prime-phylo →
1.0.11-7 →
armhf → 2018-11-09 12:09:43
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| prime-phylo 1.0.11-7 (armhf) Fri, 09 Nov 2018 11:54:16 +0000 |
+==============================================================================+
Package: prime-phylo
Version: 1.0.11-7
Source Version: 1.0.11-7
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-788499f5-711d-4786-a2e5-e60a696fe0ee' 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 [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
Fetched 24.0 MB in 9s (2785 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: 'prime-phylo' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/prime-phylo.git
Please use:
git clone https://salsa.debian.org/med-team/prime-phylo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 759 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main prime-phylo 1.0.11-7 (dsc) [2168 B]
Get:2 http://172.17.0.1/private buster-staging/main prime-phylo 1.0.11-7 (tar) [751 kB]
Get:3 http://172.17.0.1/private buster-staging/main prime-phylo 1.0.11-7 (diff) [6136 B]
Fetched 759 kB in 0s (2566 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/prime-phylo-d5czM6/prime-phylo-1.0.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/prime-phylo-d5czM6' 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-iJucbq/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-iJucbq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-iJucbq/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-iJucbq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.7 kB/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 dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libperl5.26 libsasl2-modules
libssl1.1 openssl perl-modules-5.26 systemd-sysv
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 11 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 17628 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 (>= 11~), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-prime-phylo-dummy' in '/<<BUILDDIR>>/resolver-iJucbq/apt_archive/sbuild-build-depends-prime-phylo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-prime-phylo-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-iJucbq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Sources [579 B]
Get:5 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ Packages [659 B]
Fetched 2571 B in 0s (13.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install prime-phylo 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 dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd libperl5.26 libsasl2-modules
openssl perl-modules-5.26 systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bison bsdmainutils cmake
cmake-data cpp debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex
g++ gcc gengetopt gettext gettext-base gfortran gfortran-8 gir1.2-glib-2.0
gir1.2-harfbuzz-0.0 groff-base ibverbs-providers icu-devtools
intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-dev
libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.62-dev
libboost-mpi1.62.0 libboost-serialization-dev libboost-serialization1.62-dev
libboost-serialization1.62.0 libboost1.62-dev libbsd0 libcroco3 libcurl4
libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libfreetype6 libgfortran-8-dev libgfortran5
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev
libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libjsoncpp1 liblapack-dev
liblapack3 libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libmpdec2
libnghttp2-14 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi3
libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpmix2 libpsl5 libpython3-stdlib libpython3.6-minimal
libpython3.6-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libtool libuv1
libxml2 libxml2-dev m4 man-db mime-support mpi-default-dev
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist
whois vacation cmake-doc ninja-build cpp-doc dh-make flex-doc gcc-multilib
manpages-dev gdb gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-8-doc libgfortran5-dbg libcoarrays-dev groff lrzip
liblapack-doc libboost-doc libboost-graph1.62-dev libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph-parallel1.62-dev
libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev libglib2.0-doc
libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils libgraphite2-utils
libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gcj-jdk
m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere
ssh-askpass libmail-box-perl python3-doc python3-tk python3-venv
python3.6-venv python3.6-doc binfmt-support
Recommended packages:
libfl-dev curl | wget | lynx libarchive-cpio-perl shared-mime-info
xdg-user-dirs libcoarrays-openmpi-dev publicsuffix xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bison bsdmainutils cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex
gengetopt gettext gettext-base gfortran gfortran-8 gir1.2-glib-2.0
gir1.2-harfbuzz-0.0 groff-base ibverbs-providers icu-devtools
intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-dev
libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.62-dev
libboost-mpi1.62.0 libboost-serialization-dev libboost-serialization1.62-dev
libboost-serialization1.62.0 libboost1.62-dev libbsd0 libcroco3 libcurl4
libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libfreetype6 libgfortran-8-dev libgfortran5
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev
libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libjsoncpp1 liblapack-dev
liblapack3 libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libmpdec2
libnghttp2-14 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi3
libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpmix2 libpsl5 libpython3-stdlib libpython3.6-minimal
libpython3.6-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libtool libuv1
libxml2 libxml2-dev m4 man-db mime-support mpi-default-dev
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal sbuild-build-depends-prime-phylo-dummy
zlib1g-dev
The following packages will be upgraded:
cpp g++ gcc
3 upgraded, 122 newly installed, 0 to remove and 8 not upgraded.
Need to get 60.7 MB/69.8 MB of archives.
After this operation, 362 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-iJucbq/apt_archive ./ sbuild-build-depends-prime-phylo-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2+b1 [1160 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf flex armhf 2.6.4-6.2 [427 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.7-1 [567 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.7-1 [1380 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.7-1 [36.4 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.7-1 [1639 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.7-1 [240 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.7-1 [19.9 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.7-1 [61.4 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.9p1-1 [683 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libbison-dev armhf 2:3.0.4.dfsg-1+b1 [433 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf bison armhf 2:3.0.4.dfsg-1+b1 [743 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.12.3-3 [1437 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.10-0.1 [48.4 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-5 [266 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.34.0-1 [73.4 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.61.0-1 [282 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.6-3 [97.1 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.23.2-1 [94.3 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.12.3-3 [2526 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf g++ armhf 4:8.2.0-2+rpi1 [1628 B]
Get:47 http://172.17.0.1/private buster-staging/main armhf gcc armhf 4:8.2.0-2+rpi1 [5196 B]
Get:48 http://172.17.0.1/private buster-staging/main armhf cpp armhf 4:8.2.0-2+rpi1 [19.5 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.044-1 [20.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.044-1 [12.3 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.1 [992 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf gengetopt armhf 2.22.6+dfsg0-3 [156 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-8+rpi1 [205 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-8+rpi1 [248 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-8+rpi1 [5812 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.2.0-2+rpi1 [1432 B]
Get:65 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.58.0-1 [78.2 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.58.0-1 [143 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.9.0-1+rpi1 [657 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.9.0-1+rpi1 [665 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 20.0-1 [43.2 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 20.0-1 [19.9 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1+b1 [104 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1+b1 [113 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-10+b1 [7003 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62.0 armhf 1.62.0+dfsg-10+b1 [109 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62-dev armhf 1.62.0+dfsg-10+b1 [174 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-6 [387 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.11-2+rpi1 [86.0 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.11-2+rpi1 [16.0 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.0.2-2 [344 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.2-6+rpi1 [1794 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libboost-mpi1.62.0 armhf 1.62.0+dfsg-10+b1 [54.8 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.2-6+rpi1 [162 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 20.0-1 [108 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-6 [159 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.11-2+rpi1 [142 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.2-6+rpi1 [194 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.2-6+rpi1 [954 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf mpi-default-dev armhf 1.13 [5476 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf libboost-mpi1.62-dev armhf 1.62.0+dfsg-10+b1 [74.0 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libboost-mpi-dev armhf 1.62.0.1+b8 [3790 B]
Get:98 http://172.17.0.1/private buster-staging/main armhf libboost-serialization-dev armhf 1.62.0.1+b8 [3926 B]
Get:99 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.58.1-2 [1105 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.58.1-2 [114 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.1-1 [78.7 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.1-1 [144 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.58.1-2 [151 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.58.1-2 [1237 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.9.0-1+rpi1 [650 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.9.0-1+rpi1 [944 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1+b1 [1493 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1+b1 [1550 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-7 [672 kB]
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Setting up cpp (4:8.2.0-2+rpi1) ...
Setting up libboost-serialization1.62.0:armhf (1.62.0+dfsg-10+b1) ...
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Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.34.0-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-10+b1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libuv1:armhf (1.23.2-1) ...
Setting up libpsl5:armhf (0.20.2-2) ...
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No schema files found: removed existing output file.
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Setting up libpipeline1:armhf (1.5.0-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up gcc (4:8.2.0-2+rpi1) ...
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Setting up libbsd0:armhf (0.9.1-1) ...
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Setting up libfreetype6:armhf (2.8.1-2) ...
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Setting up librhash0:armhf (1.3.6-3) ...
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Setting up gir1.2-glib-2.0:armhf (1.58.0-1) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Setting up libglib2.0-data (2.58.1-2) ...
Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Setting up openmpi-common (3.1.2-6+rpi1) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
Setting up dwz (0.12-2) ...
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Setting up libltdl7:armhf (2.4.6-6) ...
Setting up libbison-dev:armhf (2:3.0.4.dfsg-1+b1) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up g++ (4:8.2.0-2+rpi1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-11+rpi1) ...
Setting up libpcre32-3:armhf (2:8.39-11+rpi1) ...
Setting up libpcre16-3:armhf (2:8.39-11+rpi1) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up bison (2:3.0.4.dfsg-1+b1) ...
update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode
Setting up ocl-icd-libopencl1:armhf (2.2.12-1) ...
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Setting up autopoint (0.19.8.1-8) ...
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Setting up liblzo2-2:armhf (2.10-0.1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.044-1) ...
Setting up libjsoncpp1:armhf (1.7.4-3) ...
Setting up libedit2:armhf (3.1-20180525-1) ...
Setting up libboost-serialization-dev:armhf (1.62.0.1+b8) ...
Setting up libpython3.6-stdlib:armhf (3.6.7-1) ...
Setting up libpcre3-dev:armhf (2:8.39-11+rpi1) ...
Setting up python3.6 (3.6.7-1) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up python3 (3.6.7-1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up gfortran-8 (8.2.0-8+rpi1) ...
Setting up liblapack3:armhf (3.8.0-1+b1) ...
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Setting up gir1.2-harfbuzz-0.0:armhf (1.9.0-1+rpi1) ...
Setting up ibverbs-providers:armhf (20.0-1) ...
Setting up python3-lib2to3 (3.7.1-1) ...
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Setting up python3-distutils (3.7.1-1) ...
Setting up liblapack-dev:armhf (3.8.0-1+b1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up gfortran (4:8.2.0-2+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libglib2.0-dev-bin (2.58.1-2) ...
Setting up libglib2.0-dev:armhf (2.58.1-2) ...
Setting up dh-autoreconf (19) ...
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Setting up dh-strip-nondeterminism (0.044-1) ...
Setting up libicu60:armhf (60.2-6) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libhwloc-plugins:armhf (1.11.11-2+rpi1) ...
Setting up icu-devtools (60.2-6) ...
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Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up gettext (0.19.8.1-8) ...
Setting up libarchive13:armhf (3.2.2-5) ...
Setting up libpmix2:armhf (3.0.2-2) ...
Setting up libicu-dev (60.2-6) ...
Setting up libxml2-dev:armhf (2.9.4+dfsg1-7) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up cmake (3.12.3-3) ...
Setting up libopenmpi3:armhf (3.1.2-6+rpi1) ...
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Setting up openmpi-bin (3.1.2-6+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: error: no alternatives for mpi
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up debhelper (11.5.1) ...
Setting up libboost-mpi1.62.0 (1.62.0+dfsg-10+b1) ...
Setting up libopenmpi-dev:armhf (3.1.2-6+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.13) ...
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Setting up libboost-mpi-dev (1.62.0.1+b8) ...
Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-7+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-8+rpi1 gcc-8_8.2.0-8+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-8+rpi1 libstdc++6_8.2.0-8+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-7+rpi1 binutils-arm-linux-gnueabihf_2.31.1-7+rpi1 binutils-common_2.31.1-7+rpi1 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 cmake_3.12.3-3 cmake-data_3.12.3-3 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-8+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.5.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.044-1 diffutils_1:3.6-1 dirmngr_2.2.10-3+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20181018-1 flex_2.6.4-6.2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-8+rpi1 gcc_4:8.2.0-2+rpi1 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_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-8+rpi1 gcc-8-base_8.2.0-8+rpi1 gengetopt_2.22.6+dfsg0-3 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gfortran_4:8.2.0-2+rpi1 gfortran-8_8.2.0-8+rpi1 gir1.2-glib-2.0_1.58.0-1 gir1.2-harfbuzz-0.0_1.9.0-1+rpi1 gnupg_2.2.10-3+rpi1 gnupg-agent_2.2.10-3+rpi1 gnupg-l10n_2.2.10-3+rpi1 gnupg-utils_2.2.10-3+rpi1 gpg_2.2.10-3+rpi1 gpg-agent_2.2.10-3+rpi1 gpg-wks-client_2.2.10-3+rpi1 gpg-wks-server_2.2.10-3+rpi1 gpgconf_2.2.10-3+rpi1 gpgsm_2.2.10-3+rpi1 gpgv_2.2.10-3+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 ibverbs-providers_20.0-1 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-5 init-system-helpers_1.55 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libarchive13_3.2.2-5 libargon2-1_0~20171227-0.1 libasan5_8.2.0-8+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-7+rpi1 libbison-dev_2:3.0.4.dfsg-1+b1 libblas-dev_3.8.0-1+b1 libblas3_3.8.0-1+b1 libblkid1_2.32.1-0.1 libboost-dev_1.62.0.1+b8 libboost-mpi-dev_1.62.0.1+b8 libboost-mpi1.62-dev_1.62.0+dfsg-10+b1 libboost-mpi1.62.0_1.62.0+dfsg-10+b1 libboost-serialization-dev_1.62.0.1+b8 libboost-serialization1.62-dev_1.62.0+dfsg-10+b1 libboost-serialization1.62.0_1.62.0+dfsg-10+b1 libboost1.62-dev_1.62.0+dfsg-10+b1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-8+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.5-1 libcryptsetup4_2:1.7.5-1 libcurl4_7.61.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.044-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-8+rpi1 libgcc1_1:8.2.0-8+rpi1 libgcrypt20_1.8.4-3 libgdbm-compat4_1.18.1-1 libgdbm3_1.8.3-14 libgdbm6_1.18.1-1 libgfortran-8-dev_8.2.0-8+rpi1 libgfortran5_8.2.0-8+rpi1 libgirepository-1.0-1_1.58.0-1 libglib2.0-0_2.58.1-2 libglib2.0-bin_2.58.1-2 libglib2.0-data_2.58.1-2 libglib2.0-dev_2.58.1-2 libglib2.0-dev-bin_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-8+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgraphite2-3_1.3.12-1 libgraphite2-dev_1.3.12-1 libgssapi-krb5-2_1.16.1-1 libharfbuzz-dev_1.9.0-1+rpi1 libharfbuzz-gobject0_1.9.0-1+rpi1 libharfbuzz-icu0_1.9.0-1+rpi1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libhwloc-dev_1.11.11-2+rpi1 libhwloc-plugins_1.11.11-2+rpi1 libhwloc5_1.11.11-2+rpi1 libibverbs-dev_20.0-1 libibverbs1_20.0-1 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.1-2 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 liblapack-dev_3.8.0-1+b1 liblapack3_3.8.0-1+b1 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libltdl-dev_2.4.6-6 libltdl7_2.4.6-6 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4-1 libnghttp2-14_1.34.0-1 libnl-3-200_3.4.0-1 libnl-route-3-200_3.4.0-1 libnpth0_1.6-1 libnss-systemd_239-10+rpi1 libopenmpi-dev_3.1.2-6+rpi1 libopenmpi3_3.1.2-6+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpciaccess0_0.14-1 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7+b1 libperl5.28_5.28.0-3 libpipeline1_1.5.0-2 libplymouth4_0.9.3-3 libpmix2_3.0.2-2 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython3-stdlib_3.6.7-1 libpython3.6-minimal_3.6.7-1 libpython3.6-stdlib_3.6.7-1 libreadline7_7.0-5 librhash0_1.3.6-3 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.1-2 libstdc++-8-dev_8.2.0-8+rpi1 libstdc++6_8.2.0-8+rpi1 libsystemd0_239-10+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-8+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libuv1_1.23.2-1 libxml2_2.9.4+dfsg1-7 libxml2-dev_2.9.4+dfsg1-7 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-2+b1 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 mpi-default-dev_1.13 multiarch-support_2.27-6+rpi1 nano_3.1-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.4 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.1.2-6+rpi1 openmpi-common_3.1.2-6+rpi1 openssh-client_1:7.9p1-1 openssl_1.1.1-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.7-1 python3-distutils_3.7.1-1 python3-lib2to3_3.7.1-1 python3-minimal_3.6.7-1 python3.6_3.6.7-1 python3.6-minimal_3.6.7-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.11 tar_1.30+dfsg-2 tzdata_2018g-1 udev_239-10+rpi1 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 4 07:35:57 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-7.dsc
dpkg-source: info: extracting prime-phylo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz
dpkg-source: info: unpacking prime-phylo_1.0.11-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix-ftbfs-with-Boost160.patch
dpkg-source: info: applying fix-gcc-8.patch
dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.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-788499f5-711d-4786-a2e5-e60a696fe0ee
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package prime-phylo
dpkg-buildpackage: info: source version 1.0.11-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=cmake
dh_auto_clean -O--buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules build-arch
dh build-arch --buildsystem=cmake
dh_update_autotools_config -a -O--buildsystem=cmake
dh_autoreconf -a -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-Dofficial_binary_packaging=on \
-Dprime_dynamic=on \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \
-DCMAKE_BUILD_TYPE=RELEASE
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -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 -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE ..
-- The CXX compiler identification is GNU 8.2.0
-- 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
-- The Fortran compiler identification is GNU 8.2.0
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- The C compiler identification is GNU 8.2.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
hittade /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found BISON: /usr/bin/bison (found version "3.0.4")
-- Found FLEX: /usr/bin/flex (found version "2.6.4")
-- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI_Fortran: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Boost version: 1.62.0
-- Found the following Boost libraries:
-- mpi
-- serialization
-- Found LibXml2: /usr/lib/arm-linux-gnueabihf/libxml2.so (found version "2.9.4")
mpilib is /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi;/usr/lib/arm-linux-gnueabihf/openmpi/include
included path is
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "primeDTLSR". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "primeDLRS". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "showtree". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at CMakeLists.txt:120 (if):
Policy CMP0053 is not set: Simplify variable reference and escape sequence
evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
For input:
'@CMAKE_SOURCE_DIR@/excluded_from_release'
the old evaluation rules produce:
'/<<PKGBUILDDIR>>/excluded_from_release'
but the new evaluation rules produce:
'@CMAKE_SOURCE_DIR@/excluded_from_release'
Using the old result for compatibility since the policy is not set.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true"
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/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 1%] [BISON][MyParser2] Building parser with bison 3.0.4
[ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c gb.y
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/flex -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l
gb.y: warning: 1 nonterminal useless in grammar [-Wother]
gb.y: warning: 1 rule useless in grammar [-Wother]
gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry [-Wother]
%type <entry> gb_entry fasta_entry ig_entry darwin_entry
^^^^^^^^^^^^
gb.y:258.19-61: warning: rule useless in grammar [-Wother]
darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */}
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo-sfile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o
[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c
[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c: In function 'main':
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration]
if (!strcmp(argv[opt], "-d")) {
^~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c:1237:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration]
yychar = yylex ();
^~~~~
gb.y: In function 'yyerror':
gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration]
gb.y: In function 'add_to_seq':
gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable]
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function 'seq_print':
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
printf("%9d", char_counter + 1);
^~~~~ ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable]
char *top, *date;
^~~~
seqreader.l: In function 'seq_read':
seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable]
At top level:
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1864:16: warning: 'input' defined but not used [-Wunused-function]
static int input (void)
^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1821:17: warning: 'yyunput' defined but not used [-Wunused-function]
static void yyunput (int c, char * yy_bp )
^~~~~~~
[ 4%] Linking C shared library libprime-phylo-sfile.so
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,::::::::::::::::::::
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 4%] Built target prime-phylo-sfile
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 5%] [BISON][MyParser] Building parser with bison 3.0.4
[ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c NHXparse.y
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o
[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o
[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o
[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXtree.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c:155:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
fprintf(stderr, "BW:\t%d\n", l->arg.t);
~^ ~~~~~~~~
%f
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1597:16: warning: 'input' defined but not used [-Wunused-function]
static int input (void)
^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1554:17: warning: 'yyunput' defined but not used [-Wunused-function]
static void yyunput (int c, char * yy_bp )
^~~~~~~
[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c
[ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/AnError.cc
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c: In function 'yytree_parse':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c:64:25: warning: implicit declaration of function 'yytree_lex'; did you mean 'yytree_parse'? [-Wimplicit-function-declaration]
#define yylex yytree_lex
^~~~~~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c:1280:16: note: in expansion of macro 'yylex'
yychar = yylex ();
^~~~~
[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.cc
NHXparse.y: In function 'read_tree':
NHXparse.y:351:5: warning: implicit declaration of function 'close'; did you mean 'pclose'? [-Wimplicit-function-declaration]
NHXparse.y: In function 'read_tree_string':
NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string'; did you mean 'read_tree_string'? [-Wimplicit-function-declaration]
NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' [-Wimplicit-function-declaration]
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Hacks.cc
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PRNG.cc
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive]
static const Real C2 = 1.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive]
static const Real C3 = 3.0 / 10.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive]
static const Real C4 = 4.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive]
static const Real C5 = 8.0 / 9.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive]
static const Real A21 = 1.0 / 5.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive]
static const Real A31 = 3.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive]
static const Real A32 = 9.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive]
static const Real A41 = 44.0 / 45.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive]
static const Real A42 = -56.0 / 15.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive]
static const Real A43 = 32.0 / 9.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive]
static const Real A51 = 19372.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive]
static const Real A52 = -25360.0 / 2187.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive]
static const Real A53 = 64448.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive]
static const Real A54 = -212.0 / 729.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive]
static const Real A61 = 9017.0 / 3168.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive]
static const Real A62 = -355.0 / 33.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive]
static const Real A63 = 46732.0 / 5247.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive]
static const Real A64 = 49.0 / 176.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive]
static const Real A65 = -5103.0 / 18656.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive]
static const Real A71 = 35.0 / 384.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive]
static const Real A73 = 500.0 / 1113.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive]
static const Real A74 = 125.0 / 192.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive]
static const Real A75 = -2187.0 / 6784.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive]
static const Real A76 = 11.0 / 84.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive]
static const Real E1 = 71.0 / 57600.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive]
static const Real E3 = -71.0 / 16695.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive]
static const Real E4 = 71.0 / 1920.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive]
static const Real E5 = -17253.0 / 339200.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive]
static const Real E6 = 22.0 / 525.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive]
static const Real E7 = -1.0 / 40.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive]
static const Real D1 = -12715105075.0 / 11282082432.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive]
static const Real D3 = 87487479700.0 / 32700410799.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive]
static const Real D4 = -10690763975.0 / 1880347072.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive]
static const Real D5 = 701980252875.0 / 199316789632.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive]
static const Real D6 = -1453857185.0 / 822651844.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive]
static const Real D7 = 69997945.0 / 29380423.0;
^~
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::__cxx11::string&, unsigned int, std::vector<beep::UserSubstMatrixParams>&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:405:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
catch(std::exception e)
^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:423:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
catch(std::exception e)
^
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc:5:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscreteGamma.cc
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc:5:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::option::BeepOptionMap::parseUserSubstModel(beep::option::UserSubstModelOption*, int&, int, char**)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.cc
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<double> beep::option::BeepOptionMap::getDoubleX3(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:12,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:1:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:12,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::__cxx11::string&, unsigned int, std::vector<beep::UserSubstMatrixParams>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::TmplPrimeOption<T>::parseParams(std::__cxx11::string&, unsigned int, std::vector<T>&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tokenizer.cc
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TimeEstimator.cc
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.cc
[ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscTree.cc
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void beep::DiscTree::createGridTimes()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc:5:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc:5:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'beep::EpochPtSet::EpochPtSet(std::vector<const beep::Node*>, beep::Real, beep::Real, unsigned int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvMRCA.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMin(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:188:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound)
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMax(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound)
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:438:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMin(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:188:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound)
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMax(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound)
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:438:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q,
^~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Node.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void set(unsigned i, unsigned j, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(const EpochTime&, beep::EpochPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:173:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void set(const EpochTime& tm, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:403:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void set(unsigned i, unsigned j, unsigned p, unsigned q,
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(beep::EpochTime, beep::EpochTime, beep::EpochPtPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:418:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
inline void set(EpochTime tm1, EpochTime tm2, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void set(unsigned i, unsigned j, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(const EpochTime&, beep::EpochPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:173:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void set(const EpochTime& tm, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:403:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void set(unsigned i, unsigned j, unsigned p, unsigned q,
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(beep::EpochTime, beep::EpochTime, beep::EpochPtPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:418:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
inline void set(EpochTime tm1, EpochTime tm2, const_iterator start)
^~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc:7:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::EpochPtSet}; _Tp = beep::EpochPtSet; _Alloc = std::allocator<beep::EpochPtSet>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::EpochPtSet>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::EpochPtSet*, std::vector<beep::EpochPtSet> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::EpochPtSet}; _Tp = beep::EpochPtSet; _Alloc = std::allocator<beep::EpochPtSet>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::EpochPtSet*, std::vector<beep::EpochPtSet> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.cc
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeNodeMap.cc
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/RandomTreeGenerator.cc
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StrStrMap.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeAnalysis.cc
[ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc:7:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc:4:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc:6:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc:4:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void beep::EquiSplitEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector<double>&) const':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void beep::StepSizeEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector<double>&) const':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc:6:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::TreeDiscretizerOld::update()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc:7:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIOTraits.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const Real&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
sprAccPropCnt(0, 0)
^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreePerturbationEvent.cc
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ConstRateModel.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null]
buf[ bytes_read ]=NULL;
^~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.hh:6,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator' {aka '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void beep::OrthologyMCMC::estimateOrthology(bool)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const beep::Tree&}; _Tp = beep::Tree; _Alloc = std::allocator<beep::Tree>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::Tree>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const beep::Tree&}; _Tp = beep::Tree; _Alloc = std::allocator<beep::Tree>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::Tree>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, beep::StrStrMap*, std::map<const beep::Node*, beep::Node*>*, std::map<const beep::Node*, unsigned int>*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized]
new_node = S.addNode(l, r, idInt, name);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive]
static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2PMCMC.cc
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<beep::Tree> beep::TreeIO::readAllBeepTrees(const beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC.cc
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<beep::Tree> beep::TreeInputOutput::readAllBeepTrees(beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateModel_common.cc
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function 'void beep::EdgeRateMCMC_common<Templ_EdgeRateModel>::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable 'fparam' [-Wunused-variable]
Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime);
^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable]
Real rparam = variance * (rtime + ltime);
^~~~~~
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.cc
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int i = 0; i < t.size(); i++)
~~^~~~~~~~~~
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LengthRateModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive]
static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
^~
[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.cc
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.cc
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/VarRateModel.cc
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.cc
[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DummyMCMC.cc
[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCModel.cc
[ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCObject.cc
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMCPostSample.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable]
unsigned check_number_nonupdate = 0;
^~~~~~~~~~~~~~~~~~~~~~
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleML.cc
[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/MCMCSampler.cc
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/GSRSampler.cc
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc
[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleObserver.cc
[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMCMC.cc
[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MultiGSR.cc
[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc
[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point]
p[++i] = geneFams[i]->initStateProb();//updateDataProbability();
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point]
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point]
[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathMCMC.cc
[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.cc
In file included from /usr/include/c++/8/map:60,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:2684,
from /usr/include/boost/mpi/config.hpp:20,
from /usr/include/boost/mpi/environment.hpp:16,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:8,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.cc:1:
/usr/include/c++/8/bits/stl_tree.h: In member 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<beep::Node* const&>, std::tuple<>}; _Key = beep::Node*; _Val = std::pair<beep::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<beep::Node* const, double> >; _Compare = std::less<beep::Node*>; _Alloc = std::allocator<std::pair<beep::Node* const, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:2684,
from /usr/include/boost/mpi/config.hpp:20,
from /usr/include/boost/mpi/environment.hpp:16,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:8,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.cc:1:
/usr/include/c++/8/bits/stl_map.h: In member function 'beep::Node* beep::BDTreeGenerator::generateV(beep::Node*)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'beep::Node* beep::BDTreeGenerator::generateX(beep::Node*, beep::Real)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual bool beep::BDTreeGenerator::generateTree(beep::Tree&, bool)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/archive/detail/helper_collection.hpp:20,
from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
from /usr/include/boost/archive/detail/oserializer.hpp:64,
from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
from /usr/include/boost/mpi/datatype.hpp:27,
from /usr/include/boost/mpi/communicator.hpp:21,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.hh:11,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::SeriGSRvars}; _Tp = beep::SeriGSRvars; _Alloc = std::allocator<beep::SeriGSRvars>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::SeriGSRvars>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::SeriGSRvars*, std::vector<beep::SeriGSRvars> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void beep::MpiMultiGSR::updateGvars(unsigned int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::SeriGSRvars*, std::vector<beep::SeriGSRvars> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscBDProbs.cc
[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const beep::Probability&}; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator' {aka '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:288:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/8/bits/stl_vector.h: In copy constructor 'beep::DiscBirthDeathProbs::DiscBirthDeathProbs(const beep::DiscBirthDeathProbs&)':
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator' {aka '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/8/bits/stl_vector.h: In member function 'const beep::Node* beep::DiscBirthDeathProbs::getConstLinValsForPath(std::vector<beep::Probability, std::allocator<beep::Probability> >&, beep::DiscTree::Point, beep::DiscTree::Point, bool) const':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::DiscBirthDeathProbs::copyLeafBProbs(std::vector<beep::Probability, std::allocator<beep::Probability> >&, unsigned int)':
/usr/include/c++/8/bits/stl_vector.h:1512:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
{ _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
^~~~~~~~~~~~~
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:8:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder]
bool m_calculatedAtAndBelow;
^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder]
bool m_calculatedAtBars;
^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder]
EdgeDiscGSR::EdgeDiscGSR(Tree* G,
^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int i = 0; i < m_G->getNumberOfNodes(); i++) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable]
Point xpt = x.getPt();
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int i = 0; i < m_G->getNumberOfNodes(); i++) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable]
Node *parent = u->getParent();
^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable]
Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first);
^~~~~~~~
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive]
static const Real C2 = 1.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive]
static const Real C3 = 3.0 / 10.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive]
static const Real C4 = 4.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive]
static const Real C5 = 8.0 / 9.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive]
static const Real A21 = 1.0 / 5.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive]
static const Real A31 = 3.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive]
static const Real A32 = 9.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive]
static const Real A41 = 44.0 / 45.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive]
static const Real A42 = -56.0 / 15.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive]
static const Real A43 = 32.0 / 9.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive]
static const Real A51 = 19372.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive]
static const Real A52 = -25360.0 / 2187.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive]
static const Real A53 = 64448.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive]
static const Real A54 = -212.0 / 729.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive]
static const Real A61 = 9017.0 / 3168.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive]
static const Real A62 = -355.0 / 33.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive]
static const Real A63 = 46732.0 / 5247.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive]
static const Real A64 = 49.0 / 176.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive]
static const Real A65 = -5103.0 / 18656.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive]
static const Real A71 = 35.0 / 384.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive]
static const Real A73 = 500.0 / 1113.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive]
static const Real A74 = 125.0 / 192.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive]
static const Real A75 = -2187.0 / 6784.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive]
static const Real A76 = 11.0 / 84.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive]
static const Real E1 = 71.0 / 57600.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive]
static const Real E3 = -71.0 / 16695.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive]
static const Real E4 = 71.0 / 1920.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive]
static const Real E5 = -17253.0 / 339200.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive]
static const Real E6 = 22.0 / 525.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive]
static const Real E7 = -1.0 / 40.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive]
static const Real D1 = -12715105075.0 / 11282082432.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive]
static const Real D3 = 87487479700.0 / 32700410799.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive]
static const Real D4 = -10690763975.0 / 1880347072.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive]
static const Real D5 = 701980252875.0 / 199316789632.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive]
static const Real D6 = -1453857185.0 / 822651844.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive]
static const Real D7 = 69997945.0 / 29380423.0;
^~
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive]
static const Real REL_TOL = 1e-6;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive]
static const Real ABS_TOL = 1e-6;
^~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive]
static const Real C2 = 1.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive]
static const Real C3 = 3.0 / 10.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive]
static const Real C4 = 4.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive]
static const Real C5 = 8.0 / 9.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive]
static const Real A21 = 1.0 / 5.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive]
static const Real A31 = 3.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive]
static const Real A32 = 9.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive]
static const Real A41 = 44.0 / 45.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive]
static const Real A42 = -56.0 / 15.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive]
static const Real A43 = 32.0 / 9.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive]
static const Real A51 = 19372.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive]
static const Real A52 = -25360.0 / 2187.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive]
static const Real A53 = 64448.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive]
static const Real A54 = -212.0 / 729.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive]
static const Real A61 = 9017.0 / 3168.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive]
static const Real A62 = -355.0 / 33.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive]
static const Real A63 = 46732.0 / 5247.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive]
static const Real A64 = 49.0 / 176.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive]
static const Real A65 = -5103.0 / 18656.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive]
static const Real A71 = 35.0 / 384.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive]
static const Real A73 = 500.0 / 1113.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive]
static const Real A74 = 125.0 / 192.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive]
static const Real A75 = -2187.0 / 6784.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive]
static const Real A76 = 11.0 / 84.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive]
static const Real E1 = 71.0 / 57600.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive]
static const Real E3 = -71.0 / 16695.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive]
static const Real E4 = 71.0 / 1920.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive]
static const Real E5 = -17253.0 / 339200.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive]
static const Real E6 = 22.0 / 525.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive]
static const Real E7 = -1.0 / 40.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive]
static const Real D1 = -12715105075.0 / 11282082432.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive]
static const Real D3 = 87487479700.0 / 32700410799.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive]
static const Real D4 = -10690763975.0 / 1880347072.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive]
static const Real D5 = 701980252875.0 / 199316789632.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive]
static const Real D6 = -1453857185.0 / 822651844.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive]
static const Real D7 = 69997945.0 / 29380423.0;
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive]
static const Real C2 = 1.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive]
static const Real C3 = 3.0 / 10.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive]
static const Real C4 = 4.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive]
static const Real C5 = 8.0 / 9.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive]
static const Real A21 = 1.0 / 5.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive]
static const Real A31 = 3.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive]
static const Real A32 = 9.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive]
static const Real A41 = 44.0 / 45.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive]
static const Real A42 = -56.0 / 15.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive]
static const Real A43 = 32.0 / 9.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive]
static const Real A51 = 19372.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive]
static const Real A52 = -25360.0 / 2187.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive]
static const Real A53 = 64448.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive]
static const Real A54 = -212.0 / 729.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive]
static const Real A61 = 9017.0 / 3168.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive]
static const Real A62 = -355.0 / 33.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive]
static const Real A63 = 46732.0 / 5247.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive]
static const Real A64 = 49.0 / 176.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive]
static const Real A65 = -5103.0 / 18656.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive]
static const Real A71 = 35.0 / 384.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive]
static const Real A73 = 500.0 / 1113.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive]
static const Real A74 = 125.0 / 192.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive]
static const Real A75 = -2187.0 / 6784.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive]
static const Real A76 = 11.0 / 84.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive]
static const Real E1 = 71.0 / 57600.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive]
static const Real E3 = -71.0 / 16695.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive]
static const Real E4 = 71.0 / 1920.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive]
static const Real E5 = -17253.0 / 339200.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive]
static const Real E6 = 22.0 / 525.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive]
static const Real E7 = -1.0 / 40.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive]
static const Real D1 = -12715105075.0 / 11282082432.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive]
static const Real D3 = 87487479700.0 / 32700410799.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive]
static const Real D4 = -10690763975.0 / 1880347072.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive]
static const Real D5 = 701980252875.0 / 199316789632.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive]
static const Real D6 = -1453857185.0 / 822651844.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive]
static const Real D7 = 69997945.0 / 29380423.0;
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive]
static const Real REL_TOL = 1e-6;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive]
static const Real ABS_TOL = 1e-6;
^~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive]
static const Real REL_TOL = 1e-6;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive]
static const Real ABS_TOL = 1e-6;
^~~~~~~
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaMap.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:6:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::EpochBDTProbs::appendInitVals(beep::EpochBDTProbs::realvec&) const':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.cc
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumerateReconciliationModel.cc
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc
[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LambdaMap.cc
[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MaxReconciledTreeModel.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'beep::fastGEM_BirthDeathProbs::fastGEM_BirthDeathProbs(beep::Tree&, unsigned int, std::vector<double>*, const Real&, const Real&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PerturbationObservable.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:136:14: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable]
Probability topRateProb = df->operator()(rate);
^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printSa()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
Real zeroTotalQuotient = 0.0;
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLb()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1325:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
Real zeroTotalQuotient = 0.0;
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLt()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
Real zeroTotalQuotient = 0.0;
^~~~~~~~~~~~~~~~~
[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeModel.cc
[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.cc
[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc
[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::__cxx11::string beep::ReconciliationTimeModel::table4os() const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs]
typedef std::map<unsigned, unsigned>::const_iterator MapIter;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable]
Probability p = calculateDataProbability();
^
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc
[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DLRSOrthoCalculator.cc
[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SetOfNodes.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const string beep::ReconciliationTimeSampler::table4os() const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs]
typedef std::map<unsigned, unsigned>::const_iterator MapIter;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const string&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self]
ReconciliationTreeGenerator::
^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TopTimeMCMC.cc
[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridBranchSwapping.cc
[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTree.cc
[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc
[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTree.cc:367:43: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive]
if(rootNode && bTree.getRootNode() == false)
^~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const beep::HybridTree&}; _Tp = beep::HybridTree; _Alloc = std::allocator<beep::HybridTree>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::HybridTree>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<beep::HybridTree> beep::HybridTreeIO::readAllHybridTrees(beep::TreeIOTraits, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const beep::HybridTree&}; _Tp = beep::HybridTree; _Alloc = std::allocator<beep::HybridTree>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::HybridTree>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc
[ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<beep::HybridTree> beep::HybridTreeInputOutput::readAllHybridTrees(beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridBDTreeGenerator.cc
[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc
[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridGuestTreeModel.cc
[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeMCMC.cc
[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/archive/detail/helper_collection.hpp:20,
from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
from /usr/include/boost/archive/detail/oserializer.hpp:64,
from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
from /usr/include/boost/mpi/datatype.hpp:27,
from /usr/include/boost/mpi/communicator.hpp:21,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc
In file included from /usr/include/c++/8/vector:64,
from /usr/include/boost/archive/detail/helper_collection.hpp:20,
from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
from /usr/include/boost/archive/detail/oserializer.hpp:64,
from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
from /usr/include/boost/mpi/datatype.hpp:27,
from /usr/include/boost/mpi/communicator.hpp:21,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/CacheSubstitutionModel.cc
[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc
In file included from /usr/include/c++/8/ext/hash_map:60,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1:
/usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
#warning \
^~~~~~~
[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MatrixCache.cc
[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TransitionHandler.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LambdaMap.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaMap.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.hh:8,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::ReconciledTreeTimeModel}; _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator<beep::ReconciledTreeTimeModel>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::ReconciledTreeTimeModel>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::ReconciledTreeTimeModel*, std::vector<beep::ReconciledTreeTimeModel> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::GuestTreeModel}; _Tp = beep::GuestTreeModel; _Alloc = std::allocator<beep::GuestTreeModel>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<beep::GuestTreeModel>::iterator' {aka '__gnu_cxx::__normal_iterator<beep::GuestTreeModel*, std::vector<beep::GuestTreeModel> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void beep::EnumHybridGuestTreeModel::inits()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::ReconciledTreeTimeModel*, std::vector<beep::ReconciledTreeTimeModel> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::GuestTreeModel*, std::vector<beep::GuestTreeModel> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MatrixTransitionHandler.cc
[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SeqIO.cc
[ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceGenerator.cc
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceGenerator.hh:15,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceGenerator.cc:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SubstitutionModel.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)' has not been declared within 'beep'
ostream& beep::operator<<(ostream& os, const SequenceType& dt)
^~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc:8:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend'
friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt);
^~~~~~~~
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SubstitutionMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SubstitutionModel.cc:9:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map<char, double> beep::SequenceData::getBaseFrequencies()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int i = 0; i < seqType.alphabetSize(); i++)
~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int j = 0; j < seq.length(); j++) {
~~^~~~~~~~~~~~~~
[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Vector.cc
[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: 'beep::LA_Matrix::dim' is initialized with itself [-Winit-self]
LA_Matrix::LA_Matrix()
^~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc:20:13: warning: '*<unknown>.beep::LA_Matrix::dim' is used uninitialized in this function [-Wuninitialized]
: dim(dim),
^~~
[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_DiagonalMatrix.cc
In file included from /usr/include/c++/8/map:60,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:2:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const char, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::map<char, double> beep::SequenceData::getBaseFrequencies()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 81%] Linking CXX shared library libprime-phylo.so
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo.so -o libprime-phylo.so CMakeFiles/prime-phylo.dir/NHXnode.c.o CMakeFiles/prime-phylo.dir/NHXtree.c.o CMakeFiles/prime-phylo.dir/NHXannotation.c.o CMakeFiles/prime-phylo.dir/lexer.c.o CMakeFiles/prime-phylo.dir/NHXparse.c.o CMakeFiles/prime-phylo.dir/AnError.cc.o CMakeFiles/prime-phylo.dir/Beep.cc.o CMakeFiles/prime-phylo.dir/BeepOption.cc.o CMakeFiles/prime-phylo.dir/Hacks.cc.o CMakeFiles/prime-phylo.dir/ODESolver.cc.o CMakeFiles/prime-phylo.dir/PRNG.cc.o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o CMakeFiles/prime-phylo.dir/Probability.cc.o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o CMakeFiles/prime-phylo.dir/DiscTree.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o CMakeFiles/prime-phylo.dir/EpochTree.cc.o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o CMakeFiles/prime-phylo.dir/Node.cc.o CMakeFiles/prime-phylo.dir/NodeMap.cc.o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o CMakeFiles/prime-phylo.dir/Tree.cc.o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o CMakeFiles/prime-phylo.dir/TreeIO.cc.o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o CMakeFiles/prime-phylo.dir/SimpleML.cc.o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o CMakeFiles/prime-phylo.dir/GammaMap.cc.o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/fastGEM.cc.o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o CMakeFiles/prime-phylo.dir/HybridTree.cc.o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o CMakeFiles/prime-phylo.dir/SeqIO.cc.o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o CMakeFiles/prime-phylo.dir/SequenceType.cc.o CMakeFiles/prime-phylo.dir/SequenceData.cc.o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -L/usr/lib/arm-linux-gnueabihf/liblapack.so -L/usr/lib/arm-linux-gnueabihf/libblas.so -Wl,-rpath,/usr/lib/arm-linux-gnueabihf/liblapack.so:/usr/lib/arm-linux-gnueabihf/libblas.so:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../sfile/libprime-phylo-sfile.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 81%] Built target prime-phylo
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend
make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.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/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 82%] Generating cmdline.c, cmdline.h
[ 83%] Generating cmdline.c, cmdline.h
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize
Scanning dependencies of target primeDTLSR
Scanning dependencies of target primeDLRS
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color=
[ 83%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o
[ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS -I/<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS/primeDLRS.cc
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR -I/<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc
Scanning dependencies of target treesize
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build
Scanning dependencies of target primeGEM
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 83%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o
[ 83%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<<PKGBUILDDIR>>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/treesize.dir/treesize.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/<<PKGBUILDDIR>>/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeGEM/troyo.cc
/<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
switch(args_info.input_format_arg)
^
/<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
[ 84%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<<PKGBUILDDIR>>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/treesize.dir/cmdline.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c: In function 'update_arg':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c:395:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable]
char *stop_char = 0;
^~~~~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c:483:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
int check_required;
^~~~~~~~~~~~~~
[ 85%] Linking CXX executable treesize
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 85%] Built target treesize
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 85%] Generating cmdline.c, cmdline.h
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color=
Scanning dependencies of target showtree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/<<PKGBUILDDIR>>/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/showtree.dir/showtree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)':
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable 'nw' set but not used [-Wunused-but-set-variable]
bool et, nt, bl, nw;
^~
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc:174:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<beep::Tree>::size_type' {aka 'unsigned int'} [-Wsign-compare]
if(args_info.tree_number_arg >= Tvec.size())
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e)
^
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.hh:11,
from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:11:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive]
static const Real MIN_SPLICE_DELTA = 0.0001;
^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:13:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive]
static const Real C2 = 1.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive]
static const Real C3 = 3.0 / 10.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive]
static const Real C4 = 4.0 / 5.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive]
static const Real C5 = 8.0 / 9.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive]
static const Real A21 = 1.0 / 5.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive]
static const Real A31 = 3.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive]
static const Real A32 = 9.0 / 40.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive]
static const Real A41 = 44.0 / 45.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive]
static const Real A42 = -56.0 / 15.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive]
static const Real A43 = 32.0 / 9.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive]
static const Real A51 = 19372.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive]
static const Real A52 = -25360.0 / 2187.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive]
static const Real A53 = 64448.0 / 6561.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive]
static const Real A54 = -212.0 / 729.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive]
static const Real A61 = 9017.0 / 3168.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive]
static const Real A62 = -355.0 / 33.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive]
static const Real A63 = 46732.0 / 5247.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive]
static const Real A64 = 49.0 / 176.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive]
static const Real A65 = -5103.0 / 18656.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive]
static const Real A71 = 35.0 / 384.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive]
static const Real A73 = 500.0 / 1113.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive]
static const Real A74 = 125.0 / 192.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive]
static const Real A75 = -2187.0 / 6784.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive]
static const Real A76 = 11.0 / 84.0;
^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive]
static const Real E1 = 71.0 / 57600.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive]
static const Real E3 = -71.0 / 16695.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive]
static const Real E4 = 71.0 / 1920.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive]
static const Real E5 = -17253.0 / 339200.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive]
static const Real E6 = 22.0 / 525.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive]
static const Real E7 = -1.0 / 40.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive]
static const Real D1 = -12715105075.0 / 11282082432.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive]
static const Real D3 = 87487479700.0 / 32700410799.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive]
static const Real D4 = -10690763975.0 / 1880347072.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive]
static const Real D5 = 701980252875.0 / 199316789632.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive]
static const Real D6 = -1453857185.0 / 822651844.0;
^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive]
static const Real D7 = 69997945.0 / 29380423.0;
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:13:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive]
static const Real REL_TOL = 1e-6;
^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive]
static const Real ABS_TOL = 1e-6;
^~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:16:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive]
static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:17:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS/primeDLRS.cc:13:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive]
static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS/primeDLRS.cc:14:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive]
static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
^~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc:23:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
In file included from /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS/primeDLRS.cc:22:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive]
static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
^~~
/<<PKGBUILDDIR>>/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/applications/primeGEM/troyo.cc:197:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch(AnError e)
^
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int check_required;
^~~~~~~~~~~~~~
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/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
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Scanning dependencies of target reconcile
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/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc
[ 94%] Linking CXX executable primeDTLSR
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/arm-linux-gnueabihf/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *ofilename = "mpr.out";
^~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)':
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for (int i = 0; i < gtree.getNumberOfNodes(); i++) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 94%] Built target primeDTLSR
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 94%] Generating cmdline.c, cmdline.h
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color=
Scanning dependencies of target chainsaw
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 95%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
switch(args_info.input_format_arg)
^
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
[ 96%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c: In function 'update_arg':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c:388:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable]
char *stop_char = 0;
^~~~~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c:472:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
int check_required;
^~~~~~~~~~~~~~
[ 97%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<<PKGBUILDDIR>>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/reconcile.dir/cmdline.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c
[ 97%] Linking CXX executable tree2leafnames
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
[ 97%] Linking CXX executable reconcile
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
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[ 97%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c:539:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
int check_required;
^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 98%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/<<PKGBUILDDIR>>/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/reroot.dir/cmdline.c.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.c
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector<beep::SetOfNodes>*, beep::StrStrMap*)':
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch]
switch(ai.guest_tree_format_arg)
^
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)':
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value 'host_tree_format__NULL' not handled in switch [-Wswitch]
switch(ai.host_tree_format_arg)
^
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:163:17: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
/<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
switch(args_info.input_format_arg)
^
/<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=]
catch (AnError e) {
^
[ 99%] Linking CXX executable chainsaw
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[100%] Linking CXX executable reroot
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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dh_auto_test -a -O--buildsystem=cmake
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 81%] Built target prime-phylo
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend
make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.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/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.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/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.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/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.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/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.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/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/treesize/CMakeFiles/treesize.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 86%] Built target primeGEM
[ 86%] Built target treesize
[ 87%] Built target primeDLRS
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend
[ 88%] Built target primeDTLSR
make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend
make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend
make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.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/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.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/cxx/tools/reconcile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.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/cxx/tools/reroot /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.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/cxx/tools/tree2leafnames /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build
make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/showtree/CMakeFiles/showtree.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/reroot/CMakeFiles/reroot.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Built target showtree
[ 96%] Built target reroot
[ 96%] Built target reconcile
[ 98%] Built target tree2leafnames
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.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/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target chainsaw
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Debug"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/chainsaw.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeDLRS.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeGEM.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/reconcile.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/reroot.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/showtree.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/treesize.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeGEM
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDTLSR
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDLRS
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/treesize
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/showtree
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reconcile
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reroot
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/tree2leafnames
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/chainsaw
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/mcmc_analysis
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_install -a -O--buildsystem=cmake
dh_installdocs -a -O--buildsystem=cmake
dh_installchangelogs -a -O--buildsystem=cmake
dh_installexamples -a -O--buildsystem=cmake
dh_installman -a -O--buildsystem=cmake
dh_installcatalogs -a -O--buildsystem=cmake
dh_installcron -a -O--buildsystem=cmake
dh_installdebconf -a -O--buildsystem=cmake
dh_installemacsen -a -O--buildsystem=cmake
dh_installifupdown -a -O--buildsystem=cmake
dh_installinfo -a -O--buildsystem=cmake
dh_installinit -a -O--buildsystem=cmake
dh_installsystemd -a -O--buildsystem=cmake
dh_installsystemduser -a -O--buildsystem=cmake
dh_installmenu -a -O--buildsystem=cmake
dh_installmime -a -O--buildsystem=cmake
dh_installmodules -a -O--buildsystem=cmake
dh_installlogcheck -a -O--buildsystem=cmake
dh_installlogrotate -a -O--buildsystem=cmake
dh_installpam -a -O--buildsystem=cmake
dh_installppp -a -O--buildsystem=cmake
dh_installudev -a -O--buildsystem=cmake
dh_installgsettings -a -O--buildsystem=cmake
dh_bugfiles -a -O--buildsystem=cmake
dh_ucf -a -O--buildsystem=cmake
dh_lintian -a -O--buildsystem=cmake
dh_gconf -a -O--buildsystem=cmake
dh_icons -a -O--buildsystem=cmake
dh_perl -a -O--buildsystem=cmake
dh_usrlocal -a -O--buildsystem=cmake
dh_link -a -O--buildsystem=cmake
dh_installwm -a -O--buildsystem=cmake
dh_installxfonts -a -O--buildsystem=cmake
dh_strip_nondeterminism -a -O--buildsystem=cmake
dh_compress -a -O--buildsystem=cmake
dh_fixperms -a -O--buildsystem=cmake
dh_missing -a -O--buildsystem=cmake
dh_strip -a -O--buildsystem=cmake
debian/rules override_dh_makeshlibs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_shlibdeps -a -O--buildsystem=cmake
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/showtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/tree2leafnames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/treesize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDLRS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeGEM contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDTLSR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reroot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/chainsaw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reconcile contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/treesize debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/reconcile were not linked against libmpi_cxx.so.40 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=cmake
dh_gencontrol -a -O--buildsystem=cmake
dh_md5sums -a -O--buildsystem=cmake
dh_builddeb -a -O--buildsystem=cmake
dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-7_armhf.deb'.
dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../prime-phylo_1.0.11-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-11-09T12:09:40Z
Finished
--------
I: Built successfully
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| Changes |
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prime-phylo_1.0.11-7_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sun, 04 Nov 2018 08:29:40 +0100
Source: prime-phylo
Binary: prime-phylo
Architecture: armhf
Version: 1.0.11-7
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
prime-phylo - bayesian estimation of gene trees taking the species tree into ac
Closes: 912781
Changes:
prime-phylo (1.0.11-7) unstable; urgency=medium
.
[ Giovanni Mascellani ]
* Fix build with Boost 1.67
Closes: #912781
.
[ Andreas Tille ]
* Standards-Version: 4.2.1
* Secure URI in copyright format
* Remove trailing whitespace in debian/copyright
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
prime-phylo-dbgsym_1.0.11-7_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 12747788 bytes: control archive=1052 bytes.
800 bytes, 12 lines control
1166 bytes, 11 lines md5sums
Package: prime-phylo-dbgsym
Source: prime-phylo
Version: 1.0.11-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13138
Depends: prime-phylo (= 1.0.11-7)
Section: debug
Priority: optional
Description: debug symbols for prime-phylo
Build-Ids: 22932b0774dea362b44c72e483eb3afa3cc1de54 2b6f8ae317c7af5b656ffa4f15df5fa7e9d80252 345c44c8f08b0dfdfb8b2680692e84311297a1c7 359285692f1af406c8d664fe72ac39ad828f7faf 6178b1e615900de903643ce178147a9e27cb808a 670d83512582239a7226c3866a2d369fc2a110e4 8fa7bc7da5de3a7484127f0d8de4d59290ef489f 986cfc07e20504f5c335487da7d87c1d57998450 9c7cdf5167f52239fda9a8f047ac6feadd7a4081 c8fbc1514b1fc03c5a21d6908448c0e37a863e38 dc5896f488c946352c2e4f7d8dd32edb70753105
drwxr-xr-x root/root 0 2018-11-04 07:29 ./
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 306280 2018-11-04 07:29 ./usr/lib/debug/.build-id/22/932b0774dea362b44c72e483eb3afa3cc1de54.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 190476 2018-11-04 07:29 ./usr/lib/debug/.build-id/2b/6f8ae317c7af5b656ffa4f15df5fa7e9d80252.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 107132 2018-11-04 07:29 ./usr/lib/debug/.build-id/34/5c44c8f08b0dfdfb8b2680692e84311297a1c7.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/35/
-rw-r--r-- root/root 70828 2018-11-04 07:29 ./usr/lib/debug/.build-id/35/9285692f1af406c8d664fe72ac39ad828f7faf.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root 75064 2018-11-04 07:29 ./usr/lib/debug/.build-id/61/78b1e615900de903643ce178147a9e27cb808a.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 133196 2018-11-04 07:29 ./usr/lib/debug/.build-id/67/0d83512582239a7226c3866a2d369fc2a110e4.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/8f/
-rw-r--r-- root/root 11871932 2018-11-04 07:29 ./usr/lib/debug/.build-id/8f/a7bc7da5de3a7484127f0d8de4d59290ef489f.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/98/
-rw-r--r-- root/root 342388 2018-11-04 07:29 ./usr/lib/debug/.build-id/98/6cfc07e20504f5c335487da7d87c1d57998450.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 74812 2018-11-04 07:29 ./usr/lib/debug/.build-id/9c/7cdf5167f52239fda9a8f047ac6feadd7a4081.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/c8/
-rw-r--r-- root/root 42828 2018-11-04 07:29 ./usr/lib/debug/.build-id/c8/fbc1514b1fc03c5a21d6908448c0e37a863e38.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 210084 2018-11-04 07:29 ./usr/lib/debug/.build-id/dc/5896f488c946352c2e4f7d8dd32edb70753105.debug
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-11-04 07:29 ./usr/share/doc/prime-phylo-dbgsym -> prime-phylo
prime-phylo_1.0.11-7_armhf.deb
------------------------------
new Debian package, version 2.0.
size 659416 bytes: control archive=1588 bytes.
1051 bytes, 19 lines control
1579 bytes, 25 lines md5sums
Package: prime-phylo
Version: 1.0.11-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2356
Depends: perl:any, libblas3 | libblas.so.3, libboost-mpi1.62.0, libboost-serialization1.62.0, libc6 (>= 2.23), libgcc1 (>= 1:3.5), liblapack3 | liblapack.so.3, libopenmpi3, libstdc++6 (>= 5.2), libxml2 (>= 2.7.4)
Suggests: njplot, treeviewx, muscle, probalign, mafft, python-biopython, mrbayes, phyml, raxml
Section: science
Priority: optional
Homepage: http://prime.sbc.su.se
Description: bayesian estimation of gene trees taking the species tree into account
PrIME (Probabilistic Integrated Models of Evolution) is a package
supporting inference of evolutionary parameters in a Bayesian framework
using Markov chain Monte Carlo simulation. A distinguishing feature of
PrIME is that the species tree is taken into account when analyzing gene
trees.
.
The input data to PrIME is a multiple sequence alignment in FASTA format
and the output data contains trees in Newick format.
drwxr-xr-x root/root 0 2018-11-04 07:29 ./
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/bin/
-rwxr-xr-x root/root 26304 2018-11-04 07:29 ./usr/bin/chainsaw
-rwxr-xr-x root/root 33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis
-rwxr-xr-x root/root 79368 2018-11-04 07:29 ./usr/bin/primeDLRS
-rwxr-xr-x root/root 83464 2018-11-04 07:29 ./usr/bin/primeDTLSR
-rwxr-xr-x root/root 34792 2018-11-04 07:29 ./usr/bin/primeGEM
lrwxrwxrwx root/root 0 2018-11-04 07:29 ./usr/bin/primeGSRf -> primeDLRS
-rwxr-xr-x root/root 34444 2018-11-04 07:29 ./usr/bin/reconcile
-rwxr-xr-x root/root 46828 2018-11-04 07:29 ./usr/bin/reroot
-rwxr-xr-x root/root 26440 2018-11-04 07:29 ./usr/bin/showtree
-rwxr-xr-x root/root 18036 2018-11-04 07:29 ./usr/bin/tree2leafnames
-rwxr-xr-x root/root 18056 2018-11-04 07:29 ./usr/bin/treesize
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/lib/prime-phylo/
-rw-r--r-- root/root 42408 2018-11-04 07:29 ./usr/lib/prime-phylo/libprime-phylo-sfile.so
-rw-r--r-- root/root 1926660 2018-11-04 07:29 ./usr/lib/prime-phylo/libprime-phylo.so
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/doc/prime-phylo/
-rw-r--r-- root/root 845 2018-11-04 07:29 ./usr/share/doc/prime-phylo/changelog.Debian.gz
-rw-r--r-- root/root 505 2012-12-17 15:52 ./usr/share/doc/prime-phylo/changelog.gz
-rw-r--r-- root/root 7287 2018-11-04 07:29 ./usr/share/doc/prime-phylo/copyright
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/man/
drwxr-xr-x root/root 0 2018-11-04 07:29 ./usr/share/man/man1/
-rw-r--r-- root/root 653 2018-11-04 07:29 ./usr/share/man/man1/chainsaw.1.gz
-rw-r--r-- root/root 1284 2018-11-04 07:29 ./usr/share/man/man1/mcmc_analysis.1.gz
-rw-r--r-- root/root 2154 2018-11-04 07:29 ./usr/share/man/man1/primeDLRS.1.gz
-rw-r--r-- root/root 1992 2018-11-04 07:29 ./usr/share/man/man1/primeDTLSR.1.gz
-rw-r--r-- root/root 987 2018-11-04 07:29 ./usr/share/man/man1/primeGEM.1.gz
lrwxrwxrwx root/root 0 2018-11-04 07:29 ./usr/share/man/man1/primeGSRf.1.gz -> primeDLRS.1.gz
-rw-r--r-- root/root 654 2018-11-04 07:29 ./usr/share/man/man1/reconcile.1.gz
-rw-r--r-- root/root 886 2018-11-04 07:29 ./usr/share/man/man1/reroot.1.gz
-rw-r--r-- root/root 904 2018-11-04 07:29 ./usr/share/man/man1/showtree.1.gz
-rw-r--r-- root/root 494 2018-11-04 07:29 ./usr/share/man/man1/tree2leafnames.1.gz
-rw-r--r-- root/root 608 2018-11-04 07:29 ./usr/share/man/man1/treesize.1.gz
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 147904
Build-Time: 282
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 625
Job: prime-phylo_1.0.11-7
Machine Architecture: armhf
Package: prime-phylo
Package-Time: 924
Source-Version: 1.0.11-7
Space: 147904
Status: successful
Version: 1.0.11-7
--------------------------------------------------------------------------------
Finished at 2018-11-09T12:09:40Z
Build needed 00:15:24, 147904k disk space