Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 15:43:57.422411143 +0000 +++ b2/build.log 2024-04-30 16:08:56.214588010 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 2 09:48:12 -12 2025 -I: pbuilder-time-stamp: 1748900892 +I: Current time: Wed May 1 05:44:01 +14 2024 +I: pbuilder-time-stamp: 1714491841 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2326818/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 30 15:44 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6f9c87a7c78748c39d9986a44449b0cd' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2326818' - PS1='# ' - PS2='> ' + INVOCATION_ID=241c9c9278204a8e9b9a3a14235d072d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2596749 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WJ8m6id1/pbuilderrc_rBWW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WJ8m6id1/b1 --logfile b1/build.log iqtree_2.0.7+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WJ8m6id1/pbuilderrc_GPYw --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WJ8m6id1/b2 --logfile b2/build.log iqtree_2.0.7+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 19:07 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2326818/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -361,7 +393,7 @@ Get: 130 http://deb.debian.org/debian trixie/main amd64 libsprng2-dev amd64 2.0a-13 [77.9 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.15 [3152 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 time amd64 1.9-0.2 [50.8 kB] -Fetched 168 MB in 2s (68.4 MB/s) +Fetched 168 MB in 5s (33.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). @@ -915,7 +947,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1004,8 +1040,8 @@ -- clang-tidy not found. --- Configuring done (3.1s) --- Generating done (0.1s) +-- Configuring done (8.3s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -1167,7 +1203,7 @@ -- clang-tidy not found. --- Configuring done (8.3s) +-- Configuring done (7.6s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -1186,208 +1222,191 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' dh_auto_build -Bbuild.omp - cd build.omp && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.omp && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend +[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" +[ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c +[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp +[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp +[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +[ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp +[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +[ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +[ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 0%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -[ 0%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -[ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp -[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp -[ 4%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o -[ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o -[ 5%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -[ 5%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +[ 5%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c -[ 6%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -[ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp -[ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build -[ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -[ 8%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o -[ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp -[ 11%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -[ 11%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -[ 11%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c -[ 11%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -[ 12%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -[ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -[ 12%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c -[ 12%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c -[ 13%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -[ 13%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c -[ 13%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp -[ 13%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c -[ 13%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c -[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -[ 12%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -[ 14%] Building C object pll/CMakeFiles/pll.dir/models.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp -[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -[ 16%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp +[ 6%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c +[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c -[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp -[ 17%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c -[ 18%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c +[ 8%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' + 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); + | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 9%] Linking CXX static library libvectorclass.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c +[ 9%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +[ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_function.h:1438: +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 10%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c +[ 10%] Built target vectorclass +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +[ 11%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 12%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp +[ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1417,47 +1436,12 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 19%] Building C object booster/CMakeFiles/booster.dir/booster.c.o -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' - 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); - | ^~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c -[ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': -/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); - | ^~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27: -/build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { - | ^~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' - 191 | unsigned int tell_size_of_one_tree(char* filename); - | ~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1470,90 +1454,16 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' - 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' - 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -[ 20%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -[ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c -[ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' - 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' - 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); - | ^~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX static library libvectorclass.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 23%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' - 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' - 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); - | ^~~~~~~~~~~~~~~~~~ -/usr/bin/ranlib libvectorclass.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 23%] Built target vectorclass -[ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp -[ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp -[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -[ 23%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +[ 14%] Building C object booster/CMakeFiles/booster.dir/io.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c +[ 14%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp -[ 24%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +[ 15%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp +[ 15%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c -[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp -[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1569,18 +1479,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 24%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c -[ 24%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp -[ 25%] Linking C static library libsprng.a +[ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +[ 16%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp +[ 16%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1596,59 +1503,34 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 26%] Built target sprng -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp -[ 27%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp -[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp -[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp -[ 29%] Linking CXX static library libgsl.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp +[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp +[ 16%] Built target sprng +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 16%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c +[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +[ 17%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: @@ -1665,60 +1547,63 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o -/usr/bin/ranlib libgsl.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_function.h:1438: -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -[ 29%] Built target gsl -[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp -[ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c +[ 18%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c +[ 19%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' + 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' + 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +[ 20%] Building C object pll/CMakeFiles/pll.dir/models.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1732,24 +1617,88 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +[ 21%] Linking CXX static library libgsl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp +[ 21%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libgsl.a +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 22%] Built target gsl +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 22%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 23%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c +[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' + 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' + 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' + 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' + 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); + | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1763,15 +1712,69 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 26%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c +/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': +/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); + | ^~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27: +/build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { + | ^~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' + 191 | unsigned int tell_size_of_one_tree(char* filename); + | ~~~~~~^~~~~~~~ +[ 26%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c +[ 26%] Linking CXX static library liblbfgsb.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 26%] Built target lbfgsb +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp +[ 26%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c -[ 32%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +[ 27%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c -[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp +[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1785,8 +1788,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +[ 29%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c +[ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +[ 30%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1802,12 +1809,67 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c +[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp +[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp +[ 32%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 33%] Linking C static library libbooster.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +/usr/bin/ranlib libbooster.a +[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 35%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +[ 35%] Built target booster +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +[ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 35%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp +[ 35%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp +[ 35%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c +[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1821,8 +1883,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 36%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c +[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1836,10 +1906,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1847,16 +1916,24 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 38%] Linking C static library libpllavx.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +[ 38%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 38%] Built target pllavx In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1870,119 +1947,64 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c +[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 33%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c -[ 33%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c -[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 36%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +[ 40%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: +[ 40%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c +[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: +[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp +[ 41%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c +[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: +[ 42%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c +[ 42%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 37%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 38%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c -[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp -[ 40%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -1996,101 +2018,60 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 41%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -[ 41%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c -[ 41%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c -[ 42%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c -[ 42%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -[ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp +[ 44%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c +[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp -[ 43%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp -[ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +[ 44%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp -[ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: +[ 46%] Linking CXX static library libwhtest.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 46%] Linking C static library libbooster.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +/usr/bin/ranlib libwhtest.a +[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 46%] Built target booster -[ 47%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +[ 46%] Built target whtest +[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp +[ 47%] Linking CXX static library libterraphast.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +/usr/bin/ranlib libterraphast.a [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o +[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 48%] Built target terraphast [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 48%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c [ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp -[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -[ 50%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c -[ 50%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2133,7 +2114,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' @@ -2149,138 +2129,49 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 50%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Linking CXX static library libnclextra.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -/usr/bin/ranlib libnclextra.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 53%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 53%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp -[ 57%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp -[ 60%] Linking C static library libpllavx.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -[ 60%] Linking CXX static library liblbfgsb.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 60%] Built target pllavx -[ 60%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 60%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -[ 60%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -[ 60%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp -[ 61%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +[ 51%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp -[ 62%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp -[ 62%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -[ 62%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp -[ 63%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp -[ 64%] Linking C static library libpll.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -[ 65%] Linking CXX static library libwhtest.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -/usr/bin/ranlib libpll.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 65%] Built target whtest -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2289,15 +2180,19 @@ from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 65%] Built target pll +[ 52%] Linking C static library libpll.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2305,81 +2200,117 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libpll.a +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 53%] Built target pll +[ 53%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp +[ 57%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp +[ 57%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 57%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +[ 58%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: @@ -2393,7 +2324,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2409,46 +2340,87 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 59%] Linking CXX static library libnclextra.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: +In file included from /usr/include/c++/13/string:49, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +/usr/bin/ranlib libnclextra.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 59%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp +[ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2468,25 +2440,26 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2496,45 +2469,45 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2546,80 +2519,75 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 65%] Linking CXX static library libterraphast.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o -/usr/bin/ranlib libterraphast.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 65%] Built target terraphast -[ 65%] Linking CXX static library libncl.a +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp +[ 64%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp /usr/bin/ranlib libncl.a -[ 66%] Linking CXX static library libyaml-cpp.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 66%] Built target ncl +[ 65%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -/usr/bin/ranlib libyaml-cpp.a -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 69%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, @@ -2628,11 +2596,25 @@ /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2640,26 +2622,24 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2683,10 +2663,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2701,33 +2684,12 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2737,31 +2699,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 68%] Linking CXX static library libyaml-cpp.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2771,58 +2721,37 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 69%] Linking CXX static library libpda.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a +/usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 69%] Built target pda -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp +[ 69%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 70%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp -[ 70%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o -[ 71%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -[ 71%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp -[ 71%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ +[ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2830,35 +2759,40 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -2869,137 +2803,79 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ -[ 71%] Linking CXX static library libutils.a +[ 69%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 71%] Built target utils -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ +[ 69%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -[ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -[ 74%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp -[ 75%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 75%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -[ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp +[ 74%] Linking CXX static library libpda.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +/usr/bin/ranlib libpda.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 74%] Built target pda +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 75%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3016,15 +2892,23 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3032,9 +2916,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3048,9 +2931,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3064,8 +2947,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3079,16 +2963,15 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3097,8 +2980,10 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3112,9 +2997,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3129,8 +3012,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3144,9 +3026,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3156,31 +3037,11 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { - | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3194,9 +3055,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3210,27 +3071,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3241,25 +3082,161 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /usr/include/c++/13/string:49, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +[ 75%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 76%] Linking CXX static library libphyloYAML.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o +/usr/bin/ranlib libphyloYAML.a +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 242 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 76%] Built target phyloYAML +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 77%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3269,14 +3246,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3304,8 +3286,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3319,7 +3300,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3329,12 +3310,36 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3348,7 +3353,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3358,21 +3363,42 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3382,17 +3408,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3402,11 +3424,37 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] + 180 | } + | ^ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] + 257 | } + | ^ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3421,10 +3469,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3434,87 +3480,24 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] - 180 | } - | ^ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] - 257 | } - | ^ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -[ 83%] Linking CXX static library libphyloYAML.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 -/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -[ 83%] Built target phyloYAML -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3527,6 +3510,22 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3545,49 +3544,40 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 242 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3600,6 +3590,26 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3624,18 +3634,8 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3651,32 +3651,24 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -3700,6 +3692,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3712,18 +3717,49 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ [ 84%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 @@ -3731,29 +3767,29 @@ /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 84%] Built target main -[ 85%] Linking CXX static library libkernelsse.a -/usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake -/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 -/usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -/usr/bin/ranlib libkernelsse.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 85%] Built target kernelsse -[ 86%] Linking CXX static library libkernelfma.a +[ 85%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' -[ 86%] Built target kernelfma +[ 85%] Built target kernelfma +[ 86%] Linking CXX static library libkernelsse.a +/usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake +/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 +/usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +/usr/bin/ranlib libkernelsse.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 86%] Built target kernelsse [ 86%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' +[ 86%] Built target kernelavx [ 86%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake -[ 86%] Built target kernelavx cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a @@ -3773,74 +3809,62 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3854,8 +3878,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3867,8 +3890,9 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3880,17 +3904,14 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3898,13 +3919,14 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -3924,22 +3946,6 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: @@ -3955,7 +3961,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3970,9 +3977,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3985,8 +3991,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -3999,19 +4005,7 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4021,17 +4015,11 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4050,18 +4038,20 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: @@ -4072,7 +4062,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4085,8 +4075,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4101,7 +4091,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4115,62 +4107,40 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4183,7 +4153,10 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4196,7 +4169,8 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4209,8 +4183,38 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4223,6 +4227,22 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } @@ -4231,6 +4251,22 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -4301,7 +4337,7 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial - cd build.serial && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.serial && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks @@ -4317,182 +4353,108 @@ make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build +[ 0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build -make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" +[ 0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp -[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" -[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp -[ 3%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c +[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 3%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -[ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp -[ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +[ 3%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp -[ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -[ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -[ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -[ 8%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o -[ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp +[ 4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o [ 5%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +[ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o +[ 6%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c -[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp -[ 9%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp -[ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -[ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c -[ 10%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp -[ 10%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp +[ 6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +[ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp +[ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +[ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 9%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o -[ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -[ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp -[ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp -[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -[ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp -[ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -[ 11%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -[ 14%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -[ 15%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c +make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp -[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp -[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -[ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c -[ 16%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c -[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 7%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp -[ 17%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c -[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 8%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +[ 8%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -4504,38 +4466,29 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Linking C static library libsprng.a -[ 18%] Building C object booster/CMakeFiles/booster.dir/io.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp +[ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c +[ 9%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c +[ 9%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' - 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' - 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); - | ^~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +[ 10%] Linking C static library libsprng.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libsprng.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4561,55 +4514,46 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -[ 19%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o -/usr/bin/ranlib libsprng.a -[ 19%] Linking CXX static library libvectorclass.a -[ 19%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp -[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 20%] Built target sprng -[ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp -/usr/bin/ranlib libvectorclass.a +[ 11%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 22%] Built target vectorclass -[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp -[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp -[ 23%] Linking CXX static library libgsl.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 -/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o -/usr/bin/ranlib libgsl.a -[ 24%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +[ 12%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c +[ 12%] Built target sprng +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" +[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 24%] Built target gsl -[ 25%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 14%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c +[ 15%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +[ 15%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c +[ 16%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c -[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' + 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' + 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); + | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); @@ -4624,67 +4568,46 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ -[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 26%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 26%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c -[ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 16%] Linking CXX static library libvectorclass.a +[ 17%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp +[ 17%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp -[ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -[ 28%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 17%] Built target vectorclass +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" +[ 17%] Linking CXX static library libgsl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +[ 17%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 17%] Built target gsl +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 17%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -4700,30 +4623,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp -[ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c +[ 17%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c +[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +[ 17%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c +[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp +[ 17%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4737,16 +4663,23 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c -[ 32%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp +[ 19%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c -[ 32%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp -[ 32%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c +[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +[ 21%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c +[ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4760,18 +4693,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 21%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c +[ 22%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp -[ 33%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c -[ 33%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4785,21 +4719,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c -[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp -[ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c -[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: +[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ @@ -4816,6 +4742,27 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ +[ 23%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 24%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 24%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); @@ -4824,86 +4771,80 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' - 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' - 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' - 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' - 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); - | ^~~~~~~~~~~~~~~~~~ -[ 35%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 36%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -[ 36%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c +[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c +[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 26%] Linking C static library libbooster.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +/usr/bin/ranlib libbooster.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 26%] Linking CXX static library liblbfgsb.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +[ 26%] Built target booster +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c +[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +[ 28%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build +/usr/bin/ranlib liblbfgsb.a +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp +[ 28%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); @@ -4911,9 +4852,15 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp +[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp +[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4921,30 +4868,67 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 30%] Linking C static library libpllavx.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 31%] Built target pllavx +[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp +[ 31%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +[ 32%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 32%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 33%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp +[ 33%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp +[ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4958,26 +4942,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -4991,18 +4958,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp -[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp -[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5010,22 +4968,33 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp -[ 40%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c -[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp -[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp +[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' + 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' + 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); + | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5039,44 +5008,89 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 42%] Linking C static library libbooster.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -[ 43%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 43%] Built target booster -[ 43%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' + 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' + 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); + | ^~~~~~~~~~~~~~~~~~ +[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +[ 36%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 38%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp +[ 38%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 38%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +[ 39%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c +[ 40%] Linking CXX static library libwhtest.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +/usr/bin/ranlib libwhtest.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 40%] Built target whtest +[ 40%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5090,45 +5104,53 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c +[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 41%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp +[ 41%] Linking CXX static library libterraphast.a +[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +[ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5142,38 +5164,59 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp -[ 45%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -[ 45%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c -[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp -[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp +/usr/bin/ranlib libterraphast.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 43%] Built target terraphast +[ 44%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 48%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +[ 44%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp +[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 48%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c +[ 47%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c +[ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c +[ 48%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5187,38 +5230,73 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp -[ 49%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c -[ 49%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c -[ 50%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c -[ 50%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 50%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 49%] Linking CXX static library libnclextra.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +/usr/bin/ranlib libnclextra.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 49%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +[ 49%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp +[ 49%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -5280,85 +5358,49 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp +[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 49%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp -[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp -[ 52%] Linking CXX static library liblbfgsb.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 52%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp -[ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp -[ 56%] Linking C static library libpllavx.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 57%] Linking CXX static library libwhtest.a -[ 57%] Built target pllavx -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 57%] Built target whtest In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5366,29 +5408,30 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5396,92 +5439,100 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 58%] Linking CXX static library libnclextra.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -/usr/bin/ranlib libnclextra.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 58%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp +[ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp +[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp +[ 53%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp +[ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp +[ 57%] Linking C static library libpll.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp +[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 57%] Built target pll +[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp +[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -5489,8 +5540,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5502,39 +5553,39 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/13/string:49, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Linking CXX static library libterraphast.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5544,14 +5595,29 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp +[ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp +[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp +[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp +[ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5561,37 +5627,23 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/ranlib libterraphast.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, @@ -5606,7 +5658,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Built target terraphast +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -5625,35 +5682,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 65%] Linking CXX static library libncl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o +/usr/bin/ranlib libncl.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 65%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -5669,72 +5707,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 65%] Linking C static library libpll.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -/usr/bin/ranlib libpll.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 65%] Built target pll -[ 65%] Linking CXX static library libncl.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -/usr/bin/ranlib libncl.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 65%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp +[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp -[ 69%] Linking CXX static library libyaml-cpp.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" -/usr/bin/ranlib libyaml-cpp.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, @@ -5746,18 +5731,34 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -5766,7 +5767,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5799,49 +5801,25 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5854,7 +5832,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5869,10 +5848,11 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -5882,131 +5862,82 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Linking CXX static library libpda.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Built target pda -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 69%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -[ 71%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -[ 71%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -[ 71%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp -[ 71%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ -[ 71%] Linking CXX static library libutils.a +[ 68%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 71%] Built target utils +[ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -[ 72%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +[ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -[ 73%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp -[ 75%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -[ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -[ 79%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -6014,7 +5945,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6024,28 +5956,22 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + | ^~~~~ +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6055,11 +5981,18 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp +[ 72%] Linking CXX static library libyaml-cpp.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6069,15 +6002,58 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libyaml-cpp.a +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp +[ 73%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 73%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -6085,29 +6061,31 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -6115,7 +6093,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6131,9 +6111,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6143,11 +6122,29 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 242 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6157,7 +6154,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6170,84 +6167,62 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6257,13 +6232,26 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6273,13 +6261,37 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6289,11 +6301,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 74%] Linking CXX static library libpda.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6303,13 +6319,31 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libpda.a +[ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 75%] Built target pda +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 76%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +[ 76%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6319,13 +6353,23 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6339,9 +6383,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6351,15 +6393,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6373,9 +6417,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6385,11 +6427,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6399,11 +6447,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 79%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6413,13 +6465,18 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6429,30 +6486,27 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6467,8 +6521,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6495,12 +6549,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -6510,39 +6567,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6559,21 +6583,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); @@ -6582,22 +6591,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6613,6 +6606,8 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6625,50 +6620,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 242 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] - 180 | } - | ^ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] - 257 | } - | ^ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6681,7 +6632,10 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +[ 81%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp +[ 82%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6694,18 +6648,125 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 82%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 83%] Linking CXX static library libphyloYAML.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 +/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o +/usr/bin/ranlib libphyloYAML.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +[ 83%] Built target phyloYAML +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /usr/include/c++/13/complex:45, + from /usr/include/eigen3/Eigen/Core:50, + from /usr/include/eigen3/Eigen/Dense:1, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6718,33 +6779,14 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6760,7 +6802,7 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6789,32 +6831,18 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /usr/include/c++/13/complex:45, - from /usr/include/eigen3/Eigen/Core:50, - from /usr/include/eigen3/Eigen/Dense:1, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 83%] Linking CXX static library libphyloYAML.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 -/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 83%] Built target phyloYAML +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -6827,32 +6855,40 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] + 180 | } + | ^ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] + 257 | } + | ^ [ 84%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o -/usr/bin/ranlib libmain.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' -[ 84%] Built target main [ 85%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake +/usr/bin/ranlib libmain.a /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 85%] Built target kernelsse +[ 85%] Built target main [ 86%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 @@ -6888,78 +6924,57 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -6980,38 +6995,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7024,7 +7009,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7038,22 +7024,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7067,7 +7038,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7093,8 +7064,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7108,23 +7079,19 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7140,7 +7107,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7152,7 +7120,9 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7181,8 +7151,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7195,26 +7165,22 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7226,9 +7192,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7258,9 +7223,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7274,17 +7238,20 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -7297,8 +7264,7 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -7311,7 +7277,8 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -7325,7 +7292,7 @@ 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -7338,6 +7305,10 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } @@ -7346,6 +7317,71 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -7416,202 +7452,150 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi - cd build.mpi && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.mpi && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -[ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp -/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp +[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o +[ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp -[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp +[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +[ 1%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +[ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp +[ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c +/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp -[ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -[ 3%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp +[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp -[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp -[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -[ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -[ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -[ 6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -[ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c -[ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +[ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp -[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp -[ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -[ 7%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c -[ 8%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -[ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -[ 9%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp +[ 5%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c -[ 7%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c -[ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp -[ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -[ 11%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -[ 10%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -[ 11%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c -[ 12%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -[ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +[ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c -[ 13%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c -[ 14%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -[ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c -[ 14%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp -[ 15%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o -[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +[ 7%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c -[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp -[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o +[ 8%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp +[ 8%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c +[ 8%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7619,20 +7603,43 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c +[ 9%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c +[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp +[ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c +[ 9%] Linking CXX static library libvectorclass.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c +[ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +[ 11%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c +[ 11%] Built target vectorclass +[ 11%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c +[ 11%] Building C object booster/CMakeFiles/booster.dir/io.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' @@ -7644,22 +7651,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' - 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' - 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); - | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -7672,54 +7663,236 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp -[ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp -[ 19%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c -[ 19%] Linking CXX static library libvectorclass.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 20%] Linking C static library libsprng.a +[ 12%] Building C object booster/CMakeFiles/booster.dir/sort.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c +[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp +[ 12%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c +[ 12%] Building C object booster/CMakeFiles/booster.dir/tree.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c +[ 13%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 14%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -[ 20%] Built target vectorclass -[ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -[ 21%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp -[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp -[ 22%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp /usr/bin/ranlib libsprng.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 22%] Built target sprng -[ 22%] Building C object booster/CMakeFiles/booster.dir/io.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c -[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o +[ 14%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp -[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp -[ 23%] Building C object booster/CMakeFiles/booster.dir/sort.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c -[ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp -[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 14%] Built target sprng +[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp +[ 15%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp -[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp -[ 24%] Building C object booster/CMakeFiles/booster.dir/tree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c -[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o +[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_function.h:1438: +/usr/include/c++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +[ 15%] Linking CXX static library libgsl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 15%] Built target gsl +[ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp +[ 17%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c +[ 18%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' + 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' + 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); + | ^~~~~~~~~~~~~~~~~~ +[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp +[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp -[ 26%] Building C object booster/CMakeFiles/booster.dir/booster.c.o +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 21%] Linking C static library libpllavx.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +[ 21%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Built target pllavx +[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp +[ 22%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c +[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o +[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp +[ 23%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c +[ 24%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp +[ 25%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c +[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); @@ -7734,14 +7907,12 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ -[ 26%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp -[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp -[ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp +[ 26%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7755,14 +7926,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -[ 28%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp -[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' + 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' + 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +[ 27%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c +[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7776,9 +7966,26 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c +[ 27%] Building C object booster/CMakeFiles/booster.dir/prng.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp +[ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp +[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp +[ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp +[ 30%] Building C object booster/CMakeFiles/booster.dir/stats.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c +[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp +[ 30%] Linking CXX static library liblbfgsb.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7792,12 +7999,45 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 29%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c -[ 29%] Linking CXX static library libgsl.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 30%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 30%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp +[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 31%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp +[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp +[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp +[ 34%] Linking C static library libbooster.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake +[ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7811,13 +8051,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 -[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp -/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o -/usr/bin/ranlib libgsl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 +/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o +[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp +/usr/bin/ranlib libbooster.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7831,9 +8072,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 36%] Built target booster +[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp +[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp +[ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7847,13 +8094,25 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 30%] Built target gsl -[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp -[ 31%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7867,15 +8126,24 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: +[ 37%] Building C object pll/CMakeFiles/pll.dir/models.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp +[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 37%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7889,22 +8157,28 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp -[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_function.h:1438: -/usr/include/c++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp +[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7918,10 +8192,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp +[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp +[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp +[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7935,52 +8213,34 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp -[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp -[ 32%] Building C object booster/CMakeFiles/booster.dir/prng.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c -[ 33%] Building C object booster/CMakeFiles/booster.dir/stats.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c -[ 33%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c -[ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -[ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp -[ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp +[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp +[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp +[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp +[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -7994,10 +8254,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8011,17 +8270,27 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp -[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o +[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp -[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp -[ 38%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c +[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o +[ 44%] Linking CXX static library libwhtest.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp +[ 44%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp +[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp +[ 45%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 45%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c +/usr/bin/ranlib libwhtest.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8035,10 +8304,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 45%] Built target whtest +[ 45%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8052,56 +8327,52 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c -[ 39%] Building C object pll/CMakeFiles/pll.dir/models.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c -[ 40%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' - 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' - 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53: +[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp +[ 47%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c +[ 47%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c +[ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp +[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -8118,8 +8389,6 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -8132,185 +8401,222 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp +[ 49%] Linking CXX static library libterraphast.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 +/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp +[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp +[ 50%] Linking CXX static library libnclextra.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp -[ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +/usr/bin/ranlib libterraphast.a +/usr/bin/ranlib libnclextra.a +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 43%] Linking C static library libbooster.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake -[ 43%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 -/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o -/usr/bin/ranlib libbooster.a -[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp +[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 43%] Built target booster -[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp -[ 45%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +[ 52%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 45%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c -[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp +[ 52%] Built target nclextra In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 45%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp +[ 52%] Built target terraphast +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp +[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp +[ 54%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: -/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 46%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp -[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -[ 47%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp -[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp +[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +[ 54%] Linking CXX static library libncl.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +[ 54%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 49%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o +/usr/bin/ranlib libncl.a +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: +/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +[ 54%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 54%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +[ 55%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c +[ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp +[ 56%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, + from /usr/include/boost/math/special_functions/math_fwd.hpp:29, + from /usr/include/boost/math/special_functions/beta.hpp:13, + from /usr/include/boost/math/distributions/binomial.hpp:83, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22: +/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] + 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" + | ^~~~~~~ +[ 57%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c +[ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp -[ 49%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +[ 58%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp +[ 58%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp -[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 50%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +[ 58%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c -[ 51%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c -[ 51%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c -[ 52%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8318,56 +8624,79 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 52%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c -[ 52%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c +[ 59%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 59%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c +[ 60%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 53%] Linking C static library libpllavx.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 60%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 53%] Built target pllavx -[ 53%] Linking CXX static library liblbfgsb.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +[ 61%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData': /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8425,99 +8754,11 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 53%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -[ 55%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp -[ 55%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp -[ 55%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp -[ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp -[ 57%] Linking CXX static library libwhtest.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 57%] Built target whtest -[ 58%] Linking CXX static library libnclextra.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -/usr/bin/ranlib libnclextra.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 58%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o -[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8527,33 +8768,54 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp +[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp +[ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8571,76 +8833,85 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 66%] Linking CXX static library libyaml-cpp.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp +/usr/bin/ranlib libyaml-cpp.a +[ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 67%] Built target yaml-cpp +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build +make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 67%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp +[ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -8664,33 +8935,23 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: + from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 68%] Linking C static library libpll.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, @@ -8705,64 +8966,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27, @@ -8777,6 +8983,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 68%] Built target pll +[ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, @@ -8792,62 +9002,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Linking CXX static library libterraphast.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 -/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o -/usr/bin/ranlib libterraphast.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 64%] Built target terraphast -[ 65%] Linking C static library libpll.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -/usr/bin/ranlib libpll.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 65%] Built target pll -[ 65%] Linking CXX static library libncl.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -/usr/bin/ranlib libncl.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 65%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp -[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp -In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, - from /usr/include/boost/math/special_functions/math_fwd.hpp:29, - from /usr/include/boost/math/special_functions/beta.hpp:13, - from /usr/include/boost/math/distributions/binomial.hpp:83, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22: -/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] - 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" - | ^~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8862,48 +9020,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -8911,147 +9028,91 @@ from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Linking CXX static library libyaml-cpp.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" -/usr/bin/ranlib libyaml-cpp.a +/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + | ^~~~~ +[ 69%] Linking CXX static library libutils.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 +/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o +/usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 69%] Built target yaml-cpp -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend +[ 69%] Built target utils +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ [ 69%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 69%] Built target pda +[ 74%] Built target pda make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 70%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o -[ 70%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp -[ 70%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp -[ 71%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o -[ 71%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +In file included from /usr/include/c++/13/string:49, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -9059,7 +9120,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9069,20 +9131,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 75%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp +[ 76%] Linking CXX static library libphyloYAML.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 +/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9092,17 +9167,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libphyloYAML.a In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9112,100 +9183,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - | ^~~~~ -[ 71%] Linking CXX static library libutils.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o -/usr/bin/ranlib libutils.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 71%] Built target utils -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build -make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -[ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -[ 75%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -[ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp -[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp -[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o -[ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +[ 76%] Built target phyloYAML +/build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +[ 76%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9218,15 +9203,15 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9234,7 +9219,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9249,8 +9236,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9264,9 +9251,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9280,9 +9267,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9297,8 +9284,9 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9308,29 +9296,47 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9344,19 +9350,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9366,29 +9360,27 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9398,27 +9390,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ +[ 77%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9428,19 +9406,112 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 242 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ +[ 79%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9454,8 +9525,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9469,20 +9539,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9492,17 +9549,11 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9516,8 +9567,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9527,30 +9577,41 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1468 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { + | ^~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9560,31 +9621,42 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9594,18 +9666,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] + 180 | } + | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9615,14 +9702,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': +/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] + 257 | } + | ^ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9632,11 +9722,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -9646,6 +9741,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9658,129 +9759,8 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 242 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] - 180 | } - | ^ -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': -/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] - 257 | } - | ^ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9793,22 +9773,63 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9833,21 +9854,37 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, + from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9860,18 +9897,21 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9910,7 +9950,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -9935,46 +9975,35 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 83%] Linking CXX static library libphyloYAML.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 -/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o -/usr/bin/ranlib libphyloYAML.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 83%] Built target phyloYAML -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1468 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -[ 84%] Linking CXX static library libmain.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 -/usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o -/usr/bin/ranlib libmain.a -make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 84%] Built target main -[ 85%] Linking CXX static library libkernelsse.a +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +[ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 85%] Built target kernelsse -[ 85%] Linking CXX static library libalignment.a -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 -/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -/usr/bin/ranlib libalignment.a +[ 84%] Built target kernelsse +[ 85%] Linking CXX static library libmain.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 +/usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o +/usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 85%] Built target alignment +[ 85%] Built target main [ 86%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 @@ -9989,6 +10018,13 @@ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 86%] Built target kernelavx +[ 86%] Linking CXX static library libalignment.a +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 +/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o +/usr/bin/ranlib libalignment.a +make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' +[ 86%] Built target alignment [ 87%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -10002,75 +10038,51 @@ make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o -cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10094,60 +10106,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 146 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 153 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 160 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 167 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: @@ -10185,8 +10151,9 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10214,27 +10181,15 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: -/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 172 | : public binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -10242,8 +10197,7 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10256,8 +10210,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10270,7 +10224,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10285,8 +10240,8 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10298,24 +10253,21 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10345,8 +10297,8 @@ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10358,9 +10310,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10372,7 +10323,8 @@ | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ @@ -10386,34 +10338,36 @@ from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -10426,7 +10380,7 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -10439,6 +10393,14 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o +cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -10453,6 +10415,80 @@ /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 146 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 153 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 160 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 167 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: +/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 172 | : public binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } @@ -10539,18 +10575,18 @@ echo 'time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ... -+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy ++ /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos5-amd64 (AVX2, FMA3, 78 GB RAM) +Host: i-capture-the-hostname (AVX, 79 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -Seed: 816038 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Mon Jun 2 22:00:35 2025 -Kernel: AVX+FMA - 1 threads (42 CPU cores detected) +Seed: 424751 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue Apr 30 16:01:16 2024 +Kernel: AVX - 1 threads (20 CPU cores detected) -HINT: Use -nt option to specify number of threads because your CPU has 42 cores! +HINT: Use -nt option to specify number of threads because your CPU has 20 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected @@ -10578,128 +10614,128 @@ **** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3) -Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 seconds +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.004 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) -1. Initial log-likelihood: -21149.239 -Optimal log-likelihood: -21149.100 -Rate parameters: A-C: 3.73650 A-G: 5.18609 A-T: 3.83480 C-G: 0.41900 C-T: 15.29543 G-T: 1.00000 +1. Initial log-likelihood: -21149.241 +Optimal log-likelihood: -21148.879 +Rate parameters: A-C: 4.04634 A-G: 5.62615 A-T: 4.17804 C-G: 0.45965 C-T: 16.52262 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 -Gamma shape alpha: 0.739 -Parameters optimization took 1 rounds (0.071 sec) -Time for fast ML tree search: 1.422 seconds +Gamma shape alpha: 0.738 +Parameters optimization took 1 rounds (0.451 sec) +Time for fast ML tree search: 4.528 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC - 1 GTR+F 22701.500 39 45481.000 45482.593 45699.396 - 2 GTR+F+I 21615.547 40 43311.094 43312.770 43535.090 - 3 GTR+F+G4 21155.970 40 42391.940 42393.616 42615.936 - 4 GTR+F+I+G4 21148.849 41 42379.699 42381.459 42609.295 - 5 GTR+F+R2 21235.663 41 42553.327 42555.087 42782.923 - 6 GTR+F+R3 21147.168 43 42380.337 42382.273 42621.132 - 7 GTR+F+R4 21145.837 45 42381.675 42383.796 42633.671 - 16 SYM+G4 21317.782 37 42709.563 42710.998 42916.760 - 17 SYM+I+G4 21306.170 38 42688.341 42689.854 42901.137 + 1 GTR+F 22701.485 39 45480.970 45482.563 45699.366 + 2 GTR+F+I 21615.548 40 43311.095 43312.771 43535.091 + 3 GTR+F+G4 21155.969 40 42391.938 42393.614 42615.934 + 4 GTR+F+I+G4 21148.850 41 42379.699 42381.460 42609.295 + 5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922 + 6 GTR+F+R3 21147.207 43 42380.415 42382.351 42621.210 + 7 GTR+F+R4 21145.838 45 42381.675 42383.796 42633.671 + 16 SYM+G4 21317.781 37 42709.563 42710.998 42916.759 + 17 SYM+I+G4 21306.174 38 42688.347 42689.860 42901.144 29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870 - 30 TVM+F+I+G4 21288.270 40 42656.541 42658.217 42880.537 - 42 TVMe+G4 21422.186 36 42916.372 42917.730 43117.968 - 43 TVMe+I+G4 21407.596 37 42889.191 42890.626 43096.388 + 30 TVM+F+I+G4 21288.274 40 42656.549 42658.225 42880.545 + 42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969 + 43 TVMe+I+G4 21407.601 37 42889.203 42890.637 43096.399 55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649 - 56 TIM3+F+I+G4 21359.476 39 42796.953 42798.546 43015.349 + 56 TIM3+F+I+G4 21359.483 39 42796.966 42798.560 43015.362 68 TIM3e+G4 21717.462 35 43504.924 43506.209 43700.921 - 69 TIM3e+I+G4 21708.558 36 43489.115 43490.473 43690.711 - 81 TIM2+F+G4 21159.708 38 42395.415 42396.928 42608.212 - 82 TIM2+F+I+G4 21152.489 39 42382.979 42384.572 42601.375 + 69 TIM3e+I+G4 21708.559 36 43489.119 43490.477 43690.715 + 81 TIM2+F+G4 21159.707 38 42395.414 42396.927 42608.211 + 82 TIM2+F+I+G4 21152.490 39 42382.981 42384.574 42601.377 94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757 - 95 TIM2e+I+G4 21309.127 36 42690.254 42691.613 42891.851 -107 TIM+F+G4 21368.780 38 42813.560 42815.073 43026.356 -108 TIM+F+I+G4 21360.237 39 42798.474 42800.068 43016.871 -120 TIMe+G4 21718.131 35 43506.262 43507.546 43702.258 -121 TIMe+I+G4 21709.220 36 43490.439 43491.798 43692.036 + 95 TIM2e+I+G4 21309.130 36 42690.259 42691.618 42891.856 +107 TIM+F+G4 21368.780 38 42813.559 42815.073 43026.356 +108 TIM+F+I+G4 21360.238 39 42798.476 42800.070 43016.872 +120 TIMe+G4 21718.131 35 43506.262 43507.547 43702.259 +121 TIMe+I+G4 21709.222 36 43490.443 43491.802 43692.040 133 TPM3u+F+G4 21488.892 37 43051.785 43053.219 43258.981 -134 TPM3u+F+I+G4 21474.934 38 43025.868 43027.381 43238.664 +134 TPM3u+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 146 TPM3+F+G4 21488.892 37 43051.785 43053.219 43258.981 -147 TPM3+F+I+G4 21474.934 38 43025.868 43027.381 43238.664 +147 TPM3+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.790 -160 TPM2u+F+I+G4 21291.866 38 42659.732 42661.245 42872.529 +160 TPM2u+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.790 -173 TPM2+F+I+G4 21291.866 38 42659.732 42661.245 42872.529 +173 TPM2+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 185 K3Pu+F+G4 21489.348 37 43052.695 43054.130 43259.892 -186 K3Pu+F+I+G4 21475.443 38 43026.886 43028.399 43239.682 -198 K3P+G4 21847.491 34 43762.981 43764.193 43953.378 -199 K3P+I+G4 21833.794 35 43737.589 43738.873 43933.586 +186 K3Pu+F+I+G4 21475.448 38 43026.895 43028.408 43239.691 +198 K3P+G4 21847.490 34 43762.981 43764.193 43953.378 +199 K3P+I+G4 21833.799 35 43737.597 43738.882 43933.594 211 TN+F+G4 21369.048 37 42812.095 42813.530 43019.292 -212 TN+F+I+G4 21360.511 38 42797.021 42798.534 43009.817 +212 TN+F+I+G4 21360.518 38 42797.036 42798.550 43009.833 224 TNe+G4 21718.201 34 43504.403 43505.615 43694.799 -225 TNe+I+G4 21709.280 35 43488.559 43489.844 43684.556 +225 TNe+I+G4 21709.282 35 43488.563 43489.848 43684.560 237 HKY+F+G4 21489.737 36 43051.474 43052.832 43253.070 -238 HKY+F+I+G4 21475.767 37 43025.533 43026.968 43232.730 +238 HKY+F+I+G4 21475.770 37 43025.540 43026.974 43232.736 250 K2P+G4 21847.675 33 43761.350 43762.492 43946.146 -251 K2P+I+G4 21833.947 34 43735.895 43737.107 43926.292 +251 K2P+I+G4 21833.952 34 43735.903 43737.116 43926.300 263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152 -264 F81+F+I+G4 22019.574 36 44111.147 44112.506 44312.744 +264 F81+F+I+G4 22019.580 36 44111.159 44112.518 44312.756 276 JC+G4 22258.086 32 44580.172 44581.246 44759.368 -277 JC+I+G4 22245.552 33 44557.104 44558.247 44741.901 +277 JC+I+G4 22245.555 33 44557.111 44558.253 44741.908 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 9.288 seconds (0h:0m:9s) -Wall-clock time for ModelFinder: 17.531 seconds (0h:0m:17s) +CPU time for ModelFinder: 26.384 seconds (0h:0m:26s) +Wall-clock time for ModelFinder: 65.042 seconds (0h:1m:5s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... -Init pinv, alpha: 0.000, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748 -Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.976 -Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.640 -Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.216 -Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.516 -Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778 -Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833 -Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.812 / LogL: -21152.858 -Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876 -Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.904 -Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.516 +Init pinv, alpha: 0.000, 0.737 / Estimate: 0.000, 0.482 / LogL: -21159.748 +Init pinv, alpha: 0.038, 0.737 / Estimate: 0.043, 0.532 / LogL: -21156.975 +Init pinv, alpha: 0.076, 0.737 / Estimate: 0.085, 0.592 / LogL: -21154.640 +Init pinv, alpha: 0.114, 0.737 / Estimate: 0.120, 0.654 / LogL: -21153.216 +Init pinv, alpha: 0.153, 0.737 / Estimate: 0.153, 0.726 / LogL: -21152.514 +Init pinv, alpha: 0.191, 0.737 / Estimate: 0.183, 0.804 / LogL: -21152.778 +Init pinv, alpha: 0.229, 0.737 / Estimate: 0.187, 0.817 / LogL: -21152.912 +Init pinv, alpha: 0.267, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.863 +Init pinv, alpha: 0.305, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.873 +Init pinv, alpha: 0.343, 0.737 / Estimate: 0.187, 0.816 / LogL: -21152.902 +Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514 -Parameters optimization took 6.047 sec -Computing ML distances based on estimated model parameters... 0.010 sec +Parameters optimization took 20.545 sec +Computing ML distances based on estimated model parameters... 0.011 sec Computing BIONJ tree... 0.001 seconds -Log-likelihood of BIONJ tree: -21157.740 +Log-likelihood of BIONJ tree: -21157.741 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 0.818 second -Computing log-likelihood of 98 initial trees ... 1.901 seconds -Current best score: -21152.516 +Generating 98 parsimony trees... 0.978 second +Computing log-likelihood of 98 initial trees ... 6.070 seconds +Current best score: -21152.514 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.511 -Iteration 10 / LogL: -21152.728 / Time: 0h:0m:10s -Iteration 20 / LogL: -21153.061 / Time: 0h:0m:13s +Iteration 10 / LogL: -21157.873 / Time: 0h:0m:32s +Iteration 20 / LogL: -21152.554 / Time: 0h:0m:36s Finish initializing candidate tree set (2) -Current best tree score: -21152.511 / CPU time: 7.219 +Current best tree score: -21152.511 / CPU time: 16.051 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -21152.750 / Time: 0h:0m:16s (0h:0m:39s left) -Iteration 40 / LogL: -21152.599 / Time: 0h:0m:19s (0h:0m:30s left) -Iteration 50 / LogL: -21152.574 / Time: 0h:0m:21s (0h:0m:22s left) -Iteration 60 / LogL: -21152.566 / Time: 0h:0m:23s (0h:0m:16s left) -Iteration 70 / LogL: -21152.541 / Time: 0h:0m:25s (0h:0m:11s left) -Iteration 80 / LogL: -21152.635 / Time: 0h:0m:27s (0h:0m:7s left) -Iteration 90 / LogL: -21152.566 / Time: 0h:0m:28s (0h:0m:3s left) -Iteration 100 / LogL: -21158.279 / Time: 0h:0m:31s (0h:0m:0s left) -TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:31s +Iteration 30 / LogL: -21152.572 / Time: 0h:0m:43s (0h:1m:45s left) +Iteration 40 / LogL: -21152.589 / Time: 0h:0m:47s (0h:1m:14s left) +Iteration 50 / LogL: -21152.889 / Time: 0h:0m:56s (0h:0m:59s left) +Iteration 60 / LogL: -21157.810 / Time: 0h:1m:8s (0h:0m:47s left) +Iteration 70 / LogL: -21152.543 / Time: 0h:1m:13s (0h:0m:33s left) +Iteration 80 / LogL: -21152.555 / Time: 0h:1m:20s (0h:0m:21s left) +Iteration 90 / LogL: -21158.318 / Time: 0h:1m:26s (0h:0m:10s left) +Iteration 100 / LogL: -21153.052 / Time: 0h:1m:31s (0h:0m:0s left) +TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:1m:32s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | @@ -10708,19 +10744,19 @@ Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.511 Optimal log-likelihood: -21152.507 -Rate parameters: A-C: 5.70686 A-G: 7.79923 A-T: 5.70686 C-G: 1.00000 C-T: 23.13277 G-T: 1.00000 +Rate parameters: A-C: 5.70370 A-G: 7.79572 A-T: 5.70370 C-G: 1.00000 C-T: 23.14180 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.728 -Parameters optimization took 1 rounds (0.072 sec) +Parameters optimization took 1 rounds (0.144 sec) BEST SCORE FOUND : -21152.507 -Total tree length: 4.225 +Total tree length: 4.226 Total number of iterations: 102 -CPU time used for tree search: 11.060 sec (0h:0m:11s) -Wall-clock time used for tree search: 25.581 sec (0h:0m:25s) -Total CPU time used: 13.454 sec (0h:0m:13s) -Total wall-clock time used: 31.800 sec (0h:0m:31s) +CPU time used for tree search: 42.293 sec (0h:0m:42s) +Wall-clock time used for tree search: 71.755 sec (0h:1m:11s) +Total CPU time used: 49.392 sec (0h:0m:49s) +Total wall-clock time used: 92.778 sec (0h:1m:32s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -10728,21 +10764,23 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Mon Jun 2 22:01:25 2025 -22.75user 0.18system 0:49.36elapsed 46%CPU (0avgtext+0avgdata 16408maxresident)k -0inputs+168outputs (0major+5610minor)pagefaults 0swaps -+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo +Date and Time: Tue Apr 30 16:03:54 2024 + +real 2m37.917s +user 1m15.799s +sys 0m0.323s ++ /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos5-amd64 (AVX2, FMA3, 78 GB RAM) +Host: i-capture-the-hostname (AVX, 79 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo -Seed: 191817 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Mon Jun 2 22:01:25 2025 -Kernel: AVX+FMA - 1 threads (42 CPU cores detected) +Seed: 343764 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue Apr 30 16:03:54 2024 +Kernel: AVX - 1 threads (20 CPU cores detected) -HINT: Use -nt option to specify number of threads because your CPU has 42 cores! +HINT: Use -nt option to specify number of threads because your CPU has 20 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected @@ -10775,123 +10813,123 @@ Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) -1. Initial log-likelihood: -21149.239 -Optimal log-likelihood: -21149.100 -Rate parameters: A-C: 3.73650 A-G: 5.18609 A-T: 3.83480 C-G: 0.41900 C-T: 15.29543 G-T: 1.00000 +1. Initial log-likelihood: -21149.241 +Optimal log-likelihood: -21148.879 +Rate parameters: A-C: 4.04634 A-G: 5.62615 A-T: 4.17804 C-G: 0.45965 C-T: 16.52262 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 -Gamma shape alpha: 0.739 -Parameters optimization took 1 rounds (0.184 sec) -Time for fast ML tree search: 1.947 seconds +Gamma shape alpha: 0.738 +Parameters optimization took 1 rounds (0.194 sec) +Time for fast ML tree search: 3.080 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC - 1 GTR+F 22701.500 39 45481.000 45482.593 45699.396 - 2 GTR+F+I 21615.547 40 43311.094 43312.770 43535.090 - 3 GTR+F+G4 21155.970 40 42391.940 42393.616 42615.936 - 4 GTR+F+I+G4 21148.849 41 42379.699 42381.459 42609.295 - 5 GTR+F+R2 21235.663 41 42553.327 42555.087 42782.923 - 6 GTR+F+R3 21147.168 43 42380.337 42382.273 42621.132 - 7 GTR+F+R4 21145.837 45 42381.675 42383.796 42633.671 - 16 SYM+G4 21317.782 37 42709.563 42710.998 42916.760 - 17 SYM+I+G4 21306.170 38 42688.341 42689.854 42901.137 + 1 GTR+F 22701.485 39 45480.970 45482.563 45699.366 + 2 GTR+F+I 21615.548 40 43311.095 43312.771 43535.091 + 3 GTR+F+G4 21155.969 40 42391.938 42393.614 42615.934 + 4 GTR+F+I+G4 21148.850 41 42379.699 42381.460 42609.295 + 5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922 + 6 GTR+F+R3 21147.207 43 42380.415 42382.351 42621.210 + 7 GTR+F+R4 21145.838 45 42381.675 42383.796 42633.671 + 16 SYM+G4 21317.781 37 42709.563 42710.998 42916.759 + 17 SYM+I+G4 21306.174 38 42688.347 42689.860 42901.144 29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870 - 30 TVM+F+I+G4 21288.270 40 42656.541 42658.217 42880.537 - 42 TVMe+G4 21422.186 36 42916.372 42917.730 43117.968 - 43 TVMe+I+G4 21407.596 37 42889.191 42890.626 43096.388 + 30 TVM+F+I+G4 21288.274 40 42656.549 42658.225 42880.545 + 42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969 + 43 TVMe+I+G4 21407.601 37 42889.203 42890.637 43096.399 55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649 - 56 TIM3+F+I+G4 21359.476 39 42796.953 42798.546 43015.349 + 56 TIM3+F+I+G4 21359.483 39 42796.966 42798.560 43015.362 68 TIM3e+G4 21717.462 35 43504.924 43506.209 43700.921 - 69 TIM3e+I+G4 21708.558 36 43489.115 43490.473 43690.711 - 81 TIM2+F+G4 21159.708 38 42395.415 42396.928 42608.212 - 82 TIM2+F+I+G4 21152.489 39 42382.979 42384.572 42601.375 + 69 TIM3e+I+G4 21708.559 36 43489.119 43490.477 43690.715 + 81 TIM2+F+G4 21159.707 38 42395.414 42396.927 42608.211 + 82 TIM2+F+I+G4 21152.490 39 42382.981 42384.574 42601.377 94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757 - 95 TIM2e+I+G4 21309.127 36 42690.254 42691.613 42891.851 -107 TIM+F+G4 21368.780 38 42813.560 42815.073 43026.356 -108 TIM+F+I+G4 21360.237 39 42798.474 42800.068 43016.871 -120 TIMe+G4 21718.131 35 43506.262 43507.546 43702.258 -121 TIMe+I+G4 21709.220 36 43490.439 43491.798 43692.036 + 95 TIM2e+I+G4 21309.130 36 42690.259 42691.618 42891.856 +107 TIM+F+G4 21368.780 38 42813.559 42815.073 43026.356 +108 TIM+F+I+G4 21360.238 39 42798.476 42800.070 43016.872 +120 TIMe+G4 21718.131 35 43506.262 43507.547 43702.259 +121 TIMe+I+G4 21709.222 36 43490.443 43491.802 43692.040 133 TPM3u+F+G4 21488.892 37 43051.785 43053.219 43258.981 -134 TPM3u+F+I+G4 21474.934 38 43025.868 43027.381 43238.664 +134 TPM3u+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 146 TPM3+F+G4 21488.892 37 43051.785 43053.219 43258.981 -147 TPM3+F+I+G4 21474.934 38 43025.868 43027.381 43238.664 +147 TPM3+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.790 -160 TPM2u+F+I+G4 21291.866 38 42659.732 42661.245 42872.529 +160 TPM2u+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.790 -173 TPM2+F+I+G4 21291.866 38 42659.732 42661.245 42872.529 +173 TPM2+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 185 K3Pu+F+G4 21489.348 37 43052.695 43054.130 43259.892 -186 K3Pu+F+I+G4 21475.443 38 43026.886 43028.399 43239.682 -198 K3P+G4 21847.491 34 43762.981 43764.193 43953.378 -199 K3P+I+G4 21833.794 35 43737.589 43738.873 43933.586 +186 K3Pu+F+I+G4 21475.448 38 43026.895 43028.408 43239.691 +198 K3P+G4 21847.490 34 43762.981 43764.193 43953.378 +199 K3P+I+G4 21833.799 35 43737.597 43738.882 43933.594 211 TN+F+G4 21369.048 37 42812.095 42813.530 43019.292 -212 TN+F+I+G4 21360.511 38 42797.021 42798.534 43009.817 +212 TN+F+I+G4 21360.518 38 42797.036 42798.550 43009.833 224 TNe+G4 21718.201 34 43504.403 43505.615 43694.799 -225 TNe+I+G4 21709.280 35 43488.559 43489.844 43684.556 +225 TNe+I+G4 21709.282 35 43488.563 43489.848 43684.560 237 HKY+F+G4 21489.737 36 43051.474 43052.832 43253.070 -238 HKY+F+I+G4 21475.767 37 43025.533 43026.968 43232.730 +238 HKY+F+I+G4 21475.770 37 43025.540 43026.974 43232.736 250 K2P+G4 21847.675 33 43761.350 43762.492 43946.146 -251 K2P+I+G4 21833.947 34 43735.895 43737.107 43926.292 +251 K2P+I+G4 21833.952 34 43735.903 43737.116 43926.300 263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152 -264 F81+F+I+G4 22019.574 36 44111.147 44112.506 44312.744 +264 F81+F+I+G4 22019.580 36 44111.159 44112.518 44312.756 276 JC+G4 22258.086 32 44580.172 44581.246 44759.368 -277 JC+I+G4 22245.552 33 44557.104 44558.247 44741.901 +277 JC+I+G4 22245.555 33 44557.111 44558.253 44741.908 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 9.295 seconds (0h:0m:9s) -Wall-clock time for ModelFinder: 25.598 seconds (0h:0m:25s) +CPU time for ModelFinder: 27.640 seconds (0h:0m:27s) +Wall-clock time for ModelFinder: 43.879 seconds (0h:0m:43s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... -Init pinv, alpha: 0.000, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748 -Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.976 -Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.640 -Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.216 -Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.516 -Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778 -Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833 -Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.812 / LogL: -21152.858 -Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876 -Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.904 -Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.516 +Init pinv, alpha: 0.000, 0.737 / Estimate: 0.000, 0.482 / LogL: -21159.748 +Init pinv, alpha: 0.038, 0.737 / Estimate: 0.043, 0.532 / LogL: -21156.975 +Init pinv, alpha: 0.076, 0.737 / Estimate: 0.085, 0.592 / LogL: -21154.640 +Init pinv, alpha: 0.114, 0.737 / Estimate: 0.120, 0.654 / LogL: -21153.216 +Init pinv, alpha: 0.153, 0.737 / Estimate: 0.153, 0.726 / LogL: -21152.514 +Init pinv, alpha: 0.191, 0.737 / Estimate: 0.183, 0.804 / LogL: -21152.778 +Init pinv, alpha: 0.229, 0.737 / Estimate: 0.187, 0.817 / LogL: -21152.912 +Init pinv, alpha: 0.267, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.863 +Init pinv, alpha: 0.305, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.873 +Init pinv, alpha: 0.343, 0.737 / Estimate: 0.187, 0.816 / LogL: -21152.902 +Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514 -Parameters optimization took 6.155 sec -Computing ML distances based on estimated model parameters... 0.010 sec +Parameters optimization took 7.903 sec +Computing ML distances based on estimated model parameters... 0.013 sec Computing BIONJ tree... -0.002 seconds -Log-likelihood of BIONJ tree: -21157.740 +0.001 seconds +Log-likelihood of BIONJ tree: -21157.741 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 1.021 second -Computing log-likelihood of 98 initial trees ... 2.150 seconds -Current best score: -21152.516 +Generating 98 parsimony trees... 0.428 second +Computing log-likelihood of 98 initial trees ... 3.633 seconds +Current best score: -21152.514 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.511 -Iteration 10 / LogL: -21152.536 / Time: 0h:0m:11s -Iteration 20 / LogL: -21152.728 / Time: 0h:0m:14s +Iteration 10 / LogL: -21152.618 / Time: 0h:0m:14s +Iteration 20 / LogL: -21152.514 / Time: 0h:0m:18s Finish initializing candidate tree set (2) -Current best tree score: -21152.511 / CPU time: 7.964 +Current best tree score: -21152.511 / CPU time: 10.196 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -21152.938 / Time: 0h:0m:16s (0h:0m:41s left) -Iteration 40 / LogL: -21157.823 / Time: 0h:0m:19s (0h:0m:30s left) -Iteration 50 / LogL: -21152.559 / Time: 0h:0m:22s (0h:0m:23s left) -Iteration 60 / LogL: -21152.555 / Time: 0h:0m:24s (0h:0m:17s left) -Iteration 70 / LogL: -21152.519 / Time: 0h:0m:27s (0h:0m:12s left) -Iteration 80 / LogL: -21152.841 / Time: 0h:0m:30s (0h:0m:8s left) -Iteration 90 / LogL: -21152.584 / Time: 0h:0m:33s (0h:0m:4s left) -Iteration 100 / LogL: -21153.024 / Time: 0h:0m:36s (0h:0m:0s left) -TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:36s +Iteration 30 / LogL: -21152.602 / Time: 0h:0m:21s (0h:0m:53s left) +Iteration 40 / LogL: -21157.860 / Time: 0h:0m:24s (0h:0m:38s left) +Iteration 50 / LogL: -21152.604 / Time: 0h:0m:27s (0h:0m:29s left) +Iteration 60 / LogL: -21152.534 / Time: 0h:0m:31s (0h:0m:21s left) +Iteration 70 / LogL: -21152.523 / Time: 0h:0m:34s (0h:0m:15s left) +Iteration 80 / LogL: -21157.740 / Time: 0h:0m:37s (0h:0m:10s left) +Iteration 90 / LogL: -21153.364 / Time: 0h:0m:40s (0h:0m:5s left) +Iteration 100 / LogL: -21152.518 / Time: 0h:0m:43s (0h:0m:0s left) +TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:44s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | @@ -10900,19 +10938,19 @@ Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.511 Optimal log-likelihood: -21152.507 -Rate parameters: A-C: 5.70686 A-G: 7.79923 A-T: 5.70686 C-G: 1.00000 C-T: 23.13277 G-T: 1.00000 +Rate parameters: A-C: 5.70370 A-G: 7.79572 A-T: 5.70370 C-G: 1.00000 C-T: 23.14180 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.728 -Parameters optimization took 1 rounds (0.072 sec) +Parameters optimization took 1 rounds (0.060 sec) BEST SCORE FOUND : -21152.507 -Total tree length: 4.225 +Total tree length: 4.226 Total number of iterations: 102 -CPU time used for tree search: 11.054 sec (0h:0m:11s) -Wall-clock time used for tree search: 30.280 sec (0h:0m:30s) -Total CPU time used: 13.462 sec (0h:0m:13s) -Total wall-clock time used: 36.692 sec (0h:0m:36s) +CPU time used for tree search: 36.287 sec (0h:0m:36s) +Wall-clock time used for tree search: 36.552 sec (0h:0m:36s) +Total CPU time used: 43.262 sec (0h:0m:43s) +Total wall-clock time used: 44.649 sec (0h:0m:44s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -10920,12 +10958,14 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Mon Jun 2 22:02:27 2025 -22.77user 0.16system 1:02.33elapsed 36%CPU (0avgtext+0avgdata 15352maxresident)k -0inputs+208outputs (0major+6477minor)pagefaults 0swaps -+ rm -rf /tmp/iqtree-test.DMtamU -45.56user 0.36system 1:51.84elapsed 41%CPU (0avgtext+0avgdata 16408maxresident)k -0inputs+456outputs (0major+13513minor)pagefaults 0swaps +Date and Time: Tue Apr 30 16:05:22 2024 + +real 1m28.573s +user 1m10.913s +sys 0m0.339s ++ rm -rf /tmp/iqtree-test.KdclG2 +146.74user 0.71system 4:06.82elapsed 59%CPU (0avgtext+0avgdata 15732maxresident)k +0inputs+608outputs (0major+9382minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg' create-stamp debian/debhelper-build-stamp @@ -10934,7 +10974,7 @@ make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi - cd build.serial && make -j42 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.serial && make -j20 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -10952,7 +10992,7 @@ -- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi - cd build.mpi && make -j42 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.mpi && make -j20 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -11024,12 +11064,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2596749/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2326818 and its subdirectories -I: Current time: Mon Jun 2 10:06:56 -12 2025 -I: pbuilder-time-stamp: 1748902016 +I: removing directory /srv/workspace/pbuilder/2596749 and its subdirectories +I: Current time: Wed May 1 06:08:55 +14 2024 +I: pbuilder-time-stamp: 1714493335