Diff of the two buildlogs: -- --- b1/build.log 2024-11-18 14:39:52.343314599 +0000 +++ b2/build.log 2024-11-18 14:46:05.994403850 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 21 08:48:07 -12 2025 -I: pbuilder-time-stamp: 1766350087 +I: Current time: Tue Nov 19 04:39:55 +14 2024 +I: pbuilder-time-stamp: 1731940795 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/258957/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2541068/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +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 Nov 18 14:40 /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/2541068/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2541068/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='4662a16e4925448aab72e9feecc7556c' - 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='258957' - PS1='# ' - PS2='> ' + INVOCATION_ID=264f694925324cba8c0c3c710b3dea44 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2541068 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.bkfPDvra/pbuilderrc_EoAw --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bkfPDvra/b1 --logfile b1/build.log bali-phy_3.6.1+dfsg-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.bkfPDvra/pbuilderrc_kwWy --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bkfPDvra/b2 --logfile b2/build.log bali-phy_3.6.1+dfsg-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/258957/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2541068/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +329,7 @@ Get: 161 http://deb.debian.org/debian unstable/main arm64 nlohmann-json3-dev all 3.11.3-1 [261 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] -Fetched 88.6 MB in 1s (87.0 MB/s) +Fetched 88.6 MB in 0s (220 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) @@ -843,8 +875,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 21 20:49:09 UTC 2025. -Universal Time is now: Sun Dec 21 20:49:09 UTC 2025. +Local time is now: Mon Nov 18 14:40:23 UTC 2024. +Universal Time is now: Mon Nov 18 14:40:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-3.2+b1) ... @@ -981,7 +1013,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bali-phy-3.6.1+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 > ../bali-phy_3.6.1+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/2541068/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2541068/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bali-phy-3.6.1+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 > ../bali-phy_3.6.1+dfsg-3_source.changes dpkg-buildpackage: info: source package bali-phy dpkg-buildpackage: info: source version 3.6.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1090,122 +1126,121 @@ cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j12 -v [1/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/log-level.cc.o -MF src/util/libutil.a.p/log-level.cc.o.d -o src/util/libutil.a.p/log-level.cc.o -c ../src/util/log-level.cc [2/297] /usr/bin/meson --internal vcstagger ../src/git-version.h.in src/git-version.h 3.6.1 /build/reproducible-path/bali-phy-3.6.1+dfsg/src @git_message@ '(.*)' git log -n1 '--date=format:%b %d %Y %k:%M:%S' '--pretty=format:[%D commit %h] (%cd)' -[3/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc -[4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc -[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc +[3/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc +[4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc +[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc [6/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc [7/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_sanitize.cc.o -MF src/util/libutil.a.p/string_sanitize.cc.o.d -o src/util/libutil.a.p/string_sanitize.cc.o -c ../src/util/string/sanitize.cc -[8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/mapping.cc.o -MF src/util/libutil.a.p/mapping.cc.o.d -o src/util/libutil.a.p/mapping.cc.o -c ../src/util/mapping.cc -[9/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc -[10/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/permute.cc.o -MF src/util/libutil.a.p/permute.cc.o.d -o src/util/libutil.a.p/permute.cc.o -c ../src/util/permute.cc -[11/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/rng.cc.o -MF src/util/libutil.a.p/rng.cc.o.d -o src/util/libutil.a.p/rng.cc.o -c ../src/util/rng.cc -[12/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_newick-tokenizer.cc.o -MF src/libcommon.a.p/tree_newick-tokenizer.cc.o.d -o src/libcommon.a.p/tree_newick-tokenizer.cc.o -c ../src/tree/newick-tokenizer.cc -[13/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-paths.cc.o -MF src/util/libutil.a.p/file-paths.cc.o.d -o src/util/libutil.a.p/file-paths.cc.o -c ../src/util/file-paths.cc -[14/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/time.cc.o -MF src/util/libutil.a.p/time.cc.o.d -o src/util/libutil.a.p/time.cc.o -c ../src/util/time.cc -[15/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/io.cc.o -MF src/util/libutil.a.p/io.cc.o.d -o src/util/libutil.a.p/io.cc.o -c ../src/util/io.cc +[8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/permute.cc.o -MF src/util/libutil.a.p/permute.cc.o.d -o src/util/libutil.a.p/permute.cc.o -c ../src/util/permute.cc +[9/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/mapping.cc.o -MF src/util/libutil.a.p/mapping.cc.o.d -o src/util/libutil.a.p/mapping.cc.o -c ../src/util/mapping.cc +[10/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc +[11/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_newick-tokenizer.cc.o -MF src/libcommon.a.p/tree_newick-tokenizer.cc.o.d -o src/libcommon.a.p/tree_newick-tokenizer.cc.o -c ../src/tree/newick-tokenizer.cc +[12/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-paths.cc.o -MF src/util/libutil.a.p/file-paths.cc.o.d -o src/util/libutil.a.p/file-paths.cc.o -c ../src/util/file-paths.cc +[13/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/time.cc.o -MF src/util/libutil.a.p/time.cc.o.d -o src/util/libutil.a.p/time.cc.o -c ../src/util/time.cc +[14/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/rng.cc.o -MF src/util/libutil.a.p/rng.cc.o.d -o src/util/libutil.a.p/rng.cc.o -c ../src/util/rng.cc +[15/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-readers.cc.o -MF src/util/libutil.a.p/file-readers.cc.o.d -o src/util/libutil.a.p/file-readers.cc.o -c ../src/util/file-readers.cc +[16/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/io.cc.o -MF src/util/libutil.a.p/io.cc.o.d -o src/util/libutil.a.p/io.cc.o -c ../src/util/io.cc ../src/util/io.cc: In function ‘std::vector > load_lines(std::istream&, int, int, int)’: ../src/util/io.cc:113:21: warning: redundant move in return statement [-Wredundant-move] 113 | return std::move(lines); | ~~~~~~~~~^~~~~~~ ../src/util/io.cc:113:21: note: remove ‘std::move’ call -[16/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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-Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-random.cc.o -MF src/libcommon.a.p/alignment_alignment-random.cc.o.d -o src/libcommon.a.p/alignment_alignment-random.cc.o -c ../src/alignment/alignment-random.cc -[28/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_split.cc.o -MF src/util/libutil.a.p/string_split.cc.o.d -o src/util/libutil.a.p/string_split.cc.o -c ../src/util/string/split.cc -[29/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_statistics.cc.o -MF src/libcommon.a.p/tools_statistics.cc.o.d -o src/libcommon.a.p/tools_statistics.cc.o -c ../src/tools/statistics.cc +[27/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_sequencetree.cc.o -MF src/libcommon.a.p/tree_sequencetree.cc.o.d -o src/libcommon.a.p/tree_sequencetree.cc.o -c ../src/tree/sequencetree.cc +[28/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-random.cc.o -MF src/libcommon.a.p/alignment_alignment-random.cc.o.d -o src/libcommon.a.p/alignment_alignment-random.cc.o -c ../src/alignment/alignment-random.cc +[29/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc +[30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_statistics.cc.o -MF src/libcommon.a.p/tools_statistics.cc.o.d -o src/libcommon.a.p/tools_statistics.cc.o -c ../src/tools/statistics.cc ../src/tools/statistics.cc: In function ‘std::pair statistics::central_confidence_interval(const std::valarray&, double)’: ../src/tools/statistics.cc:132:90: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 132 | pair central_confidence_interval(const valarray& values,double P) | ^ -[30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc [31/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/models_path.cc.o -MF src/libcommon.a.p/models_path.cc.o.d -o src/libcommon.a.p/models_path.cc.o -c ../src/models/path.cc -[32/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_read-trees.cc.o -MF src/libcommon.a.p/tools_read-trees.cc.o.d -o src/libcommon.a.p/tools_read-trees.cc.o -c ../src/tools/read-trees.cc -[33/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree.cc.o -MF src/libcommon.a.p/tree_tree.cc.o.d -o src/libcommon.a.p/tree_tree.cc.o -c ../src/tree/tree.cc -[34/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_parsimony.cc.o -MF src/libcommon.a.p/tools_parsimony.cc.o.d -o src/libcommon.a.p/tools_parsimony.cc.o -c ../src/tools/parsimony.cc -[35/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_load.cc.o -MF src/libcommon.a.p/alignment_load.cc.o.d -o src/libcommon.a.p/alignment_load.cc.o -c ../src/alignment/load.cc -[36/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_alphabet.cc.o -MF src/libcommon.a.p/sequence_alphabet.cc.o.d -o src/libcommon.a.p/sequence_alphabet.cc.o -c ../src/sequence/alphabet.cc -[37/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_index-matrix.cc.o -MF src/libcommon.a.p/alignment_index-matrix.cc.o.d -o src/libcommon.a.p/alignment_index-matrix.cc.o -c ../src/alignment/index-matrix.cc +[32/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare 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-Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_read-trees.cc.o -MF src/libcommon.a.p/tools_read-trees.cc.o.d -o src/libcommon.a.p/tools_read-trees.cc.o -c ../src/tools/read-trees.cc +[34/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_alphabet.cc.o -MF src/libcommon.a.p/sequence_alphabet.cc.o.d -o src/libcommon.a.p/sequence_alphabet.cc.o -c ../src/sequence/alphabet.cc +[35/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_index-matrix.cc.o -MF src/libcommon.a.p/alignment_index-matrix.cc.o.d -o src/libcommon.a.p/alignment_index-matrix.cc.o -c ../src/alignment/index-matrix.cc +[36/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_parsimony.cc.o -MF src/libcommon.a.p/tools_parsimony.cc.o.d -o src/libcommon.a.p/tools_parsimony.cc.o -c ../src/tools/parsimony.cc +[37/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_optimize.cc.o -MF src/libcommon.a.p/tools_optimize.cc.o.d -o src/libcommon.a.p/tools_optimize.cc.o -c ../src/tools/optimize.cc [38/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment.cc.o -MF src/libcommon.a.p/alignment_alignment.cc.o.d -o src/libcommon.a.p/alignment_alignment.cc.o -c ../src/alignment/alignment.cc -[39/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-util.cc.o -MF src/libcommon.a.p/alignment_alignment-util.cc.o.d -o src/libcommon.a.p/alignment_alignment-util.cc.o -c ../src/alignment/alignment-util.cc -[40/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_findroot.cc.o -MF src/libcommon.a.p/tools_findroot.cc.o.d -o src/libcommon.a.p/tools_findroot.cc.o -c ../src/tools/findroot.cc -[41/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_optimize.cc.o -MF src/libcommon.a.p/tools_optimize.cc.o.d -o src/libcommon.a.p/tools_optimize.cc.o -c ../src/tools/optimize.cc -[42/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/object.cc.o -MF src/computation/libcomputation.a.p/object.cc.o.d -o src/computation/libcomputation.a.p/object.cc.o -c ../src/computation/object.cc -[43/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_partition.cc.o -MF src/libcommon.a.p/tools_partition.cc.o.d -o src/libcommon.a.p/tools_partition.cc.o -c ../src/tools/partition.cc -[44/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/closure.cc.o -MF src/computation/libcomputation.a.p/closure.cc.o.d -o src/computation/libcomputation.a.p/closure.cc.o -c ../src/computation/closure.cc -[45/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_tree-dist.cc.o -MF src/libcommon.a.p/tools_tree-dist.cc.o.d -o src/libcommon.a.p/tools_tree-dist.cc.o -c ../src/tools/tree-dist.cc -[46/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_distance-report.cc.o -MF src/libcommon.a.p/tools_distance-report.cc.o.d -o src/libcommon.a.p/tools_distance-report.cc.o -c ../src/tools/distance-report.cc +[39/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_partition.cc.o -MF src/libcommon.a.p/tools_partition.cc.o.d -o src/libcommon.a.p/tools_partition.cc.o -c ../src/tools/partition.cc +[40/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_distance-report.cc.o -MF src/libcommon.a.p/tools_distance-report.cc.o.d -o src/libcommon.a.p/tools_distance-report.cc.o -c ../src/tools/distance-report.cc ../src/tools/distance-report.cc: In function ‘void report_distances(const std::valarray&, const std::string&, boost::program_options::variables_map&)’: ../src/tools/distance-report.cc:35:75: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 35 | pair interval = central_confidence_interval(distances,P); | ^ +[41/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/object.cc.o -MF 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-DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_mctree.cc.o -MF src/libcommon.a.p/tools_mctree.cc.o.d -o src/libcommon.a.p/tools_mctree.cc.o -c ../src/tools/mctree.cc +[50/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_inverse.cc.o -MF src/libcommon.a.p/tools_inverse.cc.o.d -o src/libcommon.a.p/tools_inverse.cc.o -c ../src/tools/inverse.cc +[51/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/operations.cc.o -MF src/computation/libcomputation.a.p/operations.cc.o.d -o src/computation/libcomputation.a.p/operations.cc.o -c ../src/computation/operations.cc +[52/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 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-DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_joint-A-T.cc.o -MF src/libcommon.a.p/tools_joint-A-T.cc.o.d -o src/libcommon.a.p/tools_joint-A-T.cc.o -c ../src/tools/joint-A-T.cc +[54/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_stats-table.cc.o -MF src/libcommon.a.p/tools_stats-table.cc.o.d -o src/libcommon.a.p/tools_stats-table.cc.o -c ../src/tools/stats-table.cc +[55/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/param.cc.o -MF src/computation/libcomputation.a.p/param.cc.o.d -o src/computation/libcomputation.a.p/param.cc.o -c ../src/computation/param.cc +[56/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_operator.cc.o -MF src/computation/libcomputation.a.p/expression_operator.cc.o.d -o src/computation/libcomputation.a.p/expression_operator.cc.o -c ../src/computation/expression/operator.cc +[57/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_driver.cc.o -MF src/computation/libcomputation.a.p/parser_driver.cc.o.d -o src/computation/libcomputation.a.p/parser_driver.cc.o -c ../src/computation/parser/driver.cc +[58/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_constructor.cc.o -MF src/computation/libcomputation.a.p/expression_constructor.cc.o.d -o src/computation/libcomputation.a.p/expression_constructor.cc.o -c ../src/computation/expression/constructor.cc +[59/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_lexer.cc.o -MF src/computation/libcomputation.a.p/parser_lexer.cc.o.d -o src/computation/libcomputation.a.p/parser_lexer.cc.o -c ../src/computation/parser/lexer.cc [60/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/program.cc.o -MF src/computation/libcomputation.a.p/program.cc.o.d -o src/computation/libcomputation.a.p/program.cc.o -c ../src/computation/program.cc ../src/computation/program.cc: In member function ‘void Program::check_dependencies()’: ../src/computation/program.cc:155:17: warning: unused variable ‘index’ [-Wunused-variable] 155 | int index = find_module(name); | ^~~~~ -[61/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_apply.cc.o -MF src/computation/libcomputation.a.p/expression_apply.cc.o.d -o src/computation/libcomputation.a.p/expression_apply.cc.o -c ../src/computation/expression/apply.cc -[62/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_AST_node.cc.o -MF src/computation/libcomputation.a.p/expression_AST_node.cc.o.d -o src/computation/libcomputation.a.p/expression_AST_node.cc.o -c ../src/computation/expression/AST_node.cc -[63/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized 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-DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_inliner.cc.o -MF src/computation/libcomputation.a.p/optimization_inliner.cc.o.d -o src/computation/libcomputation.a.p/optimization_inliner.cc.o -c ../src/computation/optimization/inliner.cc -[100/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-array.cc.o -MF src/libbaliphy.a.p/dp_dp-array.cc.o.d -o src/libbaliphy.a.p/dp_dp-array.cc.o -c ../src/dp/dp-array.cc -[101/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_free-vars.cc.o -MF src/computation/libcomputation.a.p/optimization_free-vars.cc.o.d -o src/computation/libcomputation.a.p/optimization_free-vars.cc.o -c ../src/computation/optimization/free-vars.cc +[98/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_inliner.cc.o -MF src/computation/libcomputation.a.p/optimization_inliner.cc.o.d -o src/computation/libcomputation.a.p/optimization_inliner.cc.o -c ../src/computation/optimization/inliner.cc +[99/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_show_graph.cc.o -MF src/computation/libcomputation.a.p/machine_show_graph.cc.o.d -o src/computation/libcomputation.a.p/machine_show_graph.cc.o -c ../src/computation/machine/show_graph.cc +[100/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_free-vars.cc.o -MF src/computation/libcomputation.a.p/optimization_free-vars.cc.o.d -o src/computation/libcomputation.a.p/optimization_free-vars.cc.o -c ../src/computation/optimization/free-vars.cc In file included from ../external/immer/immer/detail/hamts/champ.hpp:12, from ../external/immer/immer/set.hpp:12, from ../src/computation/optimization/free-vars.H:6, @@ -2101,15 +2136,17 @@ ../external/immer/immer/heap/cpp_heap.hpp:27:30: note: object of size 24 allocated by ‘operator new’ 27 | return ::operator new(size); | ~~~~~~~~~~~~~~^~~~~~ -[102/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_float-out.cc.o -MF src/computation/libcomputation.a.p/optimization_float-out.cc.o.d -o src/computation/libcomputation.a.p/optimization_float-out.cc.o -c ../src/computation/optimization/float-out.cc -[103/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_hmm.cc.o -MF src/libbaliphy.a.p/dp_hmm.cc.o.d -o src/libbaliphy.a.p/dp_hmm.cc.o -c ../src/dp/hmm.cc -[104/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-cube.cc.o -MF src/libbaliphy.a.p/dp_dp-cube.cc.o.d -o src/libbaliphy.a.p/dp_dp-cube.cc.o -c ../src/dp/dp-cube.cc -[105/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c ../src/computation/optimization/simplifier.cc -[106/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-matrix.cc.o -MF src/libbaliphy.a.p/dp_dp-matrix.cc.o.d -o src/libbaliphy.a.p/dp_dp-matrix.cc.o -c ../src/dp/dp-matrix.cc -[107/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc -[108/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_2way.cc.o -MF src/libbaliphy.a.p/dp_2way.cc.o.d -o src/libbaliphy.a.p/dp_2way.cc.o -c ../src/dp/2way.cc -[109/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_3way.cc.o -MF src/libbaliphy.a.p/dp_3way.cc.o.d -o src/libbaliphy.a.p/dp_3way.cc.o -c ../src/dp/3way.cc -[110/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_set-levels.cc.o -MF src/computation/libcomputation.a.p/optimization_set-levels.cc.o.d -o src/computation/libcomputation.a.p/optimization_set-levels.cc.o -c ../src/computation/optimization/set-levels.cc +[101/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-array.cc.o -MF src/libbaliphy.a.p/dp_dp-array.cc.o.d -o src/libbaliphy.a.p/dp_dp-array.cc.o -c ../src/dp/dp-array.cc +[102/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_hmm.cc.o -MF src/libbaliphy.a.p/dp_hmm.cc.o.d -o src/libbaliphy.a.p/dp_hmm.cc.o -c ../src/dp/hmm.cc +[103/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc +[104/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-matrix.cc.o -MF src/libbaliphy.a.p/dp_dp-matrix.cc.o.d -o src/libbaliphy.a.p/dp_dp-matrix.cc.o -c ../src/dp/dp-matrix.cc +[105/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_float-out.cc.o -MF src/computation/libcomputation.a.p/optimization_float-out.cc.o.d -o src/computation/libcomputation.a.p/optimization_float-out.cc.o -c ../src/computation/optimization/float-out.cc +[106/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_occurrence.cc.o -MF src/computation/libcomputation.a.p/optimization_occurrence.cc.o.d -o src/computation/libcomputation.a.p/optimization_occurrence.cc.o -c ../src/computation/optimization/occurrence.cc +[107/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-cube.cc.o -MF src/libbaliphy.a.p/dp_dp-cube.cc.o.d -o src/libbaliphy.a.p/dp_dp-cube.cc.o -c ../src/dp/dp-cube.cc +[108/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_3way.cc.o -MF src/libbaliphy.a.p/dp_3way.cc.o.d -o src/libbaliphy.a.p/dp_3way.cc.o -c ../src/dp/3way.cc +[109/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_5way.cc.o -MF src/libbaliphy.a.p/dp_5way.cc.o.d -o src/libbaliphy.a.p/dp_5way.cc.o -c ../src/dp/5way.cc +[110/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c ../src/computation/optimization/simplifier.cc +[111/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_set-levels.cc.o -MF src/computation/libcomputation.a.p/optimization_set-levels.cc.o.d -o src/computation/libcomputation.a.p/optimization_set-levels.cc.o -c ../src/computation/optimization/set-levels.cc In file included from ../external/immer/immer/detail/hamts/champ.hpp:12, from ../external/immer/immer/set.hpp:12, from ../src/computation/optimization/free-vars.H:6, @@ -2518,62 +2555,61 @@ ../external/immer/immer/heap/cpp_heap.hpp:27:30: note: object of size 24 allocated by ‘operator new’ 27 | return ::operator new(size); | ~~~~~~~~~~~~~~^~~~~~ -[111/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ 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-DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_5way.cc.o -MF src/libbaliphy.a.p/dp_5way.cc.o.d -o src/libbaliphy.a.p/dp_5way.cc.o -c ../src/dp/5way.cc -[113/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 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-MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc +[112/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_2way.cc.o -MF src/libbaliphy.a.p/dp_2way.cc.o.d -o src/libbaliphy.a.p/dp_2way.cc.o -c ../src/dp/2way.cc +[113/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc +[114/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc [115/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -MF src/libbaliphy.a.p/mcmc_slice-sampling.cc.o.d -o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -c ../src/mcmc/slice-sampling.cc ../src/mcmc/slice-sampling.cc: In function ‘std::pair find_slice_boundaries_stepping_out(double, slice_function&, double, double, int)’: ../src/mcmc/slice-sampling.cc:373:91: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 373 | find_slice_boundaries_stepping_out(double x0,slice_function& g,double logy, double w,int m) | ^ -[116/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc -[117/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_proposals.cc.o -MF src/libbaliphy.a.p/mcmc_proposals.cc.o.d -o src/libbaliphy.a.p/mcmc_proposals.cc.o -c ../src/mcmc/proposals.cc -[118/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc -[119/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time 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-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc +[117/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc +[118/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 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-DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -MF src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -c ../src/mcmc/sample-branch-lengths.cc [121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_exponential.cc.o -MF src/libbaliphy.a.p/math_exponential.cc.o.d -o src/libbaliphy.a.p/math_exponential.cc.o -c ../src/math/exponential.cc -[122/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK 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-DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_link2.cc.o -MF src/libbaliphy.a.p/tree-align_link2.cc.o.d -o src/libbaliphy.a.p/tree-align_link2.cc.o -c ../src/tree-align/link2.cc +[136/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 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-DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_unification.cc.o -MF src/libbaliphy.a.p/models_unification.cc.o.d -o src/libbaliphy.a.p/models_unification.cc.o -c ../src/models/unification.cc [138/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parse.cc.o -MF src/libbaliphy.a.p/models_parse.cc.o.d -o src/libbaliphy.a.p/models_parse.cc.o -c ../src/models/parse.cc -[139/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_n_indels2.cc.o -MF src/libbaliphy.a.p/tree-align_n_indels2.cc.o.d -o src/libbaliphy.a.p/tree-align_n_indels2.cc.o -c ../src/tree-align/n_indels2.cc -[140/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_typecheck.cc.o -MF src/libbaliphy.a.p/models_typecheck.cc.o.d -o src/libbaliphy.a.p/models_typecheck.cc.o -c ../src/models/typecheck.cc +[139/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc +[140/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_n_indels2.cc.o -MF src/libbaliphy.a.p/tree-align_n_indels2.cc.o.d -o src/libbaliphy.a.p/tree-align_n_indels2.cc.o -c ../src/tree-align/n_indels2.cc [141/297] rm -f src/util/libutil.a && gcc-ar csrDT src/util/libutil.a src/util/libutil.a.p/string_pred.cc.o src/util/libutil.a.p/string_sanitize.cc.o src/util/libutil.a.p/string_strip.cc.o src/util/libutil.a.p/string_split.cc.o src/util/libutil.a.p/log-level.cc.o src/util/libutil.a.p/io.cc.o src/util/libutil.a.p/graph.cc.o src/util/libutil.a.p/range.cc.o src/util/libutil.a.p/demangle.cc.o src/util/libutil.a.p/mapping.cc.o src/util/libutil.a.p/cmdline.cc.o src/util/libutil.a.p/rng.cc.o src/util/libutil.a.p/permute.cc.o src/util/libutil.a.p/file-paths.cc.o src/util/libutil.a.p/ptree.cc.o src/util/libutil.a.p/text.cc.o src/util/libutil.a.p/myexception.cc.o src/util/libutil.a.p/time.cc.o src/util/libutil.a.p/file-readers.cc.o [142/297] rm -f src/libcommon.a && gcc-ar csrDT src/libcommon.a src/libcommon.a.p/tree_newick-tokenizer.cc.o src/libcommon.a.p/tree_sequencetree.cc.o src/libcommon.a.p/tree_tree.cc.o src/libcommon.a.p/tree_tree-util.cc.o src/libcommon.a.p/tree_randomtree.cc.o src/libcommon.a.p/tree-align_n_indels.cc.o src/libcommon.a.p/sequence_alphabet.cc.o src/libcommon.a.p/sequence_sequence.cc.o src/libcommon.a.p/sequence_sequence-format.cc.o src/libcommon.a.p/tools_read-trees.cc.o src/libcommon.a.p/alignment_alignment-util.cc.o src/libcommon.a.p/alignment_load.cc.o src/libcommon.a.p/alignment_alignment.cc.o src/libcommon.a.p/alignment_alignment-random.cc.o src/libcommon.a.p/alignment_index-matrix.cc.o src/libcommon.a.p/tree-align_link.cc.o src/libcommon.a.p/models_path.cc.o src/libcommon.a.p/tools_statistics.cc.o src/libcommon.a.p/tools_partition.cc.o src/libcommon.a.p/tools_tree-dist.cc.o src/libcommon.a.p/tools_parsimony.cc.o src/libcommon.a.p/tools_mctree.cc.o src/libcommon.a.p/tools_stats-table.cc.o src/libcommon.a.p/tools_findroot.cc.o src/libcommon.a.p/tools_optimize.cc.o src/libcommon.a.p/tools_distance-report.cc.o src/libcommon.a.p/tools_inverse.cc.o src/libcommon.a.p/tools_joint-A-T.cc.o src/libcommon.a.p/tools_distance-methods.cc.o src/libcommon.a.p/tools_consensus-tree.cc.o [143/297] rm -f src/computation/libcomputation.a && gcc-ar csrDT src/computation/libcomputation.a src/computation/libcomputation.a.p/object.cc.o src/computation/libcomputation.a.p/closure.cc.o src/computation/libcomputation.a.p/program.cc.o src/computation/libcomputation.a.p/preprocess.cc.o src/computation/libcomputation.a.p/module.cc.o src/computation/libcomputation.a.p/loader.cc.o src/computation/libcomputation.a.p/context.cc.o src/computation/libcomputation.a.p/operations.cc.o src/computation/libcomputation.a.p/param.cc.o src/computation/libcomputation.a.p/parser_desugar.cc.o src/computation/libcomputation.a.p/parser_desugar-case.cc.o src/computation/libcomputation.a.p/parser_rename.cc.o src/computation/libcomputation.a.p/parser_driver.cc.o src/computation/libcomputation.a.p/parser_lexer.cc.o src/computation/libcomputation.a.p/parser_parser.cc.o src/computation/libcomputation.a.p/expression_operator.cc.o src/computation/libcomputation.a.p/expression_expression.cc.o src/computation/libcomputation.a.p/expression_constructor.cc.o src/computation/libcomputation.a.p/expression_expression_ref.cc.o src/computation/libcomputation.a.p/expression_AST_node.cc.o src/computation/libcomputation.a.p/expression_apply.cc.o src/computation/libcomputation.a.p/expression_substitute.cc.o src/computation/libcomputation.a.p/expression_indexify.cc.o src/computation/libcomputation.a.p/expression_let.cc.o src/computation/libcomputation.a.p/expression_case.cc.o src/computation/libcomputation.a.p/expression_trim.cc.o src/computation/libcomputation.a.p/expression_tuple.cc.o src/computation/libcomputation.a.p/expression_list.cc.o src/computation/libcomputation.a.p/expression_var.cc.o src/computation/libcomputation.a.p/expression_lambda.cc.o src/computation/libcomputation.a.p/expression_random_variable.cc.o src/computation/libcomputation.a.p/expression_modifiable.cc.o src/computation/libcomputation.a.p/expression_reg_var.cc.o src/computation/libcomputation.a.p/expression_bool.cc.o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o src/computation/libcomputation.a.p/expression_maybe.cc.o src/computation/libcomputation.a.p/expression_do_block.cc.o src/computation/libcomputation.a.p/machine_args.cc.o src/computation/libcomputation.a.p/machine_tokens.cc.o src/computation/libcomputation.a.p/machine_graph_register.cc.o src/computation/libcomputation.a.p/machine_show_graph.cc.o src/computation/libcomputation.a.p/machine_evaluate.cc.o src/computation/libcomputation.a.p/machine_sums.cc.o src/computation/libcomputation.a.p/machine_gc.cc.o src/computation/libcomputation.a.p/machine_reroot.cc.o src/computation/libcomputation.a.p/machine_effects.cc.o src/computation/libcomputation.a.p/expression_kind.cc.o src/computation/libcomputation.a.p/optimization_free-vars.cc.o src/computation/libcomputation.a.p/optimization_set-levels.cc.o src/computation/libcomputation.a.p/optimization_float-out.cc.o src/computation/libcomputation.a.p/optimization_occurrence.cc.o src/computation/libcomputation.a.p/optimization_inliner.cc.o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -[144/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_eigenvalue.cc.o -MF src/libbaliphy.a.p/math_eigenvalue.cc.o.d -o src/libbaliphy.a.p/math_eigenvalue.cc.o -c ../src/math/eigenvalue.cc -[145/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc -[146/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -MF src/libbaliphy.a.p/alignment_alignment-constraint.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -c ../src/alignment/alignment-constraint.cc -[147/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc +[144/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_rules.cc.o -MF src/libbaliphy.a.p/models_rules.cc.o.d -o src/libbaliphy.a.p/models_rules.cc.o -c ../src/models/rules.cc +[145/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_typecheck.cc.o -MF src/libbaliphy.a.p/models_typecheck.cc.o.d -o src/libbaliphy.a.p/models_typecheck.cc.o -c ../src/models/typecheck.cc +[146/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/imodel_imodel.cc.o -MF src/libbaliphy.a.p/imodel_imodel.cc.o.d -o src/libbaliphy.a.p/imodel_imodel.cc.o -c ../src/imodel/imodel.cc +[147/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -MF src/libbaliphy.a.p/alignment_alignment-constraint.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -c ../src/alignment/alignment-constraint.cc +[148/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc +[149/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc ../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ ../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ -[148/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_rules.cc.o -MF src/libbaliphy.a.p/models_rules.cc.o.d -o src/libbaliphy.a.p/models_rules.cc.o -c ../src/models/rules.cc -[149/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/imodel_imodel.cc.o -MF src/libbaliphy.a.p/imodel_imodel.cc.o.d -o src/libbaliphy.a.p/imodel_imodel.cc.o -c ../src/imodel/imodel.cc -[150/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc +[150/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_eigenvalue.cc.o -MF src/libbaliphy.a.p/math_eigenvalue.cc.o.d -o src/libbaliphy.a.p/math_eigenvalue.cc.o -c ../src/math/eigenvalue.cc [151/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc -[152/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_model.cc.o -MF src/libbaliphy.a.p/models_model.cc.o.d -o src/libbaliphy.a.p/models_model.cc.o -c ../src/models/model.cc -[153/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/paths.cc.o -MF src/bali-phy/bali-phy.p/paths.cc.o.d -o src/bali-phy/bali-phy.p/paths.cc.o -c ../src/bali-phy/paths.cc -[154/297] c++ -Isrc/builtins/Array.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Array.so.p/Array.cc.o -MF src/builtins/Array.so.p/Array.cc.o.d -o src/builtins/Array.so.p/Array.cc.o -c ../src/builtins/Array.cc -[155/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/link-partitions.cc.o -MF src/bali-phy/bali-phy.p/link-partitions.cc.o.d -o src/bali-phy/bali-phy.p/link-partitions.cc.o -c ../src/bali-phy/link-partitions.cc -[156/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc +[152/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc +[153/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_model.cc.o -MF src/libbaliphy.a.p/models_model.cc.o.d -o src/libbaliphy.a.p/models_model.cc.o -c ../src/models/model.cc +[154/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/link-partitions.cc.o -MF src/bali-phy/bali-phy.p/link-partitions.cc.o.d -o src/bali-phy/bali-phy.p/link-partitions.cc.o -c ../src/bali-phy/link-partitions.cc +[155/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/paths.cc.o -MF src/bali-phy/bali-phy.p/paths.cc.o.d -o src/bali-phy/bali-phy.p/paths.cc.o -c ../src/bali-phy/paths.cc +[156/297] c++ -Isrc/builtins/Array.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Array.so.p/Array.cc.o -MF src/builtins/Array.so.p/Array.cc.o.d -o src/builtins/Array.so.p/Array.cc.o -c ../src/builtins/Array.cc [157/297] c++ -Isrc/builtins/Data.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Data.so.p/Data.cc.o -MF src/builtins/Data.so.p/Data.cc.o.d -o src/builtins/Data.so.p/Data.cc.o -c ../src/builtins/Data.cc [158/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_probability.cc.o -MF src/libbaliphy.a.p/probability_probability.cc.o.d -o src/libbaliphy.a.p/probability_probability.cc.o -c ../src/probability/probability.cc In file included from ../src/probability/probability.cc:22: @@ -2618,23 +2654,26 @@ 1127 | path leaf() const { return filename(); } | ^~~~ [161/297] c++ -Isrc/builtins/Prelude.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Prelude.so.p/Prelude.cc.o -MF src/builtins/Prelude.so.p/Prelude.cc.o.d -o src/builtins/Prelude.so.p/Prelude.cc.o -c ../src/builtins/Prelude.cc -[162/297] c++ -Isrc/builtins/Modifiables.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Modifiables.so.p/Modifiables.cc.o -MF src/builtins/Modifiables.so.p/Modifiables.cc.o.d -o src/builtins/Modifiables.so.p/Modifiables.cc.o -c ../src/builtins/Modifiables.cc -[163/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc -[164/297] c++ -Isrc/builtins/Alphabet.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc -[165/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc +[162/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc +[163/297] rm -f src/libbaliphy.a && gcc-ar csrDT src/libbaliphy.a src/libbaliphy.a.p/dp_dp_hmm.cc.o src/libbaliphy.a.p/dp_hmm.cc.o src/libbaliphy.a.p/dp_dp-engine.cc.o src/libbaliphy.a.p/dp_dp-array.cc.o src/libbaliphy.a.p/dp_dp-matrix.cc.o src/libbaliphy.a.p/dp_dp-cube.cc.o src/libbaliphy.a.p/dp_2way.cc.o src/libbaliphy.a.p/dp_3way.cc.o src/libbaliphy.a.p/dp_5way.cc.o src/libbaliphy.a.p/dp_alignment-sums.cc.o src/libbaliphy.a.p/mcmc_mcmc.cc.o src/libbaliphy.a.p/mcmc_proposals.cc.o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o src/libbaliphy.a.p/mcmc_AIS.cc.o src/libbaliphy.a.p/mcmc_logger.cc.o src/libbaliphy.a.p/mcmc_moves.cc.o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o src/libbaliphy.a.p/mcmc_sample-node.cc.o src/libbaliphy.a.p/mcmc_sample-cube.cc.o src/libbaliphy.a.p/mcmc_sample-tri.cc.o src/libbaliphy.a.p/mcmc_setup.cc.o src/libbaliphy.a.p/substitution_substitution.cc.o src/libbaliphy.a.p/substitution_parsimony.cc.o src/libbaliphy.a.p/math_exponential.cc.o src/libbaliphy.a.p/math_eigenvalue.cc.o src/libbaliphy.a.p/math_pow2.cc.o src/libbaliphy.a.p/models_parameters.cc.o src/libbaliphy.a.p/models_site-compression.cc.o src/libbaliphy.a.p/models_TreeInterface.cc.o src/libbaliphy.a.p/models_setup.cc.o src/libbaliphy.a.p/models_rules.cc.o src/libbaliphy.a.p/models_parse.cc.o src/libbaliphy.a.p/models_typecheck.cc.o src/libbaliphy.a.p/models_unification.cc.o src/libbaliphy.a.p/models_model.cc.o src/libbaliphy.a.p/tree-align_link2.cc.o src/libbaliphy.a.p/probability_choose.cc.o src/libbaliphy.a.p/probability_probability.cc.o src/libbaliphy.a.p/imodel_imodel.cc.o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o src/libbaliphy.a.p/alignment_alignment-util2.cc.o src/libbaliphy.a.p/tree-align_n_indels2.cc.o src/libbaliphy.a.p/tools_parsimony2.cc.o src/libbaliphy.a.p/version.cc.o +[164/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc ../src/bali-phy/bali-phy.cc: In function ‘void report_mem()’: ../src/bali-phy/bali-phy.cc:122:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 122 | system(cmd.str().c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -[166/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc -[167/297] rm -f src/libbaliphy.a && gcc-ar csrDT src/libbaliphy.a src/libbaliphy.a.p/dp_dp_hmm.cc.o src/libbaliphy.a.p/dp_hmm.cc.o src/libbaliphy.a.p/dp_dp-engine.cc.o src/libbaliphy.a.p/dp_dp-array.cc.o src/libbaliphy.a.p/dp_dp-matrix.cc.o src/libbaliphy.a.p/dp_dp-cube.cc.o src/libbaliphy.a.p/dp_2way.cc.o src/libbaliphy.a.p/dp_3way.cc.o src/libbaliphy.a.p/dp_5way.cc.o src/libbaliphy.a.p/dp_alignment-sums.cc.o src/libbaliphy.a.p/mcmc_mcmc.cc.o src/libbaliphy.a.p/mcmc_proposals.cc.o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o src/libbaliphy.a.p/mcmc_AIS.cc.o src/libbaliphy.a.p/mcmc_logger.cc.o src/libbaliphy.a.p/mcmc_moves.cc.o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o src/libbaliphy.a.p/mcmc_sample-node.cc.o src/libbaliphy.a.p/mcmc_sample-cube.cc.o src/libbaliphy.a.p/mcmc_sample-tri.cc.o src/libbaliphy.a.p/mcmc_setup.cc.o src/libbaliphy.a.p/substitution_substitution.cc.o src/libbaliphy.a.p/substitution_parsimony.cc.o src/libbaliphy.a.p/math_exponential.cc.o src/libbaliphy.a.p/math_eigenvalue.cc.o src/libbaliphy.a.p/math_pow2.cc.o src/libbaliphy.a.p/models_parameters.cc.o src/libbaliphy.a.p/models_site-compression.cc.o src/libbaliphy.a.p/models_TreeInterface.cc.o src/libbaliphy.a.p/models_setup.cc.o src/libbaliphy.a.p/models_rules.cc.o src/libbaliphy.a.p/models_parse.cc.o src/libbaliphy.a.p/models_typecheck.cc.o src/libbaliphy.a.p/models_unification.cc.o src/libbaliphy.a.p/models_model.cc.o src/libbaliphy.a.p/tree-align_link2.cc.o src/libbaliphy.a.p/probability_choose.cc.o src/libbaliphy.a.p/probability_probability.cc.o src/libbaliphy.a.p/imodel_imodel.cc.o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o src/libbaliphy.a.p/alignment_alignment-util2.cc.o src/libbaliphy.a.p/tree-align_n_indels2.cc.o src/libbaliphy.a.p/tools_parsimony2.cc.o src/libbaliphy.a.p/version.cc.o +[165/297] c++ -Isrc/builtins/Modifiables.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Modifiables.so.p/Modifiables.cc.o -MF src/builtins/Modifiables.so.p/Modifiables.cc.o.d -o src/builtins/Modifiables.so.p/Modifiables.cc.o -c ../src/builtins/Modifiables.cc +[166/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc +[167/297] c++ -Isrc/builtins/Range.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Range.so.p/Range.cc.o -MF src/builtins/Range.so.p/Range.cc.o.d -o src/builtins/Range.so.p/Range.cc.o -c ../src/builtins/Range.cc [168/297] c++ -Isrc/builtins/Distribution.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Distribution.so.p/Distribution.cc.o -MF src/builtins/Distribution.so.p/Distribution.cc.o.d -o src/builtins/Distribution.so.p/Distribution.cc.o -c ../src/builtins/Distribution.cc -[169/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc -[170/297] c++ -Isrc/builtins/Range.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Range.so.p/Range.cc.o -MF src/builtins/Range.so.p/Range.cc.o.d -o src/builtins/Range.so.p/Range.cc.o -c ../src/builtins/Range.cc -[171/297] c++ -Isrc/builtins/PopGen.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/PopGen.so.p/PopGen.cc.o -MF src/builtins/PopGen.so.p/PopGen.cc.o.d -o src/builtins/PopGen.so.p/PopGen.cc.o -c ../src/builtins/PopGen.cc -[172/297] c++ -Isrc/builtins/Real.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc -[173/297] c++ -Isrc/builtins/Vector.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc -[174/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc +[169/297] c++ -Isrc/builtins/Vector.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc +[170/297] c++ -Isrc/builtins/Environment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc +[171/297] c++ -Isrc/builtins/Alphabet.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc +[172/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc +[173/297] c++ -Isrc/builtins/Alignment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alignment.so.p/Alignment.cc.o -MF src/builtins/Alignment.so.p/Alignment.cc.o.d -o src/builtins/Alignment.so.p/Alignment.cc.o -c ../src/builtins/Alignment.cc +[174/297] c++ -Isrc/builtins/PopGen.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/PopGen.so.p/PopGen.cc.o -MF src/builtins/PopGen.so.p/PopGen.cc.o.d -o src/builtins/PopGen.so.p/PopGen.cc.o -c ../src/builtins/PopGen.cc +[175/297] c++ -Isrc/builtins/Real.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc +[176/297] c++ -Isrc/builtins/Text.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Text.so.p/Text.cc.o -MF src/builtins/Text.so.p/Text.cc.o.d -o src/builtins/Text.so.p/Text.cc.o -c ../src/builtins/Text.cc +[177/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc ../src/bali-phy/loggers.cc: In function ‘owned_ptr > > construct_table_function(owned_ptr&, const std::vector >&)’: ../src/bali-phy/loggers.cc:247:29: warning: possibly dangling reference to a temporary [-Wdangling-reference] 247 | const alphabet& a = (*P)[i].get_alphabet(); @@ -2642,133 +2681,130 @@ ../src/bali-phy/loggers.cc:247:53: note: the temporary was destroyed at the end of the full expression ‘(& P.owned_ptr::operator*())->Parameters::operator[](i).mutable_data_partition::data_partition.data_partition::get_alphabet()’ 247 | const alphabet& a = (*P)[i].get_alphabet(); | ~~~~~~~~~~~~~~~~~~~~^~ -[175/297] c++ -Isrc/builtins/Environment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc -[176/297] c++ -Isrc/builtins/Text.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ 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-I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c ../src/tools/mctree-mean-lengths.cc [203/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-cat.p/tools_alignment-cat.cc.o -MF src/alignment-cat.p/tools_alignment-cat.cc.o.d -o src/alignment-cat.p/tools_alignment-cat.cc.o -c ../src/tools/alignment-cat.cc -[204/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include 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-DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-consensus.p/tools_trees-consensus.cc.o -MF src/trees-consensus.p/tools_trees-consensus.cc.o.d -o src/trees-consensus.p/tools_trees-consensus.cc.o -c ../src/tools/trees-consensus.cc +[204/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-distances.p/tools_trees-distances.cc.o -MF src/trees-distances.p/tools_trees-distances.cc.o.d -o src/trees-distances.p/tools_trees-distances.cc.o -c ../src/tools/trees-distances.cc +[205/297] c++ -o src/bali-phy/bali-phy src/bali-phy/bali-phy.p/link-partitions.cc.o src/bali-phy/bali-phy.p/bali-phy.cc.o src/bali-phy/bali-phy.p/help.cc.o src/bali-phy/bali-phy.p/A-T-model.cc.o src/bali-phy/bali-phy.p/files.cc.o src/bali-phy/bali-phy.p/loggers.cc.o src/bali-phy/bali-phy.p/system.cc.o src/bali-phy/bali-phy.p/cmd_line.cc.o src/bali-phy/bali-phy.p/paths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-export-dynamic -Wl,--whole-archive -Wl,--start-group src/util/libutil.a src/libcommon.a src/computation/libcomputation.a src/libbaliphy.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -ldl -lm -Wl,--end-group [206/297] c++ -o src/builtins/Array.so src/builtins/Array.so.p/Array.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group [207/297] c++ -o src/builtins/Data.so src/builtins/Data.so.p/Data.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[208/297] c++ -o src/bali-phy/bali-phy src/bali-phy/bali-phy.p/link-partitions.cc.o src/bali-phy/bali-phy.p/bali-phy.cc.o src/bali-phy/bali-phy.p/help.cc.o src/bali-phy/bali-phy.p/A-T-model.cc.o src/bali-phy/bali-phy.p/files.cc.o src/bali-phy/bali-phy.p/loggers.cc.o src/bali-phy/bali-phy.p/system.cc.o src/bali-phy/bali-phy.p/cmd_line.cc.o src/bali-phy/bali-phy.p/paths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-export-dynamic -Wl,--whole-archive -Wl,--start-group src/util/libutil.a src/libcommon.a src/computation/libcomputation.a src/libbaliphy.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -ldl -lm -Wl,--end-group -[209/297] c++ -o src/builtins/Prelude.so src/builtins/Prelude.so.p/Prelude.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[210/297] c++ -o src/builtins/Alphabet.so src/builtins/Alphabet.so.p/Alphabet.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[211/297] c++ -o src/builtins/Pair.so src/builtins/Pair.so.p/Pair.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[212/297] c++ -o src/builtins/Modifiables.so src/builtins/Modifiables.so.p/Modifiables.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[213/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc -[214/297] c++ -o src/builtins/Alignment.so src/builtins/Alignment.so.p/Alignment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[208/297] c++ -o src/builtins/Prelude.so src/builtins/Prelude.so.p/Prelude.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[209/297] c++ -o src/builtins/Alphabet.so src/builtins/Alphabet.so.p/Alphabet.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[210/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-tool.p/tools_tree-tool.cc.o -MF src/tree-tool.p/tools_tree-tool.cc.o.d -o src/tree-tool.p/tools_tree-tool.cc.o -c ../src/tools/tree-tool.cc +[211/297] c++ -o src/builtins/Modifiables.so src/builtins/Modifiables.so.p/Modifiables.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[212/297] c++ -o src/builtins/Pair.so src/builtins/Pair.so.p/Pair.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[213/297] c++ -o src/builtins/Alignment.so src/builtins/Alignment.so.p/Alignment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[214/297] c++ -o src/builtins/Distribution.so src/builtins/Distribution.so.p/Distribution.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group [215/297] c++ -o src/builtins/PopGen.so src/builtins/PopGen.so.p/PopGen.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[216/297] c++ -o src/builtins/Distribution.so src/builtins/Distribution.so.p/Distribution.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[217/297] c++ -o src/builtins/Range.so src/builtins/Range.so.p/Range.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[218/297] c++ -o src/builtins/SModel.so src/builtins/SModel.so.p/SModel.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[219/297] c++ -o src/builtins/Vector.so src/builtins/Vector.so.p/Vector.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[220/297] c++ -o src/builtins/MCMC.so src/builtins/MCMC.so.p/MCMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[216/297] c++ -o src/builtins/Range.so src/builtins/Range.so.p/Range.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[217/297] c++ -Isrc/trees-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-consensus.p/tools_trees-consensus.cc.o -MF src/trees-consensus.p/tools_trees-consensus.cc.o.d -o src/trees-consensus.p/tools_trees-consensus.cc.o -c ../src/tools/trees-consensus.cc +[218/297] c++ -o src/builtins/MCMC.so src/builtins/MCMC.so.p/MCMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[219/297] c++ -o src/builtins/SModel.so src/builtins/SModel.so.p/SModel.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[220/297] c++ -o src/builtins/Vector.so src/builtins/Vector.so.p/Vector.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group [221/297] c++ -o src/builtins/Environment.so src/builtins/Environment.so.p/Environment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[222/297] c++ -o src/builtins/Real.so src/builtins/Real.so.p/Real.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[223/297] c++ -o src/builtins/SMC.so src/builtins/SMC.so.p/SMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[222/297] c++ -o src/builtins/SMC.so src/builtins/SMC.so.p/SMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[223/297] c++ -o src/builtins/Real.so src/builtins/Real.so.p/Real.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group [224/297] c++ -o src/builtins/Bits.so src/builtins/Bits.so.p/Bits.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[225/297] c++ -o src/builtins/Foreign.so src/builtins/Foreign.so.p/Foreign.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[225/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc [226/297] c++ -o src/builtins/Text.so src/builtins/Text.so.p/Text.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[227/297] c++ -o src/builtins/Char.so src/builtins/Char.so.p/Char.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[228/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[229/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[230/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[231/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[232/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-tool.p/tools_tree-tool.cc.o -MF src/tree-tool.p/tools_tree-tool.cc.o.d -o src/tree-tool.p/tools_tree-tool.cc.o -c ../src/tools/tree-tool.cc -[233/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-distances.p/tools_trees-distances.cc.o -MF src/trees-distances.p/tools_trees-distances.cc.o.d -o src/trees-distances.p/tools_trees-distances.cc.o -c ../src/tools/trees-distances.cc -[234/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[235/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[227/297] c++ -o src/builtins/Foreign.so src/builtins/Foreign.so.p/Foreign.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[228/297] c++ -o src/builtins/Char.so src/builtins/Char.so.p/Char.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[229/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[230/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[231/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[232/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[233/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[234/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[235/297] c++ -o src/alignment-chop-internal src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [236/297] c++ -o src/alignment-indices src/alignment-indices.p/tools_alignment-indices.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[237/297] c++ -o src/alignment-chop-internal src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[238/297] c++ -o src/alignment-info src/alignment-info.p/tools_alignment-info.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[239/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[237/297] c++ -o src/alignment-info src/alignment-info.p/tools_alignment-info.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[238/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[239/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [240/297] c++ -o src/alignment-translate src/alignment-translate.p/tools_alignment-translate.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[241/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[242/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[241/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[242/297] c++ -o src/mctree-mean-lengths src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [243/297] c++ -o src/pickout src/pickout.p/tools_pickout.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [244/297] c++ -o src/tree-mean-lengths src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[245/297] c++ -o src/mctree-mean-lengths src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[246/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[247/297] c++ -o src/trees-to-SRQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[248/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[245/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[246/297] c++ -o src/trees-to-SRQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[247/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[248/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [249/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[250/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 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--capture doc/model_P.1 -- /usr/bin/pandoc -s -t man ../doc/man/model_P.md +[250/297] /usr/bin/meson --internal exe --capture doc/model_P.1 -- /usr/bin/pandoc -s -t man ../doc/man/model_P.md +[251/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-thin.p/tools_alignment-thin.cc.o -MF src/alignment-thin.p/tools_alignment-thin.cc.o.d -o src/alignment-thin.p/tools_alignment-thin.cc.o -c ../src/tools/alignment-thin.cc +[252/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc +[253/297] /usr/bin/meson --internal exe --capture doc/statreport.1 -- /usr/bin/pandoc -s -t man ../doc/man/statreport.md [254/297] /usr/bin/meson --internal exe --capture doc/stats-select.1 -- /usr/bin/pandoc -s -t man ../doc/man/stats-select.md [255/297] /usr/bin/meson --internal exe --capture doc/alignment-gild.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-gild.md -[256/297] /usr/bin/meson --internal exe --capture doc/alignment-consensus.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-consensus.md -[257/297] /usr/bin/meson --internal exe --capture doc/bali-phy.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy.md -[258/297] /usr/bin/meson --internal exe --capture doc/alignment-max.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-max.md -[259/297] /usr/bin/meson --internal exe --capture 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/usr/bin/pandoc -s -t man ../doc/man/alignment-distances.md -[275/297] /usr/bin/meson --internal exe --capture doc/alignment-thin.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-thin.md -[276/297] /usr/bin/meson --internal exe --capture doc/alignment-draw.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-draw.md -[277/297] /usr/bin/meson --internal exe --capture doc/trees-bootstrap.1 -- /usr/bin/pandoc -s -t man ../doc/man/trees-bootstrap.md -[278/297] /usr/bin/meson --internal exe --capture doc/extract-ancestors.1 -- /usr/bin/pandoc -s -t man ../doc/man/extract-ancestors.md +[256/297] /usr/bin/meson --internal exe --capture doc/bali-phy.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy.md +[257/297] /usr/bin/meson --internal exe --capture doc/alignment-consensus.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-consensus.md +[258/297] c++ -o src/alignment-thin src/alignment-thin.p/tools_alignment-thin.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[259/297] /usr/bin/meson --internal exe --capture doc/alignment-max.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-max.md +[260/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[261/297] /usr/bin/meson --internal exe --capture doc/alignment-chop-internal.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-chop-internal.md +[262/297] /usr/bin/meson --internal exe --capture doc/alignment-indices.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-indices.md +[263/297] /usr/bin/meson --internal exe --capture doc/alignment-info.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-info.md +[264/297] /usr/bin/meson --internal exe 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../doc/man/cut-range.md +[272/297] /usr/bin/meson --internal exe --capture doc/pickout.1 -- /usr/bin/pandoc -s -t man ../doc/man/pickout.md +[273/297] /usr/bin/meson --internal exe --capture doc/trees-distances.1 -- /usr/bin/pandoc -s -t man ../doc/man/trees-distances.md +[274/297] /usr/bin/meson --internal exe --capture doc/alignment-thin.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-thin.md +[275/297] /usr/bin/meson --internal exe --capture doc/alignments-diff.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignments-diff.md +[276/297] /usr/bin/meson --internal exe --capture doc/tree-tool.1 -- /usr/bin/pandoc -s -t man ../doc/man/tree-tool.md +[277/297] /usr/bin/meson --internal exe --capture doc/alignment-draw.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-draw.md +[278/297] /usr/bin/meson --internal exe --capture doc/alignment-distances.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-distances.md [279/297] /usr/bin/meson --internal exe --capture doc/draw-tree.1 -- /usr/bin/pandoc -s -t man ../doc/man/draw-tree.md -[280/297] /usr/bin/meson --internal exe --capture doc/summarize-ancestors.1 -- /usr/bin/pandoc -s -t man ../doc/man/summarize-ancestors.md -[281/297] /usr/bin/meson --internal exe --capture doc/bali-subsample.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-subsample.md -[282/297] /usr/bin/meson --internal exe --capture doc/bp-analyze.1 -- /usr/bin/pandoc -s -t man ../doc/man/bp-analyze.md -[283/297] /usr/bin/meson --internal exe --capture doc/bali-phy-pkg.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy-pkg.md -[284/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc -[285/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[280/297] /usr/bin/meson --internal exe --capture doc/trees-bootstrap.1 -- /usr/bin/pandoc -s -t man ../doc/man/trees-bootstrap.md +[281/297] /usr/bin/meson --internal exe --capture doc/summarize-ancestors.1 -- /usr/bin/pandoc -s -t man ../doc/man/summarize-ancestors.md +[282/297] /usr/bin/meson --internal exe --capture doc/extract-ancestors.1 -- /usr/bin/pandoc -s -t man ../doc/man/extract-ancestors.md +[283/297] /usr/bin/meson --internal exe --capture doc/bali-subsample.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-subsample.md +[284/297] /usr/bin/meson --internal exe --capture doc/bp-analyze.1 -- /usr/bin/pandoc -s -t man ../doc/man/bp-analyze.md +[285/297] /usr/bin/meson --internal exe --capture doc/bali-phy-pkg.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy-pkg.md [286/297] c++ -Isrc/bali-subsample.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-subsample.p/tools_subsample.cc.o -MF src/bali-subsample.p/tools_subsample.cc.o.d -o src/bali-subsample.p/tools_subsample.cc.o -c ../src/tools/subsample.cc [287/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [288/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc [289/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[290/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc -[291/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[292/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc +[290/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc ../src/tools/trees-bootstrap.cc: In function ‘std::pair am_sdsf(const tree_sample_collection&, int, const std::map, p_counts>&, double)’: ../src/tools/trees-bootstrap.cc:567:117: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 567 | am_sdsf(const tree_sample_collection& tree_dists, int d, const map, p_counts>& counts, double min_f) | ^ -[293/297] c++ -o src/trees-bootstrap src/trees-bootstrap.p/tools_trees-bootstrap.cc.o src/trees-bootstrap.p/tools_bootstrap.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[291/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc +[292/297] c++ -o src/trees-bootstrap src/trees-bootstrap.p/tools_trees-bootstrap.cc.o src/trees-bootstrap.p/tools_bootstrap.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[293/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [294/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc [295/297] c++ -o src/summarize-ancestors src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group [296/297] c++ -Isrc/draw-tree.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc @@ -2781,42 +2817,42 @@ cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=12 meson test ninja: Entering directory `/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-aarch64-linux-gnu' [1/4] Generating src/git-version.h with a custom command - 1/36 bali-phy version OK 0.30s - 2/36 bali-phy help OK 0.29s - 3/36 model_P --help OK 0.16s - 4/36 statreport --help OK 0.14s - 5/36 stats-select --help OK 0.12s - 6/36 alignment-gild --help OK 0.10s - 7/36 alignment-consensus --help OK 0.08s - 8/36 alignment-max --help OK 0.23s - 9/36 alignment-chop-internal --help OK 0.20s -10/36 alignment-indices --help OK 0.17s -11/36 alignment-info --help OK 0.14s -12/36 alignment-cat --help OK 0.12s -13/36 alignment-translate --help OK 0.10s -14/36 alignment-find --help OK 0.10s -15/36 trees-consensus --help OK 0.25s -16/36 tree-mean-lengths --help OK 0.25s -17/36 mctree-mean-lengths --help OK 0.24s -18/36 trees-to-SRQ --help OK 0.21s -19/36 pickout --help OK 0.19s -20/36 cut-range --help OK 0.16s -21/36 trees-distances --help OK 0.13s -22/36 alignment-thin --help OK 0.11s -23/36 alignments-diff --help OK 0.23s -24/36 tree-tool --help OK 0.21s -25/36 alignment-distances --help OK 0.21s -26/36 alignment-draw --help OK 0.18s -27/36 trees-bootstrap --help OK 0.15s -28/36 draw-tree --help OK 0.13s -29/36 extract-ancestors --help OK 0.12s -30/36 summarize-ancestors --help OK 0.10s -31/36 subsample --help OK 0.07s -32/36 bali-phy 5d test OK 5.95s -33/36 bali-phy 5d -A 200 OK 10.06s -34/36 bali-phy 5d +A 50 OK 13.11s -35/36 bali-phy 48 +A 3 OK 23.31s -36/36 bali-phy testsuite OK 414.15s + 1/36 bali-phy version OK 0.10s + 2/36 bali-phy help OK 0.09s + 3/36 model_P --help OK 0.06s + 4/36 statreport --help OK 0.05s + 5/36 stats-select --help OK 0.05s + 6/36 alignment-gild --help OK 0.04s + 7/36 alignment-consensus --help OK 0.04s + 8/36 alignment-max --help OK 0.03s + 9/36 alignment-chop-internal --help OK 0.07s +10/36 alignment-indices --help OK 0.06s +11/36 alignment-info --help OK 0.06s +12/36 alignment-cat --help OK 0.05s +13/36 alignment-translate --help OK 0.04s +14/36 alignment-find --help OK 0.04s +15/36 trees-consensus --help OK 0.03s +16/36 tree-mean-lengths --help OK 0.08s +17/36 mctree-mean-lengths --help OK 0.07s +18/36 trees-to-SRQ --help OK 0.07s +19/36 pickout --help OK 0.06s +20/36 cut-range --help OK 0.05s +21/36 trees-distances --help OK 0.05s +22/36 alignment-thin --help OK 0.04s +23/36 alignments-diff --help OK 0.04s +24/36 tree-tool --help OK 0.08s +25/36 alignment-distances --help OK 0.07s +26/36 alignment-draw --help OK 0.07s +27/36 trees-bootstrap --help OK 0.06s +28/36 draw-tree --help OK 0.06s +29/36 extract-ancestors --help OK 0.05s +30/36 summarize-ancestors --help OK 0.04s +31/36 subsample --help OK 0.04s +32/36 bali-phy 5d test OK 2.11s +33/36 bali-phy 5d -A 200 OK 3.90s +34/36 bali-phy 5d +A 50 OK 5.12s +35/36 bali-phy 48 +A 3 OK 9.61s +36/36 bali-phy testsuite OK 157.91s Ok: 36 Expected Fail: 0 @@ -3436,8 +3472,8 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'bali-phy' in '../bali-phy_3.6.1+dfsg-3_arm64.deb'. dpkg-deb: building package 'bali-phy-dbgsym' in '../bali-phy-dbgsym_3.6.1+dfsg-3_arm64.deb'. +dpkg-deb: building package 'bali-phy' in '../bali-phy_3.6.1+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bali-phy_3.6.1+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../bali-phy_3.6.1+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3445,12 +3481,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2541068/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2541068/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/258957 and its subdirectories -I: Current time: Sun Dec 21 09:02:49 -12 2025 -I: pbuilder-time-stamp: 1766350969 +I: removing directory /srv/workspace/pbuilder/2541068 and its subdirectories +I: Current time: Tue Nov 19 04:46:03 +14 2024 +I: pbuilder-time-stamp: 1731941163