Diff of the two buildlogs: -- --- b1/build.log 2024-01-06 13:10:18.826891301 +0000 +++ b2/build.log 2024-01-06 13:15:45.941109955 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 7 07:26:41 -12 2025 -I: pbuilder-time-stamp: 1738956401 +I: Current time: Sat Feb 8 09:33:24 +14 2025 +I: pbuilder-time-stamp: 1738956804 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./bali-phy_3.6.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.kGWfV1W0/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.DzPU34se/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 7 07:51:21 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -28,49 +28,80 @@ dpkg-source: info: unpacking bali-phy_3.6.0+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1037046/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3718235/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Feb 7 19:33 /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/3718235/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3718235/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:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b063b67325df4474a75280257dfabc7d' - 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='1037046' - PS1='# ' - PS2='> ' + INVOCATION_ID=ab0ddb8d75c146229e9bcfc49f0afe80 + 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=3718235 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.Fyw8kbF0/pbuilderrc_0FsP --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fyw8kbF0/b1 --logfile b1/build.log bali-phy_3.6.0+dfsg-1.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://192.168.101.104:3128' + 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.Fyw8kbF0/pbuilderrc_OtZT --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fyw8kbF0/b2 --logfile b2/build.log bali-phy_3.6.0+dfsg-1.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://192.168.101.104:3128 I: uname -a - Linux codethink03-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash @@ -130,7 +161,7 @@ -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 8 15:47 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 7 19:33 sh -> /bin/bash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jan 20 2022 su @@ -156,7 +187,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/1037046/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3718235/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -360,7 +391,7 @@ Get: 142 http://deb.debian.org/debian bullseye/main arm64 nlohmann-json3-dev all 3.9.1-1 [684 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 pandoc-data all 2.9.2.1-1+deb11u1 [377 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 pandoc arm64 2.9.2.1-1+deb11u1 [22.8 MB] -Fetched 81.3 MB in 1s (68.6 MB/s) +Fetched 81.3 MB in 1s (104 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17734 files and directories currently installed.) @@ -840,8 +871,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 7 19:27:25 UTC 2025. -Universal Time is now: Fri Feb 7 19:27:25 UTC 2025. +Local time is now: Fri Feb 7 19:33:50 UTC 2025. +Universal Time is now: Fri Feb 7 19:33:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -964,7 +995,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bali-phy-3.6.0+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_3.6.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3718235/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3718235/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bali-phy-3.6.0+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_3.6.0+dfsg-1_source.changes dpkg-buildpackage: info: source package bali-phy dpkg-buildpackage: info: source version 3.6.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1060,189 +1095,188 @@ make[1]: Leaving directory '/build/reproducible-path/bali-phy-3.6.0+dfsg' dh_auto_build -O--buildsystem=meson 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 '' /build/reproducible-path/bali-phy-3.6.0+dfsg/src @git_message@ '(.*)' /build/reproducible-path/bali-phy-3.6.0+dfsg/src/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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[6/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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-DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 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-fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/graph.cc.o -MF src/util/libutil.a.p/graph.cc.o.d -o src/util/libutil.a.p/graph.cc.o -c ../src/util/graph.cc +[21/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree-util.cc.o -MF src/libcommon.a.p/tree_tree-util.cc.o.d -o src/libcommon.a.p/tree_tree-util.cc.o -c ../src/tree/tree-util.cc +[22/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[23/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_sequence-format.cc.o -MF src/libcommon.a.p/sequence_sequence-format.cc.o.d -o src/libcommon.a.p/sequence_sequence-format.cc.o -c ../src/sequence/sequence-format.cc +[24/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/ptree.cc.o -MF src/util/libutil.a.p/ptree.cc.o.d -o src/util/libutil.a.p/ptree.cc.o -c ../src/util/ptree.cc +[25/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[26/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[27/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_sequence.cc.o -MF src/libcommon.a.p/sequence_sequence.cc.o.d -o src/libcommon.a.p/sequence_sequence.cc.o -c ../src/sequence/sequence.cc +[28/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 [29/297] rm -f src/util/libutil.a && gcc-ar csrD 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 -[30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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) | ^ -[31/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[32/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[33/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[34/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[35/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 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-I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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:155:10: warning: unused variable ‘index’ [-Wunused-variable] 155 | int index = find_module(name); | ^~~~~ -[61/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[63/297] rm -f src/libcommon.a && gcc-ar csrD 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 -[64/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_rename.cc.o -MF src/computation/libcomputation.a.p/parser_rename.cc.o.d -o src/computation/libcomputation.a.p/parser_rename.cc.o -c ../src/computation/parser/rename.cc -[65/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_expression.cc.o -MF src/computation/libcomputation.a.p/expression_expression.cc.o.d -o src/computation/libcomputation.a.p/expression_expression.cc.o -c ../src/computation/expression/expression.cc -[66/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[67/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[68/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/loader.cc.o -MF src/computation/libcomputation.a.p/loader.cc.o.d -o src/computation/libcomputation.a.p/loader.cc.o -c ../src/computation/loader.cc -[69/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar-case.cc.o -MF src/computation/libcomputation.a.p/parser_desugar-case.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar-case.cc.o -c ../src/computation/parser/desugar-case.cc -[70/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_substitute.cc.o -MF src/computation/libcomputation.a.p/expression_substitute.cc.o.d -o src/computation/libcomputation.a.p/expression_substitute.cc.o -c ../src/computation/expression/substitute.cc -[71/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar.cc.o -MF src/computation/libcomputation.a.p/parser_desugar.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar.cc.o -c ../src/computation/parser/desugar.cc -[72/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_indexify.cc.o -MF src/computation/libcomputation.a.p/expression_indexify.cc.o.d -o src/computation/libcomputation.a.p/expression_indexify.cc.o -c ../src/computation/expression/indexify.cc -[73/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_case.cc.o -MF src/computation/libcomputation.a.p/expression_case.cc.o.d -o src/computation/libcomputation.a.p/expression_case.cc.o -c ../src/computation/expression/case.cc -[74/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/module.cc.o -MF src/computation/libcomputation.a.p/module.cc.o.d -o src/computation/libcomputation.a.p/module.cc.o -c ../src/computation/module.cc -[75/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_tuple.cc.o -MF src/computation/libcomputation.a.p/expression_tuple.cc.o.d -o src/computation/libcomputation.a.p/expression_tuple.cc.o 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-I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_parser.cc.o -MF src/computation/libcomputation.a.p/parser_parser.cc.o.d -o src/computation/libcomputation.a.p/parser_parser.cc.o -c ../src/computation/parser/parser.cc -[83/297] c++ 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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 -[109/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[110/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[112/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[114/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[116/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[117/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[118/297] rm -f src/computation/libcomputation.a && gcc-ar csrD 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 -[119/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_expression.cc.o -MF src/computation/libcomputation.a.p/expression_expression.cc.o.d -o src/computation/libcomputation.a.p/expression_expression.cc.o -c ../src/computation/expression/expression.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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_rename.cc.o -MF src/computation/libcomputation.a.p/parser_rename.cc.o.d -o src/computation/libcomputation.a.p/parser_rename.cc.o -c ../src/computation/parser/rename.cc +[64/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar-case.cc.o -MF src/computation/libcomputation.a.p/parser_desugar-case.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar-case.cc.o -c ../src/computation/parser/desugar-case.cc +[65/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/loader.cc.o -MF src/computation/libcomputation.a.p/loader.cc.o.d -o src/computation/libcomputation.a.p/loader.cc.o -c ../src/computation/loader.cc +[66/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[67/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[68/297] rm -f src/libcommon.a && gcc-ar csrD 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 +[69/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[70/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_substitute.cc.o -MF src/computation/libcomputation.a.p/expression_substitute.cc.o.d -o src/computation/libcomputation.a.p/expression_substitute.cc.o -c ../src/computation/expression/substitute.cc +[71/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_case.cc.o -MF src/computation/libcomputation.a.p/expression_case.cc.o.d -o src/computation/libcomputation.a.p/expression_case.cc.o -c ../src/computation/expression/case.cc +[72/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_list.cc.o -MF src/computation/libcomputation.a.p/expression_list.cc.o.d -o src/computation/libcomputation.a.p/expression_list.cc.o -c ../src/computation/expression/list.cc +[73/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/substitution_substitution.cc.o -MF src/libbaliphy.a.p/substitution_substitution.cc.o.d -o src/libbaliphy.a.p/substitution_substitution.cc.o -c ../src/substitution/substitution.cc +[74/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_tuple.cc.o -MF src/computation/libcomputation.a.p/expression_tuple.cc.o.d -o src/computation/libcomputation.a.p/expression_tuple.cc.o -c ../src/computation/expression/tuple.cc +[75/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar.cc.o -MF src/computation/libcomputation.a.p/parser_desugar.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar.cc.o -c ../src/computation/parser/desugar.cc +[76/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops 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-fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[109/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing 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-fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[111/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[112/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[113/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[114/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[115/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[116/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[117/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[120/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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) | ^ -[120/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[121/297] rm -f src/computation/libcomputation.a && gcc-ar csrD 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 [122/297] /usr/bin/meson --internal exe --capture doc/pickout.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/pickout.md -[123/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK 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src/libbaliphy.a.p/mcmc_sample-alignment.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o -c ../src/mcmc/sample-alignment.cc +[124/297] /usr/bin/meson --internal exe --capture doc/cut-range.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/cut-range.md +[125/297] /usr/bin/meson --internal exe --capture doc/trees-distances.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-distances.md +[126/297] /usr/bin/meson --internal exe --capture doc/alignment-thin.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-thin.md +[127/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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__; | ^~~~~~~~ -[150/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[151/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[152/297] c++ 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-I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[154/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[155/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[156/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[157/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[158/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[159/297] 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,--start-group -Wl,-soname,Data.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[160/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[161/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[152/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[153/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[154/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[155/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[156/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[157/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[158/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[159/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[160/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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: /usr/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = long double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /usr/include/boost/math/tools/fraction.hpp:216:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits::result_type = long double; uintmax_t = long unsigned int]’ @@ -1255,198 +1289,199 @@ /usr/include/boost/math/special_functions/gamma.hpp:302:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 302 | result_type operator()() | ^~~~~~~~ -[162/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[163/297] 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,--start-group -Wl,-soname,Array.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[164/297] c++ -Isrc/builtins/Pair.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Pair.so.p/Pair.cc.o -MF src/builtins/Pair.so.p/Pair.cc.o.d -o src/builtins/Pair.so.p/Pair.cc.o -c ../src/builtins/Pair.cc -[165/297] 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,--start-group -Wl,-soname,Pair.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[166/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[167/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/files.cc.o -MF src/bali-phy/bali-phy.p/files.cc.o.d -o src/bali-phy/bali-phy.p/files.cc.o -c ../src/bali-phy/files.cc -[168/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[169/297] rm -f src/libbaliphy.a && gcc-ar csrD 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 -[170/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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++ -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,--start-group -Wl,-soname,Alphabet.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[173/297] 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,--start-group -Wl,-soname,Prelude.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[175/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[176/297] 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,--start-group -Wl,-soname,Modifiables.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[177/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[178/297] 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,--start-group -Wl,-soname,Range.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[179/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[180/297] 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,--start-group -Wl,-soname,Distribution.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[181/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[182/297] 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,--start-group -Wl,-soname,PopGen.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[183/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[161/297] 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,--start-group -Wl,-soname,Data.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[162/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[163/297] c++ -Isrc/builtins/Pair.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Pair.so.p/Pair.cc.o -MF src/builtins/Pair.so.p/Pair.cc.o.d -o src/builtins/Pair.so.p/Pair.cc.o -c ../src/builtins/Pair.cc +[164/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[165/297] 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,--start-group -Wl,-soname,Pair.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[166/297] 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,--start-group -Wl,-soname,Array.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[167/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[168/297] 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,--start-group -Wl,-soname,Prelude.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/files.cc.o -MF src/bali-phy/bali-phy.p/files.cc.o.d -o src/bali-phy/bali-phy.p/files.cc.o -c ../src/bali-phy/files.cc +[170/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[171/297] 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,--start-group -Wl,-soname,Alphabet.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[172/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[173/297] rm -f src/libbaliphy.a && gcc-ar csrD 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 +[174/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[175/297] 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,--start-group -Wl,-soname,Modifiables.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[176/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[178/297] 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,--start-group -Wl,-soname,Range.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[179/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[180/297] 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,--start-group -Wl,-soname,PopGen.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[181/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[182/297] 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,--start-group -Wl,-soname,Distribution.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[183/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[184/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[185/297] 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,--start-group -Wl,-soname,Environment.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[186/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[187/297] 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,--start-group -Wl,-soname,Real.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[188/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[189/297] 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,--start-group -Wl,-soname,Vector.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[190/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[191/297] 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,--start-group -Wl,-soname,Text.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[192/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[193/297] c++ -Isrc/builtins/Bits.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Bits.so.p/Bits.cc.o -MF src/builtins/Bits.so.p/Bits.cc.o.d -o src/builtins/Bits.so.p/Bits.cc.o -c ../src/builtins/Bits.cc +[194/297] c++ -Isrc/builtins/SModel.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SModel.so.p/SModel.cc.o -MF src/builtins/SModel.so.p/SModel.cc.o.d -o src/builtins/SModel.so.p/SModel.cc.o -c ../src/builtins/SModel.cc +[195/297] 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,--start-group -Wl,-soname,Alignment.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[196/297] 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,--start-group -Wl,-soname,Bits.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[197/297] 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,--start-group -Wl,-soname,SModel.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[198/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[199/297] c++ -Isrc/builtins/Char.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Char.so.p/Char.cc.o -MF src/builtins/Char.so.p/Char.cc.o.d -o src/builtins/Char.so.p/Char.cc.o -c ../src/builtins/Char.cc +[200/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -[184/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[185/297] 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,--start-group -Wl,-soname,Vector.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[186/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[187/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[188/297] 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,--start-group -Wl,-soname,Environment.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[189/297] 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,--start-group -Wl,-soname,Alignment.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[190/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[191/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[192/297] 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,--start-group -Wl,-soname,Real.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[193/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[194/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[195/297] 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,--start-group -Wl,-soname,Text.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[196/297] c++ -Isrc/builtins/MCMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/MCMC.so.p/MCMC.cc.o -MF src/builtins/MCMC.so.p/MCMC.cc.o.d -o src/builtins/MCMC.so.p/MCMC.cc.o -c ../src/builtins/MCMC.cc -[197/297] 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,--start-group -Wl,-soname,MCMC.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[198/297] c++ -Isrc/builtins/Bits.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Bits.so.p/Bits.cc.o -MF src/builtins/Bits.so.p/Bits.cc.o.d -o src/builtins/Bits.so.p/Bits.cc.o -c ../src/builtins/Bits.cc -[199/297] c++ -Isrc/builtins/Char.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Char.so.p/Char.cc.o -MF src/builtins/Char.so.p/Char.cc.o.d -o src/builtins/Char.so.p/Char.cc.o -c ../src/builtins/Char.cc -[200/297] c++ -Isrc/builtins/SModel.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SModel.so.p/SModel.cc.o -MF src/builtins/SModel.so.p/SModel.cc.o.d -o src/builtins/SModel.so.p/SModel.cc.o -c ../src/builtins/SModel.cc -[201/297] 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,--start-group -Wl,-soname,Bits.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[202/297] 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,--start-group -Wl,-soname,SModel.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[203/297] 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,--start-group -Wl,-soname,Char.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[204/297] c++ -Isrc/builtins/Foreign.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Foreign.so.p/Foreign.cc.o -MF src/builtins/Foreign.so.p/Foreign.cc.o.d -o src/builtins/Foreign.so.p/Foreign.cc.o -c ../src/builtins/Foreign.cc -[205/297] 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,--start-group -Wl,-soname,Foreign.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[206/297] c++ -Isrc/model_P.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/model_P.p/tools_model_P.cc.o -MF src/model_P.p/tools_model_P.cc.o.d -o src/model_P.p/tools_model_P.cc.o -c ../src/tools/model_P.cc -[207/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[208/297] c++ -Isrc/stats-select.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/stats-select.p/tools_stats-select.cc.o -MF src/stats-select.p/tools_stats-select.cc.o.d -o src/stats-select.p/tools_stats-select.cc.o -c ../src/tools/stats-select.cc -[209/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[210/297] c++ -Isrc/builtins/SMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SMC.so.p/SMC.cc.o -MF src/builtins/SMC.so.p/SMC.cc.o.d -o src/builtins/SMC.so.p/SMC.cc.o -c ../src/builtins/SMC.cc -[211/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/A-T-model.cc.o -MF src/bali-phy/bali-phy.p/A-T-model.cc.o.d -o src/bali-phy/bali-phy.p/A-T-model.cc.o -c ../src/bali-phy/A-T-model.cc -[212/297] 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,--start-group -Wl,-soname,SMC.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[213/297] c++ -Isrc/statreport.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/statreport.p/tools_statreport.cc.o -MF src/statreport.p/tools_statreport.cc.o.d -o src/statreport.p/tools_statreport.cc.o -c ../src/tools/statreport.cc +[201/297] 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,--start-group -Wl,-soname,Char.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[202/297] c++ -Isrc/builtins/MCMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/MCMC.so.p/MCMC.cc.o -MF src/builtins/MCMC.so.p/MCMC.cc.o.d -o src/builtins/MCMC.so.p/MCMC.cc.o -c ../src/builtins/MCMC.cc +[203/297] 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,--start-group -Wl,-soname,MCMC.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[204/297] c++ -Isrc/builtins/Foreign.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Foreign.so.p/Foreign.cc.o -MF src/builtins/Foreign.so.p/Foreign.cc.o.d -o src/builtins/Foreign.so.p/Foreign.cc.o -c ../src/builtins/Foreign.cc +[205/297] 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,--start-group -Wl,-soname,Foreign.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[206/297] c++ -Isrc/model_P.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/model_P.p/tools_model_P.cc.o -MF src/model_P.p/tools_model_P.cc.o.d -o src/model_P.p/tools_model_P.cc.o -c ../src/tools/model_P.cc +[207/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[208/297] c++ -Isrc/stats-select.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/stats-select.p/tools_stats-select.cc.o -MF src/stats-select.p/tools_stats-select.cc.o.d -o src/stats-select.p/tools_stats-select.cc.o -c ../src/tools/stats-select.cc +[209/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[210/297] c++ -Isrc/alignment-translate.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-translate.p/tools_alignment-translate.cc.o -MF src/alignment-translate.p/tools_alignment-translate.cc.o.d -o src/alignment-translate.p/tools_alignment-translate.cc.o -c ../src/tools/alignment-translate.cc +[211/297] c++ -Isrc/builtins/SMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SMC.so.p/SMC.cc.o -MF src/builtins/SMC.so.p/SMC.cc.o.d -o src/builtins/SMC.so.p/SMC.cc.o -c ../src/builtins/SMC.cc +[212/297] 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,--start-group -Wl,-soname,SMC.so -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group +[213/297] c++ -o src/alignment-translate src/alignment-translate.p/tools_alignment-translate.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[214/297] c++ -Isrc/statreport.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/statreport.p/tools_statreport.cc.o -MF src/statreport.p/tools_statreport.cc.o.d -o src/statreport.p/tools_statreport.cc.o -c ../src/tools/statreport.cc ../src/tools/statreport.cc: In function ‘void show_mode(const string&, const std::vector >&, int, const std::vector&, bool)’: ../src/tools/statreport.cc:300:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 300 | auto m = mode(total); | ^ -[214/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[215/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -ldl -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[216/297] c++ -Isrc/alignment-translate.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-translate.p/tools_alignment-translate.cc.o -MF src/alignment-translate.p/tools_alignment-translate.cc.o.d -o src/alignment-translate.p/tools_alignment-translate.cc.o -c ../src/tools/alignment-translate.cc -[217/297] c++ -o src/alignment-translate src/alignment-translate.p/tools_alignment-translate.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[218/297] c++ -Isrc/alignment-gild.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-gild.p/tools_alignment-gild.cc.o -MF src/alignment-gild.p/tools_alignment-gild.cc.o.d -o src/alignment-gild.p/tools_alignment-gild.cc.o -c ../src/tools/alignment-gild.cc -[219/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[220/297] c++ -Isrc/alignment-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-consensus.p/tools_alignment-consensus.cc.o -MF src/alignment-consensus.p/tools_alignment-consensus.cc.o.d -o src/alignment-consensus.p/tools_alignment-consensus.cc.o -c ../src/tools/alignment-consensus.cc -[221/297] c++ -Isrc/alignment-info.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-info.p/tools_alignment-info.cc.o -MF src/alignment-info.p/tools_alignment-info.cc.o.d -o src/alignment-info.p/tools_alignment-info.cc.o -c ../src/tools/alignment-info.cc -[222/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[223/297] c++ -Isrc/alignment-indices.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-indices.p/tools_alignment-indices.cc.o -MF src/alignment-indices.p/tools_alignment-indices.cc.o.d -o src/alignment-indices.p/tools_alignment-indices.cc.o -c ../src/tools/alignment-indices.cc -[224/297] c++ -o src/alignment-info src/alignment-info.p/tools_alignment-info.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[225/297] c++ -Isrc/alignment-chop-internal.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -MF src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o.d -o src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -c ../src/tools/alignment-chop-internal.cc -[226/297] c++ -o src/alignment-indices src/alignment-indices.p/tools_alignment-indices.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[227/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[228/297] c++ -Isrc/alignment-find.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-find.p/tools_alignment-find.cc.o -MF src/alignment-find.p/tools_alignment-find.cc.o.d -o src/alignment-find.p/tools_alignment-find.cc.o -c ../src/tools/alignment-find.cc -[229/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[230/297] c++ -Isrc/tree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -MF src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o.d -o src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -c ../src/tools/tree-mean-lengths.cc -[231/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[232/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[233/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[234/297] c++ -Isrc/mctree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[235/297] c++ -Isrc/trees-to-SRQ.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -MF src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o.d -o src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -c ../src/tools/trees-to-SRQ.cc -[236/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[237/297] c++ -Isrc/pickout.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/pickout.p/tools_pickout.cc.o -MF src/pickout.p/tools_pickout.cc.o.d -o src/pickout.p/tools_pickout.cc.o -c ../src/tools/pickout.cc -[238/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[239/297] c++ -o src/pickout src/pickout.p/tools_pickout.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[240/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_colors.cc.o -MF src/alignment-draw.p/tools_colors.cc.o.d -o src/alignment-draw.p/tools_colors.cc.o -c ../src/tools/colors.cc -[241/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_bootstrap.cc.o -MF src/trees-bootstrap.p/tools_bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_bootstrap.cc.o -c ../src/tools/bootstrap.cc -[242/297] c++ -Isrc/alignment-max.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-max.p/tools_alignment-max.cc.o -MF src/alignment-max.p/tools_alignment-max.cc.o.d -o src/alignment-max.p/tools_alignment-max.cc.o -c ../src/tools/alignment-max.cc -[243/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[244/297] c++ -Isrc/cut-range.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/cut-range.p/tools_cut-range.cc.o -MF src/cut-range.p/tools_cut-range.cc.o.d -o src/cut-range.p/tools_cut-range.cc.o -c ../src/tools/cut-range.cc -[245/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[246/297] c++ -Isrc/trees-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[247/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[248/297] /usr/bin/meson --internal exe --capture doc/bali-phy.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-phy.md -[249/297] /usr/bin/meson --internal exe --capture doc/model_P.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/model_P.md -[250/297] /usr/bin/meson --internal exe --capture doc/statreport.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/statreport.md -[251/297] /usr/bin/meson --internal exe --capture doc/stats-select.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/stats-select.md -[252/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[253/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[254/297] /usr/bin/meson --internal exe --capture doc/alignment-gild.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-gild.md -[255/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[256/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[215/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[216/297] 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/A-T-model.cc.o -MF src/bali-phy/bali-phy.p/A-T-model.cc.o.d -o src/bali-phy/bali-phy.p/A-T-model.cc.o -c ../src/bali-phy/A-T-model.cc +[217/297] c++ -Isrc/alignment-info.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-info.p/tools_alignment-info.cc.o -MF src/alignment-info.p/tools_alignment-info.cc.o.d -o src/alignment-info.p/tools_alignment-info.cc.o -c ../src/tools/alignment-info.cc +[218/297] c++ -Isrc/alignment-chop-internal.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -MF src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o.d -o src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -c ../src/tools/alignment-chop-internal.cc +[219/297] c++ -o src/alignment-info src/alignment-info.p/tools_alignment-info.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[220/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[221/297] c++ -Isrc/alignment-indices.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-indices.p/tools_alignment-indices.cc.o -MF src/alignment-indices.p/tools_alignment-indices.cc.o.d -o src/alignment-indices.p/tools_alignment-indices.cc.o -c ../src/tools/alignment-indices.cc +[222/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -ldl -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[223/297] c++ -Isrc/alignment-gild.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-gild.p/tools_alignment-gild.cc.o -MF src/alignment-gild.p/tools_alignment-gild.cc.o.d -o src/alignment-gild.p/tools_alignment-gild.cc.o -c ../src/tools/alignment-gild.cc +[224/297] c++ -o src/alignment-indices src/alignment-indices.p/tools_alignment-indices.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[225/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[226/297] c++ -Isrc/alignment-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-consensus.p/tools_alignment-consensus.cc.o -MF src/alignment-consensus.p/tools_alignment-consensus.cc.o.d -o src/alignment-consensus.p/tools_alignment-consensus.cc.o -c ../src/tools/alignment-consensus.cc +[227/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[228/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[229/297] c++ -Isrc/alignment-max.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-max.p/tools_alignment-max.cc.o -MF src/alignment-max.p/tools_alignment-max.cc.o.d -o src/alignment-max.p/tools_alignment-max.cc.o -c ../src/tools/alignment-max.cc +[230/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[231/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[232/297] c++ -Isrc/alignment-find.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-find.p/tools_alignment-find.cc.o -MF src/alignment-find.p/tools_alignment-find.cc.o.d -o src/alignment-find.p/tools_alignment-find.cc.o -c ../src/tools/alignment-find.cc +[233/297] c++ -Isrc/tree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -MF src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o.d -o src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -c ../src/tools/tree-mean-lengths.cc +[234/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[235/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[236/297] c++ -Isrc/pickout.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare 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-I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_bootstrap.cc.o -MF src/trees-bootstrap.p/tools_bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_bootstrap.cc.o -c ../src/tools/bootstrap.cc +[242/297] c++ -Isrc/trees-to-SRQ.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_ALL_NO_LIB -MD -MQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -MF src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o.d -o src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -c ../src/tools/trees-to-SRQ.cc +[243/297] c++ -Isrc/cut-range.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic 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src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[245/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[246/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[247/297] c++ -o src/tree-tool 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[252/297] /usr/bin/meson --internal exe --capture doc/model_P.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/model_P.md +[253/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[254/297] /usr/bin/meson --internal exe --capture doc/statreport.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/statreport.md +[255/297] /usr/bin/meson --internal exe --capture doc/alignment-gild.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-gild.md +[256/297] /usr/bin/meson --internal exe --capture doc/stats-select.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/stats-select.md [257/297] /usr/bin/meson --internal exe --capture doc/alignment-max.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-max.md [258/297] /usr/bin/meson --internal exe --capture doc/alignment-consensus.1 -- /usr/bin/pandoc -s -t man -f markdown-smart 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-[276/297] /usr/bin/meson --internal exe --capture doc/draw-tree.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/draw-tree.md -[277/297] /usr/bin/meson --internal exe --capture doc/extract-ancestors.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/extract-ancestors.md -[278/297] c++ -Isrc/bali-subsample.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 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/usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bp-analyze.md [283/297] /usr/bin/meson --internal exe --capture doc/bali-phy-pkg.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-phy-pkg.md -[284/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[287/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[288/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[284/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[285/297] c++ -o src/alignment-thin src/alignment-thin.p/tools_alignment-thin.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[286/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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) | ^ -[289/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[290/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[291/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[292/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -[293/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[294/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[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/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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 +[287/297] 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[288/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[289/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[290/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[291/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[292/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 +[293/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[294/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[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/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -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 -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -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 ../src/tools/draw-tree.cc: In function ‘MC_tree_with_lengths collapse_MC_tree(const MC_tree_with_lengths&)’: ../src/tools/draw-tree.cc:3351:10: warning: unused variable ‘right1’ [-Wunused-variable] 3351 | int right1 = MC1.mapping[b1]; | ^~~~~~ -[297/297] c++ -o src/draw-tree src/draw-tree.p/tools_draw-tree.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 -lm /usr/lib/aarch64-linux-gnu/libcairo.so -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[297/297] c++ -o src/draw-tree src/draw-tree.p/tools_draw-tree.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 -lm /usr/lib/aarch64-linux-gnu/libcairo.so -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX dh_auto_test -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=12 meson test ninja: Entering directory `/build/reproducible-path/bali-phy-3.6.0+dfsg/obj-aarch64-linux-gnu' [1/4] Generating git-version.h with a custom command - 1/36 bali-phy version OK 0.03s - 2/36 bali-phy help OK 0.04s - 3/36 bali-phy 5d test OK 3.53s - 4/36 bali-phy 5d +A 50 OK 7.22s - 5/36 bali-phy 48 +A 3 OK 13.82s - 6/36 bali-phy 5d -A 200 OK 5.01s + 1/36 bali-phy version OK 0.04s + 2/36 bali-phy help OK 0.03s + 3/36 bali-phy 5d test OK 2.14s + 4/36 bali-phy 5d +A 50 OK 5.20s + 5/36 bali-phy 48 +A 3 OK 9.20s + 6/36 bali-phy 5d -A 200 OK 3.80s 7/36 model_P --help OK 0.02s 8/36 statreport --help OK 0.04s 9/36 stats-select --help OK 0.02s -10/36 alignment-gild --help OK 0.03s -11/36 alignment-consensus --help OK 0.09s -12/36 alignment-max --help OK 0.05s -13/36 alignment-chop-internal --help OK 0.05s -14/36 alignment-indices --help OK 0.03s +10/36 alignment-gild --help OK 0.02s +11/36 alignment-consensus --help OK 0.04s +12/36 alignment-max --help OK 0.03s +13/36 alignment-chop-internal --help OK 0.03s +14/36 alignment-indices --help OK 0.04s 15/36 alignment-info --help OK 0.03s -16/36 alignment-cat --help OK 0.10s -17/36 alignment-translate --help OK 0.06s +16/36 alignment-cat --help OK 0.03s +17/36 alignment-translate --help OK 0.03s 18/36 alignment-find --help OK 0.03s -19/36 trees-consensus --help OK 0.07s -20/36 tree-mean-lengths --help OK 0.05s -21/36 mctree-mean-lengths --help OK 0.05s -22/36 trees-to-SRQ --help OK 0.05s +19/36 trees-consensus --help OK 0.03s +20/36 tree-mean-lengths --help OK 0.02s +21/36 mctree-mean-lengths --help OK 0.02s +22/36 trees-to-SRQ --help OK 0.03s 23/36 pickout --help OK 0.03s -24/36 cut-range --help OK 0.03s -25/36 trees-distances --help OK 0.06s +24/36 cut-range --help OK 0.02s +25/36 trees-distances --help OK 0.04s 26/36 alignment-thin --help OK 0.02s 27/36 alignments-diff --help OK 0.03s -28/36 tree-tool --help OK 0.08s -29/36 alignment-distances --help OK 0.06s -30/36 alignment-draw --help OK 0.03s -31/36 trees-bootstrap --help OK 0.05s -32/36 draw-tree --help OK 0.05s -33/36 extract-ancestors --help OK 0.05s -34/36 summarize-ancestors --help OK 0.05s -35/36 subsample --help OK 0.04s -36/36 bali-phy testsuite OK 158.85s +28/36 tree-tool --help OK 0.02s +29/36 alignment-distances --help OK 0.04s +30/36 alignment-draw --help OK 0.02s +31/36 trees-bootstrap --help OK 0.03s +32/36 draw-tree --help OK 0.03s +33/36 extract-ancestors --help OK 0.03s +34/36 summarize-ancestors --help OK 0.03s +35/36 subsample --help OK 0.02s +36/36 bali-phy testsuite OK 150.63s Ok: 36 @@ -2051,46 +2086,46 @@ dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/SMC.so contains an unresolvable reference to symbol _ZTV6Object: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Pair.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/SModel.so contains an unresolvable reference to symbol _ZN12substitution20sample_root_sequenceERK23Likelihood_Cache_BranchS2_S2_RK20pairwise_alignment_tS5_S5_RKN8bali_phy6matrixIdEE: it's probably a plugin +dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Distribution.so contains an unresolvable reference to symbol _Z11laplace_pdfddd: it's probably a plugin +dpkg-shlibdeps: warning: 32 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Char.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: it's probably a plugin +dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Text.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Bits.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Array.so contains an unresolvable reference to symbol _ZN13OperationArgs8allocateEO7closure: it's probably a plugin -dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/SMC.so contains an unresolvable reference to symbol _Z7uniformv: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Alignment.so contains an unresolvable reference to symbol _ZN9alignmentC2ERK8alphabetRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE: it's probably a plugin +dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/MCMC.so contains an unresolvable reference to symbol _ZN11constructorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi: it's probably a plugin +dpkg-shlibdeps: warning: 43 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Prelude.so contains an unresolvable reference to symbol _ZTI6Object: it's probably a plugin +dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Range.so contains an unresolvable reference to symbol _ZTI6Object: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Char.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin -dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/SModel.so contains an unresolvable reference to symbol _ZNK8Doublets9n_changesEii: it's probably a plugin -dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Text.so contains an unresolvable reference to symbol _ZTI6Object: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Vector.so contains an unresolvable reference to symbol _ZTV6Object: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Bits.so contains an unresolvable reference to symbol _ZN20pairwise_alignment_tC2Ev: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Foreign.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Prelude.so contains an unresolvable reference to symbol _ZTV6Object: it's probably a plugin -dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/MCMC.so contains an unresolvable reference to symbol log_verbose: it's probably a plugin -dpkg-shlibdeps: warning: 43 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Distribution.so contains an unresolvable reference to symbol _Z14gamma_quantileddd: it's probably a plugin -dpkg-shlibdeps: warning: 32 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Data.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Vector.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Alignment.so contains an unresolvable reference to symbol _ZN9alignment4loadERKSt6vectorI8sequenceSaIS1_EE: it's probably a plugin -dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Alphabet.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/PopGen.so contains an unresolvable reference to symbol _Z8demangleRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE: it's probably a plugin +dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Modifiables.so contains an unresolvable reference to symbol _ZTV10expression: it's probably a plugin dpkg-shlibdeps: warning: 26 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Environment.so contains an unresolvable reference to symbol _ZTI6Object: it's probably a plugin -dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Real.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Modifiables.so contains an unresolvable reference to symbol _ZN15random_variableC1Ev: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Alphabet.so contains an unresolvable reference to symbol _ZNK8TripletsclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE: it's probably a plugin dpkg-shlibdeps: warning: 26 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Foreign.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Array.so contains an unresolvable reference to symbol _ZN13OperationArgs8allocateEO7closure: it's probably a plugin +dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Data.so contains an unresolvable reference to symbol _ZTV6Object: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/PopGen.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Pair.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Environment.so contains an unresolvable reference to symbol _ZTI6Object: it's probably a plugin +dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson @@ -2104,12 +2139,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3718235/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3718235/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/1037046 and its subdirectories -I: Current time: Fri Feb 7 07:33:17 -12 2025 -I: pbuilder-time-stamp: 1738956797 +I: removing directory /srv/workspace/pbuilder/3718235 and its subdirectories +I: Current time: Sat Feb 8 09:38:44 +14 2025 +I: pbuilder-time-stamp: 1738957124