Diff of the two buildlogs: -- --- b1/build.log 2024-01-09 22:41:19.706589831 +0000 +++ b2/build.log 2024-01-09 22:47:52.106384336 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 9 10:30:37 -12 2024 -I: pbuilder-time-stamp: 1704839437 +I: Current time: Tue Feb 11 19:04:21 +14 2025 +I: pbuilder-time-stamp: 1739250261 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ 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.NCNFoquy/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.FRu2dPkn/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 7 07:51:21 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -29,51 +29,82 @@ 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/30002/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/85939/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 11 05:04 /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/85939/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/85939/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='1ae6d8d24d464222bcff48be60005a5a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='30002' - PS1='# ' - PS2='> ' + INVOCATION_ID=5fa99ae5fc5f4162869e6afdfd10b6f1 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=85939 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.jlZRmGun/pbuilderrc_Ej67 --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.jlZRmGun/b1 --logfile b1/build.log bali-phy_3.6.0+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.jlZRmGun/pbuilderrc_bh97 --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.jlZRmGun/b2 --logfile b2/build.log bali-phy_3.6.0+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash @@ -133,7 +164,7 @@ -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 7 09:24 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 11 05:04 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su @@ -159,7 +190,7 @@ -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/30002/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/85939/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -363,7 +394,7 @@ Get: 142 http://deb.debian.org/debian bullseye/main i386 nlohmann-json3-dev all 3.9.1-1 [684 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 pandoc-data all 2.9.2.1-1+deb11u1 [377 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 pandoc i386 2.9.2.1-1+deb11u1 [19.1 MB] -Fetched 79.9 MB in 15s (5351 kB/s) +Fetched 79.9 MB in 1s (53.3 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 ... 17763 files and directories currently installed.) @@ -843,8 +874,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 9 22:31:29 UTC 2024. -Universal Time is now: Tue Jan 9 22:31:29 UTC 2024. +Local time is now: Tue Feb 11 05:04:49 UTC 2025. +Universal Time is now: Tue Feb 11 05:04:49 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -967,7 +998,11 @@ 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/85939/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/85939/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 @@ -1062,366 +1097,366 @@ Found ninja-1.10.1 at /usr/bin/ninja make[1]: Leaving directory '/build/reproducible-path/bali-phy-3.6.0+dfsg' dh_auto_build -O--buildsystem=meson - cd obj-i686-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/log-level.cc.o -MF src/util/libutil.a.p/log-level.cc.o.d -o src/util/libutil.a.p/log-level.cc.o -c ../src/util/log-level.cc + cd obj-i686-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/log-level.cc.o -MF src/util/libutil.a.p/log-level.cc.o.d -o src/util/libutil.a.p/log-level.cc.o -c ../src/util/log-level.cc [2/297] /usr/bin/meson --internal vcstagger ../src/git-version.h.in src/git-version.h '' /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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc -[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_sanitize.cc.o -MF src/util/libutil.a.p/string_sanitize.cc.o.d -o src/util/libutil.a.p/string_sanitize.cc.o -c ../src/util/string/sanitize.cc -[8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/mapping.cc.o -MF src/util/libutil.a.p/mapping.cc.o.d -o src/util/libutil.a.p/mapping.cc.o -c ../src/util/mapping.cc -[9/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/permute.cc.o -MF src/util/libutil.a.p/permute.cc.o.d -o src/util/libutil.a.p/permute.cc.o -c ../src/util/permute.cc -[10/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/rng.cc.o -MF src/util/libutil.a.p/rng.cc.o.d -o src/util/libutil.a.p/rng.cc.o -c ../src/util/rng.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc +[4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc +[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc +[7/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_sanitize.cc.o -MF src/util/libutil.a.p/string_sanitize.cc.o.d -o src/util/libutil.a.p/string_sanitize.cc.o -c ../src/util/string/sanitize.cc +[8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc +[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 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/mapping.cc.o -MF src/util/libutil.a.p/mapping.cc.o.d -o src/util/libutil.a.p/mapping.cc.o -c ../src/util/mapping.cc +[10/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/permute.cc.o -MF src/util/libutil.a.p/permute.cc.o.d -o src/util/libutil.a.p/permute.cc.o -c ../src/util/permute.cc +[11/297] c++ -Isrc/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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_newick-tokenizer.cc.o -MF src/libcommon.a.p/tree_newick-tokenizer.cc.o.d -o src/libcommon.a.p/tree_newick-tokenizer.cc.o -c ../src/tree/newick-tokenizer.cc +[12/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/rng.cc.o -MF src/util/libutil.a.p/rng.cc.o.d -o src/util/libutil.a.p/rng.cc.o -c ../src/util/rng.cc ../src/util/rng.cc: In function ‘long unsigned int get_random_seed()’: ../src/util/rng.cc:42:8: warning: left shift count >= width of type [-Wshift-count-overflow] 42 | s <<= bits_per_read; | ~~^~~~~~~~~~~~~~~~~ -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc -[12/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-paths.cc.o -MF src/util/libutil.a.p/file-paths.cc.o.d -o src/util/libutil.a.p/file-paths.cc.o -c ../src/util/file-paths.cc -[13/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/io.cc.o -MF src/util/libutil.a.p/io.cc.o.d -o src/util/libutil.a.p/io.cc.o -c ../src/util/io.cc -[14/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_newick-tokenizer.cc.o -MF src/libcommon.a.p/tree_newick-tokenizer.cc.o.d -o src/libcommon.a.p/tree_newick-tokenizer.cc.o -c ../src/tree/newick-tokenizer.cc -[15/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/time.cc.o -MF src/util/libutil.a.p/time.cc.o.d -o src/util/libutil.a.p/time.cc.o -c ../src/util/time.cc -[16/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/text.cc.o -MF src/util/libutil.a.p/text.cc.o.d -o src/util/libutil.a.p/text.cc.o -c ../src/util/text.cc -[17/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/cmdline.cc.o -MF src/util/libutil.a.p/cmdline.cc.o.d -o src/util/libutil.a.p/cmdline.cc.o -c ../src/util/cmdline.cc -[18/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -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 -[19/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -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 -[20/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_randomtree.cc.o -MF src/libcommon.a.p/tree_randomtree.cc.o.d -o src/libcommon.a.p/tree_randomtree.cc.o -c ../src/tree/randomtree.cc -[21/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_split.cc.o -MF src/util/libutil.a.p/string_split.cc.o.d -o src/util/libutil.a.p/string_split.cc.o -c ../src/util/string/split.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_n_indels.cc.o -MF src/libcommon.a.p/tree-align_n_indels.cc.o.d -o src/libcommon.a.p/tree-align_n_indels.cc.o -c ../src/tree-align/n_indels.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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_sequencetree.cc.o -MF src/libcommon.a.p/tree_sequencetree.cc.o.d -o src/libcommon.a.p/tree_sequencetree.cc.o -c ../src/tree/sequencetree.cc -[24/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -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 -[25/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree.cc.o -MF src/libcommon.a.p/tree_tree.cc.o.d -o src/libcommon.a.p/tree_tree.cc.o -c ../src/tree/tree.cc -[27/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-readers.cc.o -MF src/util/libutil.a.p/file-readers.cc.o.d -o src/util/libutil.a.p/file-readers.cc.o -c ../src/util/file-readers.cc -[28/297] 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 -[29/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-random.cc.o -MF src/libcommon.a.p/alignment_alignment-random.cc.o.d -o src/libcommon.a.p/alignment_alignment-random.cc.o -c ../src/alignment/alignment-random.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_read-trees.cc.o -MF src/libcommon.a.p/tools_read-trees.cc.o.d -o src/libcommon.a.p/tools_read-trees.cc.o -c ../src/tools/read-trees.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc -[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 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_statistics.cc.o -MF src/libcommon.a.p/tools_statistics.cc.o.d -o src/libcommon.a.p/tools_statistics.cc.o -c ../src/tools/statistics.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_split.cc.o -MF src/util/libutil.a.p/string_split.cc.o.d -o src/util/libutil.a.p/string_split.cc.o -c ../src/util/string/split.cc +[29/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_read-trees.cc.o -MF src/libcommon.a.p/tools_read-trees.cc.o.d -o src/libcommon.a.p/tools_read-trees.cc.o -c ../src/tools/read-trees.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/models_path.cc.o -MF src/libcommon.a.p/models_path.cc.o.d -o src/libcommon.a.p/models_path.cc.o -c ../src/models/path.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc +[32/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-readers.cc.o -MF src/util/libutil.a.p/file-readers.cc.o.d -o src/util/libutil.a.p/file-readers.cc.o -c ../src/util/file-readers.cc +[33/297] 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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree.cc.o -MF src/libcommon.a.p/tree_tree.cc.o.d -o src/libcommon.a.p/tree_tree.cc.o -c ../src/tree/tree.cc +[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 -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_optimize.cc.o -MF src/libcommon.a.p/tools_optimize.cc.o.d -o src/libcommon.a.p/tools_optimize.cc.o -c ../src/tools/optimize.cc +[36/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_findroot.cc.o -MF src/libcommon.a.p/tools_findroot.cc.o.d -o src/libcommon.a.p/tools_findroot.cc.o -c ../src/tools/findroot.cc +[37/297] 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 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_alphabet.cc.o -MF src/libcommon.a.p/sequence_alphabet.cc.o.d -o src/libcommon.a.p/sequence_alphabet.cc.o -c ../src/sequence/alphabet.cc +[39/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-util.cc.o -MF src/libcommon.a.p/alignment_alignment-util.cc.o.d -o src/libcommon.a.p/alignment_alignment-util.cc.o -c ../src/alignment/alignment-util.cc +[40/297] c++ -Isrc/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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/object.cc.o -MF src/computation/libcomputation.a.p/object.cc.o.d -o src/computation/libcomputation.a.p/object.cc.o -c ../src/computation/object.cc +[41/297] 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=. 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-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/context.cc.o -MF src/computation/libcomputation.a.p/context.cc.o.d -o src/computation/libcomputation.a.p/context.cc.o -c ../src/computation/context.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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_AST_node.cc.o -MF src/computation/libcomputation.a.p/expression_AST_node.cc.o.d -o src/computation/libcomputation.a.p/expression_AST_node.cc.o -c ../src/computation/expression/AST_node.cc +[63/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_apply.cc.o -MF src/computation/libcomputation.a.p/expression_apply.cc.o.d -o src/computation/libcomputation.a.p/expression_apply.cc.o -c ../src/computation/expression/apply.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/program.cc.o -MF src/computation/libcomputation.a.p/program.cc.o.d -o src/computation/libcomputation.a.p/program.cc.o -c ../src/computation/program.cc ../src/computation/program.cc: In member function ‘void Program::check_dependencies()’: ../src/computation/program.cc:155:10: warning: unused variable ‘index’ [-Wunused-variable] 155 | int index = find_module(name); | ^~~~~ -[58/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 -[59/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_joint-A-T.cc.o -MF src/libcommon.a.p/tools_joint-A-T.cc.o.d -o src/libcommon.a.p/tools_joint-A-T.cc.o -c ../src/tools/joint-A-T.cc -[60/297] 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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_driver.cc.o -MF src/computation/libcomputation.a.p/parser_driver.cc.o.d -o src/computation/libcomputation.a.p/parser_driver.cc.o -c ../src/computation/parser/driver.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_lexer.cc.o -MF src/computation/libcomputation.a.p/parser_lexer.cc.o.d -o src/computation/libcomputation.a.p/parser_lexer.cc.o -c ../src/computation/parser/lexer.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_operator.cc.o -MF src/computation/libcomputation.a.p/expression_operator.cc.o.d -o src/computation/libcomputation.a.p/expression_operator.cc.o -c ../src/computation/expression/operator.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_constructor.cc.o -MF src/computation/libcomputation.a.p/expression_constructor.cc.o.d -o src/computation/libcomputation.a.p/expression_constructor.cc.o -c ../src/computation/expression/constructor.cc -[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 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-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 -[117/297] 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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_proposals.cc.o -MF src/libbaliphy.a.p/mcmc_proposals.cc.o.d -o src/libbaliphy.a.p/mcmc_proposals.cc.o -c ../src/mcmc/proposals.cc -[122/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -MF src/libbaliphy.a.p/mcmc_slice-sampling.cc.o.d -o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -c ../src/mcmc/slice-sampling.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc -[124/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -MF src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o.d -o 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src/libbaliphy.a.p/mcmc_sample-alignment.cc.o -c ../src/mcmc/sample-alignment.cc -[126/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-node.cc.o -MF src/libbaliphy.a.p/mcmc_sample-node.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-node.cc.o -c ../src/mcmc/sample-node.cc -[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 -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -MF src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -c ../src/mcmc/sample-two-nodes.cc -[128/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -MF src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -c ../src/mcmc/sample-topology-NNI.cc -[129/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[130/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[131/297] /usr/bin/meson --internal exe --capture doc/pickout.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/pickout.md -[132/297] /usr/bin/meson --internal exe --capture doc/cut-range.1 -- /usr/bin/pandoc -s -t man 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-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_var.cc.o -MF src/computation/libcomputation.a.p/expression_var.cc.o.d -o src/computation/libcomputation.a.p/expression_var.cc.o -c ../src/computation/expression/var.cc +[77/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_lambda.cc.o -MF src/computation/libcomputation.a.p/expression_lambda.cc.o.d -o src/computation/libcomputation.a.p/expression_lambda.cc.o -c ../src/computation/expression/lambda.cc +[78/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_random_variable.cc.o -MF src/computation/libcomputation.a.p/expression_random_variable.cc.o.d -o src/computation/libcomputation.a.p/expression_random_variable.cc.o -c ../src/computation/expression/random_variable.cc +[79/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_joint-A-T.cc.o -MF src/libcommon.a.p/tools_joint-A-T.cc.o.d -o src/libcommon.a.p/tools_joint-A-T.cc.o -c ../src/tools/joint-A-T.cc +[80/297] 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 +[81/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_reg_var.cc.o -MF src/computation/libcomputation.a.p/expression_reg_var.cc.o.d -o src/computation/libcomputation.a.p/expression_reg_var.cc.o -c ../src/computation/expression/reg_var.cc +[82/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_setup.cc.o -MF src/libbaliphy.a.p/mcmc_setup.cc.o.d -o src/libbaliphy.a.p/mcmc_setup.cc.o -c ../src/mcmc/setup.cc +[83/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_let.cc.o -MF src/computation/libcomputation.a.p/expression_let.cc.o.d -o src/computation/libcomputation.a.p/expression_let.cc.o -c ../src/computation/expression/let.cc +[84/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_modifiable.cc.o -MF src/computation/libcomputation.a.p/expression_modifiable.cc.o.d -o src/computation/libcomputation.a.p/expression_modifiable.cc.o -c ../src/computation/expression/modifiable.cc +[85/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_maybe.cc.o -MF src/computation/libcomputation.a.p/expression_maybe.cc.o.d -o src/computation/libcomputation.a.p/expression_maybe.cc.o -c ../src/computation/expression/maybe.cc +[86/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_bool.cc.o -MF src/computation/libcomputation.a.p/expression_bool.cc.o.d -o src/computation/libcomputation.a.p/expression_bool.cc.o -c ../src/computation/expression/bool.cc +[87/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -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 +[88/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o -MF src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o.d -o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o -c ../src/computation/expression/resolved_symbol.cc +[89/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[90/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c ../src/computation/optimization/simplifier.cc +[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 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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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc +[112/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_occurrence.cc.o -MF src/computation/libcomputation.a.p/optimization_occurrence.cc.o.d -o src/computation/libcomputation.a.p/optimization_occurrence.cc.o -c ../src/computation/optimization/occurrence.cc +[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 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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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -MF src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -c ../src/mcmc/sample-branch-lengths.cc +[121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc +[122/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-alignment.cc.o -MF 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 +[123/297] /usr/bin/meson --internal exe --capture doc/pickout.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/pickout.md +[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] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc +[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 -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_pow2.cc.o -MF src/libbaliphy.a.p/math_pow2.cc.o.d -o src/libbaliphy.a.p/math_pow2.cc.o -c ../src/math/pow2.cc +[128/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_set-levels.cc.o -MF src/computation/libcomputation.a.p/optimization_set-levels.cc.o.d -o src/computation/libcomputation.a.p/optimization_set-levels.cc.o -c ../src/computation/optimization/set-levels.cc +[129/297] 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 +[130/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_exponential.cc.o -MF src/libbaliphy.a.p/math_exponential.cc.o.d -o src/libbaliphy.a.p/math_exponential.cc.o -c ../src/math/exponential.cc +[131/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[132/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-node.cc.o -MF src/libbaliphy.a.p/mcmc_sample-node.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-node.cc.o -c ../src/mcmc/sample-node.cc +[133/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_site-compression.cc.o -MF src/libbaliphy.a.p/models_site-compression.cc.o.d -o src/libbaliphy.a.p/models_site-compression.cc.o -c ../src/models/site-compression.cc +[134/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -MF src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -c ../src/mcmc/sample-two-nodes.cc +[135/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[136/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -MF src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -c 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-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_eigenvalue.cc.o -MF src/libbaliphy.a.p/math_eigenvalue.cc.o.d -o src/libbaliphy.a.p/math_eigenvalue.cc.o -c ../src/math/eigenvalue.cc +[139/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/substitution_parsimony.cc.o -MF src/libbaliphy.a.p/substitution_parsimony.cc.o.d -o src/libbaliphy.a.p/substitution_parsimony.cc.o -c ../src/substitution/parsimony.cc +[140/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_choose.cc.o -MF src/libbaliphy.a.p/probability_choose.cc.o.d -o src/libbaliphy.a.p/probability_choose.cc.o -c ../src/probability/choose.cc +[141/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-tri.cc.o -MF src/libbaliphy.a.p/mcmc_sample-tri.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-tri.cc.o -c ../src/mcmc/sample-tri.cc +[142/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_link2.cc.o -MF src/libbaliphy.a.p/tree-align_link2.cc.o.d -o src/libbaliphy.a.p/tree-align_link2.cc.o -c ../src/tree-align/link2.cc +[143/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o -MF src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o -c ../src/mcmc/sample-topology-SPR.cc +[144/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_TreeInterface.cc.o -MF src/libbaliphy.a.p/models_TreeInterface.cc.o.d -o src/libbaliphy.a.p/models_TreeInterface.cc.o -c ../src/models/TreeInterface.cc +[145/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_n_indels2.cc.o -MF src/libbaliphy.a.p/tree-align_n_indels2.cc.o.d -o src/libbaliphy.a.p/tree-align_n_indels2.cc.o -c ../src/tree-align/n_indels2.cc +[146/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_unification.cc.o -MF src/libbaliphy.a.p/models_unification.cc.o.d -o src/libbaliphy.a.p/models_unification.cc.o -c ../src/models/unification.cc +[147/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -MF src/libbaliphy.a.p/alignment_alignment-constraint.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -c ../src/alignment/alignment-constraint.cc +[148/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc ../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ ../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc -[158/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc -[160/297] 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 -[161/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc -[162/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/link-partitions.cc.o -MF src/bali-phy/bali-phy.p/link-partitions.cc.o.d -o src/bali-phy/bali-phy.p/link-partitions.cc.o -c ../src/bali-phy/link-partitions.cc -[163/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/paths.cc.o -MF src/bali-phy/bali-phy.p/paths.cc.o.d -o src/bali-phy/bali-phy.p/paths.cc.o -c ../src/bali-phy/paths.cc -[164/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[165/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Array.so.p/Array.cc.o -MF src/builtins/Array.so.p/Array.cc.o.d -o src/builtins/Array.so.p/Array.cc.o -c ../src/builtins/Array.cc -[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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[167/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Data.so.p/Data.cc.o -MF src/builtins/Data.so.p/Data.cc.o.d -o src/builtins/Data.so.p/Data.cc.o -c ../src/builtins/Data.cc -[168/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[169/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[170/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc +[149/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/imodel_imodel.cc.o -MF src/libbaliphy.a.p/imodel_imodel.cc.o.d -o src/libbaliphy.a.p/imodel_imodel.cc.o -c ../src/imodel/imodel.cc +[150/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_logger.cc.o -MF src/libbaliphy.a.p/mcmc_logger.cc.o.d -o src/libbaliphy.a.p/mcmc_logger.cc.o -c ../src/mcmc/logger.cc +[151/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parse.cc.o -MF src/libbaliphy.a.p/models_parse.cc.o.d -o src/libbaliphy.a.p/models_parse.cc.o -c ../src/models/parse.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_rules.cc.o -MF src/libbaliphy.a.p/models_rules.cc.o.d -o src/libbaliphy.a.p/models_rules.cc.o -c ../src/models/rules.cc +[154/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_typecheck.cc.o -MF src/libbaliphy.a.p/models_typecheck.cc.o.d -o src/libbaliphy.a.p/models_typecheck.cc.o -c ../src/models/typecheck.cc +[156/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_probability.cc.o -MF src/libbaliphy.a.p/probability_probability.cc.o.d -o src/libbaliphy.a.p/probability_probability.cc.o -c ../src/probability/probability.cc +[158/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Array.so.p/Array.cc.o -MF src/builtins/Array.so.p/Array.cc.o.d -o src/builtins/Array.so.p/Array.cc.o -c ../src/builtins/Array.cc +[159/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Data.so.p/Data.cc.o -MF src/builtins/Data.so.p/Data.cc.o.d -o src/builtins/Data.so.p/Data.cc.o -c ../src/builtins/Data.cc +[160/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[162/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/paths.cc.o -MF src/bali-phy/bali-phy.p/paths.cc.o.d -o src/bali-phy/bali-phy.p/paths.cc.o -c ../src/bali-phy/paths.cc +[163/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/link-partitions.cc.o -MF src/bali-phy/bali-phy.p/link-partitions.cc.o.d -o src/bali-phy/bali-phy.p/link-partitions.cc.o -c ../src/bali-phy/link-partitions.cc +[164/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_model.cc.o -MF src/libbaliphy.a.p/models_model.cc.o.d -o src/libbaliphy.a.p/models_model.cc.o -c ../src/models/model.cc +[165/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[166/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Prelude.so.p/Prelude.cc.o -MF src/builtins/Prelude.so.p/Prelude.cc.o.d -o src/builtins/Prelude.so.p/Prelude.cc.o -c ../src/builtins/Prelude.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[169/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc +[170/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[171/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[172/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Range.so.p/Range.cc.o -MF src/builtins/Range.so.p/Range.cc.o.d -o src/builtins/Range.so.p/Range.cc.o -c ../src/builtins/Range.cc +[173/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Modifiables.so.p/Modifiables.cc.o -MF src/builtins/Modifiables.so.p/Modifiables.cc.o.d -o src/builtins/Modifiables.so.p/Modifiables.cc.o -c ../src/builtins/Modifiables.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[176/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Distribution.so.p/Distribution.cc.o -MF src/builtins/Distribution.so.p/Distribution.cc.o.d -o src/builtins/Distribution.so.p/Distribution.cc.o -c ../src/builtins/Distribution.cc +[177/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[178/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc +[179/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc +[180/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/PopGen.so.p/PopGen.cc.o -MF src/builtins/PopGen.so.p/PopGen.cc.o.d -o src/builtins/PopGen.so.p/PopGen.cc.o -c ../src/builtins/PopGen.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[188/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc +[189/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc ../src/bali-phy/bali-phy.cc: In function ‘void report_mem()’: ../src/bali-phy/bali-phy.cc:122:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 122 | system(cmd.str().c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -[171/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[172/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Prelude.so.p/Prelude.cc.o -MF src/builtins/Prelude.so.p/Prelude.cc.o.d -o src/builtins/Prelude.so.p/Prelude.cc.o -c ../src/builtins/Prelude.cc -[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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc -[175/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc -[176/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc -[177/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[178/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc -[179/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Range.so.p/Range.cc.o -MF src/builtins/Range.so.p/Range.cc.o.d -o src/builtins/Range.so.p/Range.cc.o -c ../src/builtins/Range.cc -[180/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[181/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Modifiables.so.p/Modifiables.cc.o -MF src/builtins/Modifiables.so.p/Modifiables.cc.o.d -o src/builtins/Modifiables.so.p/Modifiables.cc.o -c ../src/builtins/Modifiables.cc -[182/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[183/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Distribution.so.p/Distribution.cc.o -MF src/builtins/Distribution.so.p/Distribution.cc.o.d -o src/builtins/Distribution.so.p/Distribution.cc.o -c ../src/builtins/Distribution.cc -[184/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[185/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc -[186/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[187/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/PopGen.so.p/PopGen.cc.o -MF src/builtins/PopGen.so.p/PopGen.cc.o.d -o src/builtins/PopGen.so.p/PopGen.cc.o -c ../src/builtins/PopGen.cc -[188/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[189/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc -[190/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[191/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alignment.so.p/Alignment.cc.o -MF src/builtins/Alignment.so.p/Alignment.cc.o.d -o src/builtins/Alignment.so.p/Alignment.cc.o -c ../src/builtins/Alignment.cc -[193/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[194/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[195/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[196/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[198/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[199/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Text.so.p/Text.cc.o -MF src/builtins/Text.so.p/Text.cc.o.d -o src/builtins/Text.so.p/Text.cc.o -c ../src/builtins/Text.cc -[200/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[201/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[202/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[203/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[204/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[205/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[206/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[207/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[208/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[209/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[210/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[211/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[212/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -ldl -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[213/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[214/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group -[215/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[216/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[217/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[218/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[219/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[220/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[221/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[222/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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-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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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-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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[227/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[228/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[229/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[230/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[231/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-cat.p/tools_alignment-cat.cc.o -MF src/alignment-cat.p/tools_alignment-cat.cc.o.d -o src/alignment-cat.p/tools_alignment-cat.cc.o -c ../src/tools/alignment-cat.cc -[232/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[233/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[234/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[235/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[236/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[237/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_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 -[238/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[239/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c 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doc/mctree-mean-lengths.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/mctree-mean-lengths.md -[274/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[275/297] /usr/bin/meson --internal exe --capture doc/trees-to-SRQ.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-to-SRQ.md -[276/297] /usr/bin/meson --internal exe --capture doc/alignment-thin.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-thin.md -[277/297] /usr/bin/meson --internal exe --capture doc/tree-tool.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/tree-tool.md -[278/297] /usr/bin/meson --internal exe --capture doc/alignments-diff.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignments-diff.md -[279/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc -[280/297] /usr/bin/meson --internal exe --capture doc/alignment-draw.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-draw.md -[281/297] /usr/bin/meson --internal exe --capture doc/alignment-distances.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-distances.md -[282/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[283/297] /usr/bin/meson --internal exe --capture doc/draw-tree.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/draw-tree.md -[284/297] /usr/bin/meson --internal exe --capture doc/trees-bootstrap.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-bootstrap.md -[285/297] /usr/bin/meson --internal exe --capture doc/extract-ancestors.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/extract-ancestors.md -[286/297] /usr/bin/meson --internal exe --capture doc/summarize-ancestors.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/summarize-ancestors.md -[287/297] /usr/bin/meson --internal exe --capture doc/bali-subsample.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-subsample.md -[288/297] /usr/bin/meson --internal exe --capture doc/bp-analyze.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bp-analyze.md -[289/297] /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 -[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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc -[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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc -[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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[294/297] 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/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc +[190/297] 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 +[191/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[192/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[193/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Text.so.p/Text.cc.o -MF src/builtins/Text.so.p/Text.cc.o.d -o src/builtins/Text.so.p/Text.cc.o -c ../src/builtins/Text.cc +[194/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[195/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alignment.so.p/Alignment.cc.o -MF src/builtins/Alignment.so.p/Alignment.cc.o.d -o src/builtins/Alignment.so.p/Alignment.cc.o -c ../src/builtins/Alignment.cc +[196/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[197/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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++ -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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[200/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[201/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[203/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -Wl,--end-group +[206/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc +[207/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[208/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[209/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[210/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[215/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[216/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[217/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[218/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[219/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[220/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[221/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[222/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[223/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c ../src/tools/mctree-mean-lengths.cc +[224/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[225/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[226/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[227/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[228/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[229/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -ldl -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[230/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[231/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_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 +[232/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-consensus.p/tools_trees-consensus.cc.o -MF src/trees-consensus.p/tools_trees-consensus.cc.o.d -o src/trees-consensus.p/tools_trees-consensus.cc.o -c ../src/tools/trees-consensus.cc +[233/297] 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 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-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-subsample.p/tools_subsample.cc.o -MF src/bali-subsample.p/tools_subsample.cc.o.d -o src/bali-subsample.p/tools_subsample.cc.o -c ../src/tools/subsample.cc +[281/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[282/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc +[283/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[284/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc +[285/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-thin.p/tools_alignment-thin.cc.o -MF src/alignment-thin.p/tools_alignment-thin.cc.o.d -o src/alignment-thin.p/tools_alignment-thin.cc.o -c ../src/tools/alignment-thin.cc +[286/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX +[287/297] 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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc +[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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc +[295/297] c++ -o src/summarize-ancestors src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-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/i386-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_FILESYSTEM_DYN_LINK=1 -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc ../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]; | ^~~~~~ -[295/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm /usr/lib/i386-linux-gnu/libcairo.so -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -[296/297] 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_FILESYSTEM_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc -[297/297] 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/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm -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/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_random.so.1.74.0 -lm /usr/lib/i386-linux-gnu/libcairo.so -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX dh_auto_test -O--buildsystem=meson - cd obj-i686-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test + cd obj-i686-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=15 meson test ninja: Entering directory `/build/reproducible-path/bali-phy-3.6.0+dfsg/obj-i686-linux-gnu' [1/4] Generating git-version.h with a custom command - 1/36 bali-phy version OK 0.07s - 2/36 bali-phy help OK 0.03s - 3/36 bali-phy 5d test OK 5.42s - 4/36 bali-phy 5d +A 50 OK 14.57s - 5/36 bali-phy 48 +A 3 OK 20.31s - 6/36 bali-phy 5d -A 200 OK 11.72s - 7/36 model_P --help OK 0.04s - 8/36 statreport --help OK 0.05s - 9/36 stats-select --help OK 0.02s + 1/36 bali-phy version OK 0.02s + 2/36 bali-phy help OK 0.01s + 3/36 bali-phy 5d test OK 3.22s + 4/36 bali-phy 5d +A 50 OK 7.75s + 5/36 bali-phy 48 +A 3 OK 13.79s + 6/36 bali-phy 5d -A 200 OK 5.95s + 7/36 model_P --help OK 0.01s + 8/36 statreport --help OK 0.03s + 9/36 stats-select --help OK 0.01s 10/36 alignment-gild --help OK 0.02s 11/36 alignment-consensus --help OK 0.03s -12/36 alignment-max --help OK 0.02s -13/36 alignment-chop-internal --help OK 0.03s +12/36 alignment-max --help OK 0.01s +13/36 alignment-chop-internal --help OK 0.04s 14/36 alignment-indices --help OK 0.02s -15/36 alignment-info --help OK 0.02s -16/36 alignment-cat --help OK 0.03s -17/36 alignment-translate --help OK 0.05s -18/36 alignment-find --help OK 0.01s -19/36 trees-consensus --help OK 0.02s -20/36 tree-mean-lengths --help OK 0.02s -21/36 mctree-mean-lengths --help OK 0.03s -22/36 trees-to-SRQ --help OK 0.01s +15/36 alignment-info --help OK 0.01s +16/36 alignment-cat --help OK 0.01s +17/36 alignment-translate --help OK 0.02s +18/36 alignment-find --help OK 0.02s +19/36 trees-consensus --help OK 0.01s +20/36 tree-mean-lengths --help OK 0.01s +21/36 mctree-mean-lengths --help OK 0.01s +22/36 trees-to-SRQ --help OK 0.03s 23/36 pickout --help OK 0.01s -24/36 cut-range --help OK 0.05s -25/36 trees-distances --help OK 0.02s -26/36 alignment-thin --help OK 0.01s -27/36 alignments-diff --help OK 0.03s +24/36 cut-range --help OK 0.02s +25/36 trees-distances --help OK 0.03s +26/36 alignment-thin --help OK 0.03s +27/36 alignments-diff --help OK 0.01s 28/36 tree-tool --help OK 0.02s -29/36 alignment-distances --help OK 0.02s -30/36 alignment-draw --help OK 0.01s +29/36 alignment-distances --help OK 0.03s +30/36 alignment-draw --help OK 0.02s 31/36 trees-bootstrap --help OK 0.02s 32/36 draw-tree --help OK 0.02s -33/36 extract-ancestors --help OK 0.03s +33/36 extract-ancestors --help OK 0.01s 34/36 summarize-ancestors --help OK 0.02s -35/36 subsample --help OK 0.01s -36/36 bali-phy testsuite OK 302.29s +35/36 subsample --help OK 0.02s +36/36 bali-phy testsuite OK 222.22s Ok: 36 @@ -1440,435 +1475,435 @@ [1/5] Generating git-version.h with a custom command [1/2] Installing files. Installing subdir /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Parse.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Prelude.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Range.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/MCMC.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Tree.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/IModel.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/PopGen.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Parse.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Prelude.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SMC.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/MCMC.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Parameters.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/PopGen.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Control/DeepSeq.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Control/Monad.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Nucleotides.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Doublets.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/ReversibleMarkov.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Frequency.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Likelihood.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Codons.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/System/Environment.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/System +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Tree/Newick.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Tree Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Random.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/FakeDist.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Binomial.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Mixture.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Dirichlet.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Cauchy.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Poisson.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Discrete.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Exponential.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Laplace.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Gamma.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/ExpTransform.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Discrete.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Tree.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/List.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Uniform.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Laplace.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Bernoulli.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/RandomAlignment.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Beta.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Exponential.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Geometric.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Cauchy.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Normal.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Poisson.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/RandomAlignment.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Dirichlet.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/FakeDist.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Categorical.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Mixture.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/DirichletProcess.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Geometric.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Gamma.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/Beta.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Probability/Distribution/List.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Char.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Ord.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Bool.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Ix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Array.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Either.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/BitVector.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Eq.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Maybe.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Text.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Set.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Map.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Text.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Either.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/List.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Ord.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Function.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/JSON.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Tuple.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Matrix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Maybe.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Eq.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/ReadFile.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Function.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/List.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Control/DeepSeq.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Control/Monad.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Tree/Newick.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Tree -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Sequence.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Set.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Char.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Array.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Ix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Matrix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Bool.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Data/Tuple.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Alignment.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Alphabet.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Alignment/Matrix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio/Alignment +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Sequence.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Alignment/Pairwise.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio/Alignment -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/System/Environment.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/System -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/String.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Introspection.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Vector.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Pair.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Doublets.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/ReversibleMarkov.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Nucleotides.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Frequency.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Codons.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/SModel/Likelihood.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Bio/Alignment/Matrix.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio/Alignment +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Real.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Base.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/ST.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/IO.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Real.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Enum.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Num.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/ST.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Compiler/Enum.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Introspection.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Pair.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/String.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/Foreign/Vector.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/BAliPhy/ATModel.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/haskell/BAliPhy/ATModel/DataPartition.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy/ATModel Installing subdir /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fe.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/multiMixtureModel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/scaled_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/k80.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/branch_site.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m2a_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x3.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/multi_rate.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f1x4.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_laplace.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/shifted_exponential.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/laplace.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/symmetric_dirichlet_on.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/bernoulli.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/uniform.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/geometric.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/exponential.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/uniform_int.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/shifted_gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/symmetric_dirichlet.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/cauchy.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/poisson.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/binomial.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/beta.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/iid.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/empirical.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rs05.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mut_sel_aa.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gy94_ext.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m1a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/hky85.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m7.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/hky85_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f1x4.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gy94.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f3x4.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/k80.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gtr.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/wag_freq.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/lg08_freq.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fMutSel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/density.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2x2.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/markov_modulate_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f61.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x3.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rs07.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mut_sel_aa.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/tn93.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gtr_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/multiMixtureModel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rna_16a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/inv.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fMutSel0.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mut_sel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/get_q.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94_ext.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m3.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8a_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/pam.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m3_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/lg08.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/empirical.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gtr_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/jtt.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/wag.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/lg08_freq.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fMutSel0.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/dNdS.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x3_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/tn93_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2x2.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/parameter_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gtr.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/jc69.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gwF.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x3x3.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/tn93.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m3_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m7.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f61.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mut_sel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94k.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/wag.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x2_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f81.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/hky85.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fMutSel.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/scaled_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m2a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/f3x4.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/pam.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rs07.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m1a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rna_16a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/tn93_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gy94_ext.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/sample.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/markov_modulate_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gy94.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94k.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m2a.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/jtt.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/jc69.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/fe.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m3.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/x3_sym.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m8a_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/mg94_ext.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/branch_site.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/m2a_test.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/dNdS.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/gwF.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/rs07_relaxed_rates.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/wag_freq.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/equ.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Frequencies/uniform.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Frequencies -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/wang07.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/ts98.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/multi_rate.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/parameter_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/huelsenbeck02.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/galtier01.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Rates/log_normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Rates/free.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/ts98.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Covarion/wang07.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Frequencies/uniform.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Frequencies Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Rates/gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Rates/free.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/models/Rates/log_normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/intToDouble.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/take.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/getAminoAcids.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/codons.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/zip.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/quantile.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/getNucleotides.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/add.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sqrt.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/getAminoAcids.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/exp.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/mul.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/length.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sub.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/getNucleotides.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/cos.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/letters.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/letter_pairs.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/aa.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/dna.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/uniform_discretize.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/log.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sin.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/aa.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/map.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/tan.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/zipWith.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/letters.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/exp.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/div.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/tan.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/num_branches.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/rna.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/zip.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/letter_pairs.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/map.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/standard_code.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/unit_mixture.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/mul.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sqrt.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/replicate.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/take.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/length.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/intToDouble.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sub.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/rna.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/sin.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/uniform_discretize.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/constructors/Nil.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/functions/constructors/Cons.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/laplace.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/exponential.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/bernoulli.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/shifted_gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/normal.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/symmetric_dirichlet_on.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/uniform.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/cauchy.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/poisson.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/geometric.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/shifted_exponential.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/beta.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/log_laplace.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/gamma.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/binomial.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/symmetric_dirichlet.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/iid.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/bindings/distributions/uniform_int.json to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing subdir /build/reproducible-path/bali-phy-3.6.0+dfsg/help to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/parameters.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/Doublets.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/Codons.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/Triplets.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/genetic-code.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/Triplets.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/alphabets/Codons.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/parameters/priors.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/parameters -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/scale.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/tree.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/align.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/name.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/package-path.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/print.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/pre-burnin.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/seed.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/unalign.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/version.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/disable.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/smodel.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/enable.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/Rao-Blackwellize.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/alphabet.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/iterations.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/model.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/smodel.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/branch-lengths.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/subsample.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/align.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/scale.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/imodel.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/set.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/verbose.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/iterations.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/print.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/tree.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/link.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/seed.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/test.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/config.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/alphabet.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/verbose.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/version.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/pre-burnin.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/unalign.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/help/commands/subsample.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing subdir /build/reproducible-path/bali-phy-3.6.0+dfsg/examples to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo3.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Airline.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo4.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo1.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo5.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo6.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo2.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Coalmine.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models -Warning: trying to copy a symlink that points to a file. This will copy the file, -but this will be changed in a future version of Meson to copy the symlink as is. Please update your -build definitions so that it will not break when the change happens. -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Enolase/enolase-38-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Enolase/enolase-38.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/ITS2-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/5.8S.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/ITS1-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/some.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/globins.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/10-globins-Lunter.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/bglobin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/10-globins.xml to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/many-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/many.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/HIVSIV.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/pol-clustal.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env-clustal.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/pol.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env-clustal-codons.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/pol-common.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env-clustal.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env-common.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/env-clustal-codons.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/HIV/chain-2005/pol-clustal.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/NOTES.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/keep.pl to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.rna.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.gb to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc12.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/orig.nex to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/orig.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/README.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/config.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/config2.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/cleaned.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/Src_homology_2_domains.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/papain.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/subtilase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/xylose_isomerase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/Starch_binding_domain.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/annexin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/parvalbumin-like.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/rr_receiver.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/legume_lectin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/lectin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/lysozyme.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/haloperoxidase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Enolase/enolase-38.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Enolase/enolase-38-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/48b.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/48b-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/25-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/12d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/48b-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/orig.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/config2.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/orig.nex to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/config.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/README.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ferns/cleaned.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisF.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/EF-Tu/48b-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/trp-tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/tyr.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/trp-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/trp.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/lysozyme.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/parvalbumin-like.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/Src_homology_2_domains.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/lectin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/haloperoxidase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/Starch_binding_domain.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/legume_lectin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/xylose_isomerase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/rr_receiver.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/annexin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/papain.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Miklos-2008/subtilase.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/NOTES.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.rna.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc12.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/keep.pl to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/lrRNA/mollusc.gb to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.trees to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/trp-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/trp-tyr/trp-tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisA.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Duplications/hisA-hisF/hisF.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/paper.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/table1.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/additional.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.aln to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/other.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-WPD.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-tcoffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-tcoffee.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-WPD.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-fsa.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.command to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-c10.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-consensus.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.trees to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-fsa.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-c10.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-WPD.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-poy.command to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-fsa.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-tcoffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/table1.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.aln to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/paper.txt to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-clustalw.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/other.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/additional.accessions to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/37-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/30-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/microbotryum/76-muscle.ph to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/10-globins.xml to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/many.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/bglobin.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/globins.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/many-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/10-globins-Lunter.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/some.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Globins/few-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/48-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/5S-rRNA/25-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4.MAP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4.MAP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-muscle.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-fsa.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-mafft.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/5.8S.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/ITS1-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/sequences/ITS/ITS2-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Airline.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Coalmine.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo6.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo2.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo1.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo4.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo5.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. +Installing /build/reproducible-path/bali-phy-3.6.0+dfsg/examples/models/Demo3.hs to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Warning: trying to copy a symlink that points to a file. This will copy the file, +but this will be changed in a future version of Meson to copy the symlink as is. Please update your +build definitions so that it will not break when the change happens. Installing src/bali-phy/bali-phy to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/bin Installing src/builtins/Array.so to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy Installing src/builtins/Data.so to /build/reproducible-path/bali-phy-3.6.0+dfsg/debian/bali-phy/usr/lib/bali-phy @@ -2026,52 +2061,52 @@ 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/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 _ZN8reg_heap24set_reg_value_in_contextEiO7closurei: 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 _ZN10expressionC1ERK14expression_refRKSt6vectorIS0_SaIS0_EE: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Prelude.so contains an unresolvable reference to symbol _ZTI11constructor: 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/Bits.so contains an unresolvable reference to symbol _ZN14expression_refC1ERKb: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Bits.so contains an unresolvable reference to symbol _ZNK6Object5printB5cxx11Ev: 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 _ZNK6Object5printB5cxx11Ev: it's probably a plugin +dpkg-shlibdeps: warning: debian/bali-phy/usr/lib/bali-phy/Range.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: 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/Alignment.so contains an unresolvable reference to symbol _ZNK20pairwise_alignment_t7length1Ev: 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/SMC.so contains an unresolvable reference to symbol _Z16show_stack_traceB5cxx11i: 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/Text.so contains an unresolvable reference to symbol _ZTV6Object: 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/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/Modifiables.so contains an unresolvable reference to symbol _ZNK8reg_heap12call_for_regEi: 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/Pair.so contains an unresolvable reference to symbol _ZTV6Object: 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/Alphabet.so contains an unresolvable reference to symbol _ZN8TripletsC1ERK11Nucleotides: 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/Data.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/PopGen.so contains an unresolvable reference to symbol _ZN16checked_ifstreamC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_: 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/Vector.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: 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/SModel.so contains an unresolvable reference to symbol _ZN12substitution24peel_internal_branch_SEVEPK23Likelihood_Cache_BranchS2_RK7EVectorRKN8bali_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/Real.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/Array.so contains an unresolvable reference to symbol _ZN14expression_refC1ERK9index_var: 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/Char.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: it's probably a plugin +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/SModel.so contains an unresolvable reference to symbol _ZN12substitution20peel_leaf_branch_SEVERK7EVectorRK8alphabetS2_RKN5boost14dynamic_bitsetImSaImEEES2_: 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/PopGen.so contains an unresolvable reference to symbol _ZN16checked_ifstreamC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_: 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/Foreign.so contains an unresolvable reference to symbol _Z12is_bool_trueRK14expression_ref: 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/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/Range.so contains an unresolvable reference to symbol _ZNK14expression_ref5printB5cxx11Ev: 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/Data.so contains an unresolvable reference to symbol _ZN13OperationArgs8evaluateEi: 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/SMC.so contains an unresolvable reference to symbol _ZNK7EVectorcvSt6vectorIdSaIdEEEv: 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/Alphabet.so contains an unresolvable reference to symbol _ZTI8Doublets: 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/Modifiables.so contains an unresolvable reference to symbol _ZplRK14expression_refS1_: 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/Distribution.so contains an unresolvable reference to symbol _Z9bernoullid: 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/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/Text.so contains an unresolvable reference to symbol _ZTV6Object: 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/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) dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'bali-phy' in '../bali-phy_3.6.0+dfsg-1_i386.deb'. dpkg-deb: building package 'bali-phy-dbgsym' in '../bali-phy-dbgsym_3.6.0+dfsg-1_i386.deb'. +dpkg-deb: building package 'bali-phy' in '../bali-phy_3.6.0+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bali-phy_3.6.0+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2079,12 +2114,14 @@ 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/85939/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/85939/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/30002 and its subdirectories -I: Current time: Tue Jan 9 10:41:18 -12 2024 -I: pbuilder-time-stamp: 1704840078 +I: removing directory /srv/workspace/pbuilder/85939 and its subdirectories +I: Current time: Tue Feb 11 19:10:48 +14 2025 +I: pbuilder-time-stamp: 1739250648