Diff of the two buildlogs: -- --- b1/build.log 2025-03-14 18:42:44.602816333 +0000 +++ b2/build.log 2025-03-14 18:48:44.082612383 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 14 06:05:47 -12 2025 -I: pbuilder-time-stamp: 1741975547 +I: Current time: Fri Apr 17 15:05:46 +14 2026 +I: pbuilder-time-stamp: 1776387946 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1833660/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 17 01:05 /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/1247855/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1729d4b3fb1f429a843b9c710dc22bc0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1833660' - PS1='# ' - PS2='> ' + INVOCATION_ID=d5115e90653e423fbce89f5240c305a8 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1247855 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.uOpYys8S/pbuilderrc_qgQQ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uOpYys8S/b1 --logfile b1/build.log bali-phy_3.6.1+dfsg-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.uOpYys8S/pbuilderrc_SkuU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uOpYys8S/b2 --logfile b2/build.log bali-phy_3.6.1+dfsg-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1833660/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -286,7 +318,7 @@ Get: 154 http://deb.debian.org/debian trixie/main amd64 nlohmann-json3-dev all 3.11.3-2 [262 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] -Fetched 90.5 MB in 2s (47.4 MB/s) +Fetched 90.5 MB in 4s (22.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19803 files and directories currently installed.) @@ -804,8 +836,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 14 18:08:23 UTC 2025. -Universal Time is now: Fri Mar 14 18:08:23 UTC 2025. +Local time is now: Fri Apr 17 01:06:21 UTC 2026. +Universal Time is now: Fri Apr 17 01:06:21 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.1+b1) ... @@ -940,7 +972,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bali-phy-3.6.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bali-phy_3.6.1+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bali-phy-3.6.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bali-phy_3.6.1+dfsg-3_source.changes dpkg-buildpackage: info: source package bali-phy dpkg-buildpackage: info: source version 3.6.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1046,120 +1082,133 @@ Found ninja-1.12.1 at /usr/bin/ninja make[1]: Leaving directory '/build/reproducible-path/bali-phy-3.6.1+dfsg' dh_auto_build -O--buildsystem=meson - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j20 -v + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j42 -v [1/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/log-level.cc.o -MF src/util/libutil.a.p/log-level.cc.o.d -o src/util/libutil.a.p/log-level.cc.o -c ../src/util/log-level.cc [2/297] /usr/bin/meson --internal vcstagger ../src/git-version.h.in src/git-version.h 3.6.1 /build/reproducible-path/bali-phy-3.6.1+dfsg/src @git_message@ '(.*)' git log -n1 '--date=format:%b %d %Y %k:%M:%S' '--pretty=format:[%D commit %h] (%cd)' [3/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc -[4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc -[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc -[6/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc +[4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc +[5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc +[6/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc [7/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_sanitize.cc.o -MF src/util/libutil.a.p/string_sanitize.cc.o.d -o src/util/libutil.a.p/string_sanitize.cc.o -c ../src/util/string/sanitize.cc [8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc [9/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 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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 [14/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_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 [15/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-paths.cc.o -MF src/util/libutil.a.p/file-paths.cc.o.d -o src/util/libutil.a.p/file-paths.cc.o -c ../src/util/file-paths.cc -[16/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-readers.cc.o -MF 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-Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_optimize.cc.o -MF src/libcommon.a.p/tools_optimize.cc.o.d -o src/libcommon.a.p/tools_optimize.cc.o -c ../src/tools/optimize.cc +[22/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/object.cc.o -MF src/computation/libcomputation.a.p/object.cc.o.d -o src/computation/libcomputation.a.p/object.cc.o -c ../src/computation/object.cc +[23/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_parsimony.cc.o -MF src/libcommon.a.p/tools_parsimony.cc.o.d -o src/libcommon.a.p/tools_parsimony.cc.o -c ../src/tools/parsimony.cc +[24/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/io.cc.o -MF src/util/libutil.a.p/io.cc.o.d -o src/util/libutil.a.p/io.cc.o -c ../src/util/io.cc ../src/util/io.cc: In function ‘std::vector > load_lines(std::istream&, int, int, int)’: ../src/util/io.cc:113:21: warning: redundant move in return statement [-Wredundant-move] 113 | return std::move(lines); | ~~~~~~~~~^~~~~~~ ../src/util/io.cc:113:21: note: remove ‘std::move’ call -[19/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-random.cc.o -MF src/libcommon.a.p/alignment_alignment-random.cc.o.d -o src/libcommon.a.p/alignment_alignment-random.cc.o -c ../src/alignment/alignment-random.cc -[20/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/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 -[21/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_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 -[22/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/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 -[23/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_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 -[24/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree-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/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/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 -[26/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_statistics.cc.o -MF src/libcommon.a.p/tools_statistics.cc.o.d -o src/libcommon.a.p/tools_statistics.cc.o -c ../src/tools/statistics.cc -[27/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_sequencetree.cc.o -MF src/libcommon.a.p/tree_sequencetree.cc.o.d -o src/libcommon.a.p/tree_sequencetree.cc.o -c ../src/tree/sequencetree.cc -[28/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc -[29/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/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 -[30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. 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-Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_stats-table.cc.o -MF src/libcommon.a.p/tools_stats-table.cc.o.d -o src/libcommon.a.p/tools_stats-table.cc.o -c ../src/tools/stats-table.cc +[95/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-cube.cc.o -MF src/libbaliphy.a.p/dp_dp-cube.cc.o.d -o src/libbaliphy.a.p/dp_dp-cube.cc.o -c ../src/dp/dp-cube.cc +[96/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 +[97/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_exponential.cc.o -MF src/libbaliphy.a.p/math_exponential.cc.o.d -o src/libbaliphy.a.p/math_exponential.cc.o -c ../src/math/exponential.cc +[98/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-matrix.cc.o -MF src/libbaliphy.a.p/dp_dp-matrix.cc.o.d -o src/libbaliphy.a.p/dp_dp-matrix.cc.o -c ../src/dp/dp-matrix.cc +[99/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_hmm.cc.o -MF src/libbaliphy.a.p/dp_hmm.cc.o.d -o src/libbaliphy.a.p/dp_hmm.cc.o -c ../src/dp/hmm.cc +[100/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/program.cc.o -MF src/computation/libcomputation.a.p/program.cc.o.d -o src/computation/libcomputation.a.p/program.cc.o -c ../src/computation/program.cc ../src/computation/program.cc: In member function ‘void Program::check_dependencies()’: ../src/computation/program.cc:155:17: warning: unused variable ‘index’ [-Wunused-variable] 155 | int index = find_module(name); | ^~~~~ -[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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_args.cc.o -MF src/computation/libcomputation.a.p/machine_args.cc.o.d -o src/computation/libcomputation.a.p/machine_args.cc.o -c ../src/computation/machine/args.cc -[82/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_kind.cc.o -MF src/computation/libcomputation.a.p/expression_kind.cc.o.d -o src/computation/libcomputation.a.p/expression_kind.cc.o -c ../src/computation/expression/kind.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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_tokens.cc.o -MF src/computation/libcomputation.a.p/machine_tokens.cc.o.d -o src/computation/libcomputation.a.p/machine_tokens.cc.o -c ../src/computation/machine/tokens.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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_expression_ref.cc.o -MF src/computation/libcomputation.a.p/expression_expression_ref.cc.o.d -o src/computation/libcomputation.a.p/expression_expression_ref.cc.o -c ../src/computation/expression/expression_ref.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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_sums.cc.o -MF src/computation/libcomputation.a.p/machine_sums.cc.o.d -o src/computation/libcomputation.a.p/machine_sums.cc.o -c ../src/computation/machine/sums.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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/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 -[87/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 -[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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch 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-fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_free-vars.cc.o -MF src/computation/libcomputation.a.p/optimization_free-vars.cc.o.d -o src/computation/libcomputation.a.p/optimization_free-vars.cc.o -c ../src/computation/optimization/free-vars.cc +[102/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 +[103/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc +[104/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_5way.cc.o -MF src/libbaliphy.a.p/dp_5way.cc.o.d -o src/libbaliphy.a.p/dp_5way.cc.o -c ../src/dp/5way.cc +[105/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_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 +[106/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc +[107/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_float-out.cc.o -MF src/computation/libcomputation.a.p/optimization_float-out.cc.o.d -o src/computation/libcomputation.a.p/optimization_float-out.cc.o -c ../src/computation/optimization/float-out.cc +[108/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_2way.cc.o -MF src/libbaliphy.a.p/dp_2way.cc.o.d -o src/libbaliphy.a.p/dp_2way.cc.o -c ../src/dp/2way.cc +[109/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_show_graph.cc.o -MF src/computation/libcomputation.a.p/machine_show_graph.cc.o.d -o src/computation/libcomputation.a.p/machine_show_graph.cc.o -c ../src/computation/machine/show_graph.cc +[110/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_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 +[111/297] rm -f src/util/libutil.a && gcc-ar csrDT src/util/libutil.a src/util/libutil.a.p/string_pred.cc.o src/util/libutil.a.p/string_sanitize.cc.o src/util/libutil.a.p/string_strip.cc.o src/util/libutil.a.p/string_split.cc.o src/util/libutil.a.p/log-level.cc.o src/util/libutil.a.p/io.cc.o src/util/libutil.a.p/graph.cc.o src/util/libutil.a.p/range.cc.o src/util/libutil.a.p/demangle.cc.o src/util/libutil.a.p/mapping.cc.o src/util/libutil.a.p/cmdline.cc.o src/util/libutil.a.p/rng.cc.o src/util/libutil.a.p/permute.cc.o src/util/libutil.a.p/file-paths.cc.o src/util/libutil.a.p/ptree.cc.o src/util/libutil.a.p/text.cc.o src/util/libutil.a.p/myexception.cc.o src/util/libutil.a.p/time.cc.o src/util/libutil.a.p/file-readers.cc.o +[112/297] rm -f src/libcommon.a && gcc-ar csrDT src/libcommon.a src/libcommon.a.p/tree_newick-tokenizer.cc.o src/libcommon.a.p/tree_sequencetree.cc.o src/libcommon.a.p/tree_tree.cc.o src/libcommon.a.p/tree_tree-util.cc.o src/libcommon.a.p/tree_randomtree.cc.o src/libcommon.a.p/tree-align_n_indels.cc.o src/libcommon.a.p/sequence_alphabet.cc.o src/libcommon.a.p/sequence_sequence.cc.o src/libcommon.a.p/sequence_sequence-format.cc.o src/libcommon.a.p/tools_read-trees.cc.o src/libcommon.a.p/alignment_alignment-util.cc.o src/libcommon.a.p/alignment_load.cc.o src/libcommon.a.p/alignment_alignment.cc.o src/libcommon.a.p/alignment_alignment-random.cc.o src/libcommon.a.p/alignment_index-matrix.cc.o src/libcommon.a.p/tree-align_link.cc.o src/libcommon.a.p/models_path.cc.o src/libcommon.a.p/tools_statistics.cc.o src/libcommon.a.p/tools_partition.cc.o src/libcommon.a.p/tools_tree-dist.cc.o src/libcommon.a.p/tools_parsimony.cc.o src/libcommon.a.p/tools_mctree.cc.o src/libcommon.a.p/tools_stats-table.cc.o src/libcommon.a.p/tools_findroot.cc.o src/libcommon.a.p/tools_optimize.cc.o src/libcommon.a.p/tools_distance-report.cc.o src/libcommon.a.p/tools_inverse.cc.o src/libcommon.a.p/tools_joint-A-T.cc.o src/libcommon.a.p/tools_distance-methods.cc.o src/libcommon.a.p/tools_consensus-tree.cc.o +[113/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_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 +[114/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[115/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc +[116/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c ../src/computation/optimization/simplifier.cc +[117/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_free-vars.cc.o -MF src/computation/libcomputation.a.p/optimization_free-vars.cc.o.d -o src/computation/libcomputation.a.p/optimization_free-vars.cc.o -c ../src/computation/optimization/free-vars.cc In file included from ../external/immer/immer/detail/hamts/champ.hpp:12, from ../external/immer/immer/set.hpp:12, from ../src/computation/optimization/free-vars.H:6, @@ -2055,20 +2104,29 @@ ../external/immer/immer/heap/cpp_heap.hpp:27:30: note: object of size 24 allocated by ‘operator new’ 27 | return ::operator new(size); | ~~~~~~~~~~~~~~^~~~~~ -[105/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc -[106/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc -[107/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_float-out.cc.o -MF src/computation/libcomputation.a.p/optimization_float-out.cc.o.d -o src/computation/libcomputation.a.p/optimization_float-out.cc.o -c ../src/computation/optimization/float-out.cc 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-I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/module.cc.o -MF src/computation/libcomputation.a.p/module.cc.o.d -o src/computation/libcomputation.a.p/module.cc.o -c 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-I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc -[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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c 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-DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[120/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -MF src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -c ../src/mcmc/sample-branch-lengths.cc +[121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_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 +[122/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/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 +[123/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc +[124/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/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 +[125/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc +[126/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_proposals.cc.o -MF src/libbaliphy.a.p/mcmc_proposals.cc.o.d -o src/libbaliphy.a.p/mcmc_proposals.cc.o -c ../src/mcmc/proposals.cc +[127/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-cube.cc.o -MF src/libbaliphy.a.p/mcmc_sample-cube.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-cube.cc.o -c ../src/mcmc/sample-cube.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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_occurrence.cc.o -MF src/computation/libcomputation.a.p/optimization_occurrence.cc.o.d -o src/computation/libcomputation.a.p/optimization_occurrence.cc.o -c ../src/computation/optimization/occurrence.cc +[129/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc +../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 67 | s<<__DATE__<<" "<<__TIME__; + | ^~~~~~~~ +../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 67 | s<<__DATE__<<" "<<__TIME__; + | ^~~~~~~~ +[130/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[131/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[132/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc +[133/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc +[134/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_set-levels.cc.o -MF src/computation/libcomputation.a.p/optimization_set-levels.cc.o.d -o src/computation/libcomputation.a.p/optimization_set-levels.cc.o -c ../src/computation/optimization/set-levels.cc In file included from ../external/immer/immer/detail/hamts/champ.hpp:12, from ../external/immer/immer/set.hpp:12, from ../src/computation/optimization/free-vars.H:6, @@ -2477,65 +2535,39 @@ ../external/immer/immer/heap/cpp_heap.hpp:27:30: note: object of size 24 allocated by ‘operator new’ 27 | return ::operator new(size); | ~~~~~~~~~~~~~~^~~~~~ -[119/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc -[120/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_proposals.cc.o -MF src/libbaliphy.a.p/mcmc_proposals.cc.o.d -o src/libbaliphy.a.p/mcmc_proposals.cc.o -c ../src/mcmc/proposals.cc -[121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc -[122/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_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 -[123/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[124/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[125/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-cube.cc.o -MF src/libbaliphy.a.p/mcmc_sample-cube.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-cube.cc.o -c ../src/mcmc/sample-cube.cc -[126/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/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 -[127/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[128/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_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 -[129/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[130/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_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 -[131/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[132/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[133/297] rm -f src/util/libutil.a && gcc-ar csrDT src/util/libutil.a src/util/libutil.a.p/string_pred.cc.o src/util/libutil.a.p/string_sanitize.cc.o src/util/libutil.a.p/string_strip.cc.o src/util/libutil.a.p/string_split.cc.o src/util/libutil.a.p/log-level.cc.o src/util/libutil.a.p/io.cc.o src/util/libutil.a.p/graph.cc.o src/util/libutil.a.p/range.cc.o src/util/libutil.a.p/demangle.cc.o src/util/libutil.a.p/mapping.cc.o src/util/libutil.a.p/cmdline.cc.o src/util/libutil.a.p/rng.cc.o src/util/libutil.a.p/permute.cc.o src/util/libutil.a.p/file-paths.cc.o src/util/libutil.a.p/ptree.cc.o src/util/libutil.a.p/text.cc.o src/util/libutil.a.p/myexception.cc.o src/util/libutil.a.p/time.cc.o src/util/libutil.a.p/file-readers.cc.o -[134/297] rm -f src/libcommon.a && gcc-ar csrDT src/libcommon.a src/libcommon.a.p/tree_newick-tokenizer.cc.o src/libcommon.a.p/tree_sequencetree.cc.o src/libcommon.a.p/tree_tree.cc.o src/libcommon.a.p/tree_tree-util.cc.o src/libcommon.a.p/tree_randomtree.cc.o src/libcommon.a.p/tree-align_n_indels.cc.o src/libcommon.a.p/sequence_alphabet.cc.o src/libcommon.a.p/sequence_sequence.cc.o src/libcommon.a.p/sequence_sequence-format.cc.o src/libcommon.a.p/tools_read-trees.cc.o src/libcommon.a.p/alignment_alignment-util.cc.o src/libcommon.a.p/alignment_load.cc.o src/libcommon.a.p/alignment_alignment.cc.o src/libcommon.a.p/alignment_alignment-random.cc.o src/libcommon.a.p/alignment_index-matrix.cc.o src/libcommon.a.p/tree-align_link.cc.o src/libcommon.a.p/models_path.cc.o src/libcommon.a.p/tools_statistics.cc.o src/libcommon.a.p/tools_partition.cc.o src/libcommon.a.p/tools_tree-dist.cc.o src/libcommon.a.p/tools_parsimony.cc.o src/libcommon.a.p/tools_mctree.cc.o src/libcommon.a.p/tools_stats-table.cc.o src/libcommon.a.p/tools_findroot.cc.o src/libcommon.a.p/tools_optimize.cc.o src/libcommon.a.p/tools_distance-report.cc.o src/libcommon.a.p/tools_inverse.cc.o src/libcommon.a.p/tools_joint-A-T.cc.o src/libcommon.a.p/tools_distance-methods.cc.o src/libcommon.a.p/tools_consensus-tree.cc.o -[135/297] rm -f src/computation/libcomputation.a && gcc-ar csrDT src/computation/libcomputation.a src/computation/libcomputation.a.p/object.cc.o src/computation/libcomputation.a.p/closure.cc.o src/computation/libcomputation.a.p/program.cc.o src/computation/libcomputation.a.p/preprocess.cc.o src/computation/libcomputation.a.p/module.cc.o src/computation/libcomputation.a.p/loader.cc.o src/computation/libcomputation.a.p/context.cc.o src/computation/libcomputation.a.p/operations.cc.o src/computation/libcomputation.a.p/param.cc.o src/computation/libcomputation.a.p/parser_desugar.cc.o src/computation/libcomputation.a.p/parser_desugar-case.cc.o src/computation/libcomputation.a.p/parser_rename.cc.o src/computation/libcomputation.a.p/parser_driver.cc.o src/computation/libcomputation.a.p/parser_lexer.cc.o src/computation/libcomputation.a.p/parser_parser.cc.o src/computation/libcomputation.a.p/expression_operator.cc.o src/computation/libcomputation.a.p/expression_expression.cc.o src/computation/libcomputation.a.p/expression_constructor.cc.o src/computation/libcomputation.a.p/expression_expression_ref.cc.o src/computation/libcomputation.a.p/expression_AST_node.cc.o src/computation/libcomputation.a.p/expression_apply.cc.o src/computation/libcomputation.a.p/expression_substitute.cc.o src/computation/libcomputation.a.p/expression_indexify.cc.o src/computation/libcomputation.a.p/expression_let.cc.o src/computation/libcomputation.a.p/expression_case.cc.o src/computation/libcomputation.a.p/expression_trim.cc.o src/computation/libcomputation.a.p/expression_tuple.cc.o src/computation/libcomputation.a.p/expression_list.cc.o src/computation/libcomputation.a.p/expression_var.cc.o src/computation/libcomputation.a.p/expression_lambda.cc.o src/computation/libcomputation.a.p/expression_random_variable.cc.o src/computation/libcomputation.a.p/expression_modifiable.cc.o src/computation/libcomputation.a.p/expression_reg_var.cc.o src/computation/libcomputation.a.p/expression_bool.cc.o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o src/computation/libcomputation.a.p/expression_maybe.cc.o src/computation/libcomputation.a.p/expression_do_block.cc.o src/computation/libcomputation.a.p/machine_args.cc.o src/computation/libcomputation.a.p/machine_tokens.cc.o src/computation/libcomputation.a.p/machine_graph_register.cc.o src/computation/libcomputation.a.p/machine_show_graph.cc.o src/computation/libcomputation.a.p/machine_evaluate.cc.o src/computation/libcomputation.a.p/machine_sums.cc.o src/computation/libcomputation.a.p/machine_gc.cc.o src/computation/libcomputation.a.p/machine_reroot.cc.o src/computation/libcomputation.a.p/machine_effects.cc.o src/computation/libcomputation.a.p/expression_kind.cc.o src/computation/libcomputation.a.p/optimization_free-vars.cc.o src/computation/libcomputation.a.p/optimization_set-levels.cc.o src/computation/libcomputation.a.p/optimization_float-out.cc.o src/computation/libcomputation.a.p/optimization_occurrence.cc.o src/computation/libcomputation.a.p/optimization_inliner.cc.o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -[136/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_n_indels2.cc.o -MF src/libbaliphy.a.p/tree-align_n_indels2.cc.o.d -o src/libbaliphy.a.p/tree-align_n_indels2.cc.o -c ../src/tree-align/n_indels2.cc -[137/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[138/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/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 -[139/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_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 -[140/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc -../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 67 | s<<__DATE__<<" "<<__TIME__; - | ^~~~~~~~ -../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 67 | s<<__DATE__<<" "<<__TIME__; - | ^~~~~~~~ -[141/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc -[142/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 -[143/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc -[144/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_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 +[135/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[136/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/module.cc.o -MF src/computation/libcomputation.a.p/module.cc.o.d -o src/computation/libcomputation.a.p/module.cc.o -c ../src/computation/module.cc +[137/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc +[138/297] rm -f src/computation/libcomputation.a && gcc-ar csrDT src/computation/libcomputation.a src/computation/libcomputation.a.p/object.cc.o src/computation/libcomputation.a.p/closure.cc.o src/computation/libcomputation.a.p/program.cc.o src/computation/libcomputation.a.p/preprocess.cc.o src/computation/libcomputation.a.p/module.cc.o src/computation/libcomputation.a.p/loader.cc.o src/computation/libcomputation.a.p/context.cc.o src/computation/libcomputation.a.p/operations.cc.o src/computation/libcomputation.a.p/param.cc.o src/computation/libcomputation.a.p/parser_desugar.cc.o src/computation/libcomputation.a.p/parser_desugar-case.cc.o src/computation/libcomputation.a.p/parser_rename.cc.o src/computation/libcomputation.a.p/parser_driver.cc.o src/computation/libcomputation.a.p/parser_lexer.cc.o src/computation/libcomputation.a.p/parser_parser.cc.o src/computation/libcomputation.a.p/expression_operator.cc.o src/computation/libcomputation.a.p/expression_expression.cc.o src/computation/libcomputation.a.p/expression_constructor.cc.o src/computation/libcomputation.a.p/expression_expression_ref.cc.o src/computation/libcomputation.a.p/expression_AST_node.cc.o src/computation/libcomputation.a.p/expression_apply.cc.o src/computation/libcomputation.a.p/expression_substitute.cc.o src/computation/libcomputation.a.p/expression_indexify.cc.o src/computation/libcomputation.a.p/expression_let.cc.o src/computation/libcomputation.a.p/expression_case.cc.o src/computation/libcomputation.a.p/expression_trim.cc.o src/computation/libcomputation.a.p/expression_tuple.cc.o src/computation/libcomputation.a.p/expression_list.cc.o src/computation/libcomputation.a.p/expression_var.cc.o src/computation/libcomputation.a.p/expression_lambda.cc.o src/computation/libcomputation.a.p/expression_random_variable.cc.o src/computation/libcomputation.a.p/expression_modifiable.cc.o src/computation/libcomputation.a.p/expression_reg_var.cc.o src/computation/libcomputation.a.p/expression_bool.cc.o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o src/computation/libcomputation.a.p/expression_maybe.cc.o src/computation/libcomputation.a.p/expression_do_block.cc.o src/computation/libcomputation.a.p/machine_args.cc.o src/computation/libcomputation.a.p/machine_tokens.cc.o src/computation/libcomputation.a.p/machine_graph_register.cc.o src/computation/libcomputation.a.p/machine_show_graph.cc.o src/computation/libcomputation.a.p/machine_evaluate.cc.o src/computation/libcomputation.a.p/machine_sums.cc.o src/computation/libcomputation.a.p/machine_gc.cc.o src/computation/libcomputation.a.p/machine_reroot.cc.o src/computation/libcomputation.a.p/machine_effects.cc.o src/computation/libcomputation.a.p/expression_kind.cc.o src/computation/libcomputation.a.p/optimization_free-vars.cc.o src/computation/libcomputation.a.p/optimization_set-levels.cc.o src/computation/libcomputation.a.p/optimization_float-out.cc.o src/computation/libcomputation.a.p/optimization_occurrence.cc.o src/computation/libcomputation.a.p/optimization_inliner.cc.o src/computation/libcomputation.a.p/optimization_simplifier.cc.o +[139/297] 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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros 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src/libbaliphy.a.p/models_parse.cc.o.d -o src/libbaliphy.a.p/models_parse.cc.o -c ../src/models/parse.cc [161/297] c++ -Isrc/builtins/Prelude.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Prelude.so.p/Prelude.cc.o -MF src/builtins/Prelude.so.p/Prelude.cc.o.d -o src/builtins/Prelude.so.p/Prelude.cc.o -c ../src/builtins/Prelude.cc -[162/297] c++ -Isrc/builtins/Alphabet.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc -[163/297] c++ -Isrc/builtins/Real.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc -[164/297] c++ -Isrc/builtins/Distribution.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Distribution.so.p/Distribution.cc.o -MF src/builtins/Distribution.so.p/Distribution.cc.o.d -o src/builtins/Distribution.so.p/Distribution.cc.o -c ../src/builtins/Distribution.cc -[165/297] c++ -Isrc/builtins/Vector.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc -[166/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc -../src/bali-phy/bali-phy.cc: In function ‘void report_mem()’: -../src/bali-phy/bali-phy.cc:122:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 122 | system(cmd.str().c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~ -[167/297] c++ -Isrc/builtins/Environment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc +[162/297] 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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/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 +[163/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_probability.cc.o -MF src/libbaliphy.a.p/probability_probability.cc.o.d -o src/libbaliphy.a.p/probability_probability.cc.o -c ../src/probability/probability.cc +[164/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_typecheck.cc.o -MF src/libbaliphy.a.p/models_typecheck.cc.o.d -o src/libbaliphy.a.p/models_typecheck.cc.o -c ../src/models/typecheck.cc +[165/297] c++ -Isrc/builtins/Alphabet.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc +[166/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_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 +[167/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_model.cc.o -MF src/libbaliphy.a.p/models_model.cc.o.d -o src/libbaliphy.a.p/models_model.cc.o -c ../src/models/model.cc [168/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/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 ../src/bali-phy/files.cc: In function ‘std::string run_name(const boost::program_options::variables_map&)’: ../src/bali-phy/files.cc:100:68: warning: ‘boost::filesystem::path boost::filesystem::path::leaf() const’ is deprecated: Use path::filename() instead [-Wdeprecated-declarations] @@ -2546,19 +2578,100 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -[169/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc -[170/297] c++ -Isrc/builtins/Text.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Text.so.p/Text.cc.o -MF src/builtins/Text.so.p/Text.cc.o.d -o src/builtins/Text.so.p/Text.cc.o -c ../src/builtins/Text.cc -[171/297] 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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/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 -[172/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra 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-ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_bootstrap.cc.o -MF src/trees-bootstrap.p/tools_bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_bootstrap.cc.o -c ../src/tools/bootstrap.cc +[174/297] c++ -Isrc/model_P.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 +[175/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_rules.cc.o -MF src/libbaliphy.a.p/models_rules.cc.o.d -o src/libbaliphy.a.p/models_rules.cc.o -c ../src/models/rules.cc +[176/297] c++ -o src/builtins/Data.so src/builtins/Data.so.p/Data.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[177/297] c++ -o src/builtins/Array.so src/builtins/Array.so.p/Array.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[178/297] c++ -o src/builtins/Prelude.so src/builtins/Prelude.so.p/Prelude.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[179/297] c++ -o src/builtins/Alphabet.so src/builtins/Alphabet.so.p/Alphabet.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[180/297] c++ -o src/builtins/Modifiables.so src/builtins/Modifiables.so.p/Modifiables.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[181/297] c++ -o src/builtins/Pair.so src/builtins/Pair.so.p/Pair.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[182/297] c++ -o src/builtins/Distribution.so src/builtins/Distribution.so.p/Distribution.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[183/297] c++ -o src/builtins/PopGen.so src/builtins/PopGen.so.p/PopGen.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[184/297] c++ -o src/builtins/Range.so src/builtins/Range.so.p/Range.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[185/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc +[186/297] c++ -o src/builtins/Vector.so src/builtins/Vector.so.p/Vector.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[187/297] c++ -o src/builtins/MCMC.so src/builtins/MCMC.so.p/MCMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[188/297] c++ -o src/builtins/Environment.so src/builtins/Environment.so.p/Environment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[189/297] c++ -o src/builtins/Real.so src/builtins/Real.so.p/Real.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[190/297] c++ -o src/builtins/Text.so src/builtins/Text.so.p/Text.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[191/297] c++ -o src/builtins/Bits.so src/builtins/Bits.so.p/Bits.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[192/297] c++ -o src/builtins/Foreign.so src/builtins/Foreign.so.p/Foreign.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[193/297] c++ -o src/builtins/Char.so src/builtins/Char.so.p/Char.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group +[194/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[195/297] /usr/bin/meson --internal exe --capture doc/bali-phy.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy.md +[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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/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] /usr/bin/meson --internal exe --capture doc/statreport.1 -- /usr/bin/pandoc -s -t man ../doc/man/statreport.md +[198/297] /usr/bin/meson --internal exe --capture doc/model_P.1 -- /usr/bin/pandoc -s -t man ../doc/man/model_P.md +[199/297] /usr/bin/meson --internal exe --capture doc/stats-select.1 -- /usr/bin/pandoc -s -t man ../doc/man/stats-select.md +[200/297] /usr/bin/meson --internal exe --capture doc/alignment-gild.1 -- /usr/bin/pandoc -s -t man ../doc/man/alignment-gild.md +[201/297] c++ -Isrc/builtins/Alignment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 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doc/summarize-ancestors.1 -- /usr/bin/pandoc -s -t man ../doc/man/summarize-ancestors.md +[228/297] /usr/bin/meson --internal exe --capture doc/bp-analyze.1 -- /usr/bin/pandoc -s -t man ../doc/man/bp-analyze.md +[229/297] /usr/bin/meson --internal exe --capture doc/bali-subsample.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-subsample.md +[230/297] c++ -Isrc/alignment-find.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[231/297] /usr/bin/meson --internal exe --capture doc/bali-phy-pkg.1 -- /usr/bin/pandoc -s -t man ../doc/man/bali-phy-pkg.md +[232/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[233/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ 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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 +[235/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc +../src/bali-phy/bali-phy.cc: In function ‘void report_mem()’: +../src/bali-phy/bali-phy.cc:122:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 122 | system(cmd.str().c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~ +[236/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 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-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[240/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed 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-funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 +[242/297] c++ -o src/pickout src/pickout.p/tools_pickout.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[243/297] c++ -Isrc/alignment-indices.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[244/297] c++ -Isrc/alignment-translate.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[245/297] c++ -o src/alignment-indices src/alignment-indices.p/tools_alignment-indices.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[246/297] c++ -o src/alignment-translate src/alignment-translate.p/tools_alignment-translate.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[247/297] c++ -Isrc/mctree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c ../src/tools/mctree-mean-lengths.cc +[248/297] c++ -Isrc/alignment-gild.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[249/297] c++ -Isrc/alignment-chop-internal.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[250/297] c++ -o src/mctree-mean-lengths src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[251/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc +[252/297] c++ -o src/alignment-chop-internal src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[253/297] c++ -Isrc/tree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-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 +[254/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[255/297] c++ -Isrc/cut-range.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 +[256/297] c++ -o src/tree-mean-lengths src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[257/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[258/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc ../src/bali-phy/loggers.cc: In function ‘owned_ptr > > construct_table_function(owned_ptr&, const std::vector >&)’: ../src/bali-phy/loggers.cc:247:29: warning: possibly dangling reference to a temporary [-Wdangling-reference] 247 | const alphabet& a = (*P)[i].get_alphabet(); @@ -2566,191 +2679,162 @@ ../src/bali-phy/loggers.cc:247:53: note: the temporary was destroyed at the end of the full expression ‘(& P.owned_ptr::operator*())->Parameters::operator[](i).mutable_data_partition::data_partition.data_partition::get_alphabet()’ 247 | const alphabet& a = (*P)[i].get_alphabet(); | ~~~~~~~~~~~~~~~~~~~~^~ -[182/297] c++ -Isrc/stats-select.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 -[183/297] c++ -Isrc/alignment-find.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[184/297] c++ -Isrc/alignment-gild.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[185/297] c++ -Isrc/alignment-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[186/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/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 -[187/297] c++ -Isrc/alignment-info.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[188/297] c++ -Isrc/alignment-translate.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[189/297] c++ -Isrc/alignment-chop-internal.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[190/297] c++ -Isrc/statreport.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 -[191/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc -[192/297] rm -f src/libbaliphy.a && gcc-ar csrDT src/libbaliphy.a src/libbaliphy.a.p/dp_dp_hmm.cc.o src/libbaliphy.a.p/dp_hmm.cc.o src/libbaliphy.a.p/dp_dp-engine.cc.o src/libbaliphy.a.p/dp_dp-array.cc.o src/libbaliphy.a.p/dp_dp-matrix.cc.o src/libbaliphy.a.p/dp_dp-cube.cc.o src/libbaliphy.a.p/dp_2way.cc.o src/libbaliphy.a.p/dp_3way.cc.o src/libbaliphy.a.p/dp_5way.cc.o src/libbaliphy.a.p/dp_alignment-sums.cc.o src/libbaliphy.a.p/mcmc_mcmc.cc.o src/libbaliphy.a.p/mcmc_proposals.cc.o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o src/libbaliphy.a.p/mcmc_AIS.cc.o src/libbaliphy.a.p/mcmc_logger.cc.o src/libbaliphy.a.p/mcmc_moves.cc.o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o src/libbaliphy.a.p/mcmc_sample-node.cc.o src/libbaliphy.a.p/mcmc_sample-cube.cc.o src/libbaliphy.a.p/mcmc_sample-tri.cc.o src/libbaliphy.a.p/mcmc_setup.cc.o src/libbaliphy.a.p/substitution_substitution.cc.o src/libbaliphy.a.p/substitution_parsimony.cc.o src/libbaliphy.a.p/math_exponential.cc.o src/libbaliphy.a.p/math_eigenvalue.cc.o src/libbaliphy.a.p/math_pow2.cc.o src/libbaliphy.a.p/models_parameters.cc.o src/libbaliphy.a.p/models_site-compression.cc.o src/libbaliphy.a.p/models_TreeInterface.cc.o src/libbaliphy.a.p/models_setup.cc.o src/libbaliphy.a.p/models_rules.cc.o src/libbaliphy.a.p/models_parse.cc.o src/libbaliphy.a.p/models_typecheck.cc.o src/libbaliphy.a.p/models_unification.cc.o src/libbaliphy.a.p/models_model.cc.o src/libbaliphy.a.p/tree-align_link2.cc.o src/libbaliphy.a.p/probability_choose.cc.o src/libbaliphy.a.p/probability_probability.cc.o src/libbaliphy.a.p/imodel_imodel.cc.o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o src/libbaliphy.a.p/alignment_alignment-util2.cc.o src/libbaliphy.a.p/tree-align_n_indels2.cc.o src/libbaliphy.a.p/tools_parsimony2.cc.o src/libbaliphy.a.p/version.cc.o -[193/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_bootstrap.cc.o -MF src/trees-bootstrap.p/tools_bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_bootstrap.cc.o -c ../src/tools/bootstrap.cc -[194/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_colors.cc.o -MF src/alignment-draw.p/tools_colors.cc.o.d -o src/alignment-draw.p/tools_colors.cc.o -c ../src/tools/colors.cc -[195/297] c++ -Isrc/alignment-indices.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 -[196/297] c++ -Isrc/tree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-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 -[197/297] c++ -Isrc/pickout.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 -[198/297] c++ -o src/builtins/Array.so src/builtins/Array.so.p/Array.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[199/297] c++ -o src/builtins/Data.so src/builtins/Data.so.p/Data.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[200/297] c++ -o src/builtins/Prelude.so src/builtins/Prelude.so.p/Prelude.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[201/297] c++ -o src/builtins/Alphabet.so src/builtins/Alphabet.so.p/Alphabet.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[202/297] c++ -o src/builtins/Pair.so src/builtins/Pair.so.p/Pair.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[203/297] c++ -o src/builtins/Modifiables.so src/builtins/Modifiables.so.p/Modifiables.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[204/297] c++ -o src/builtins/Alignment.so src/builtins/Alignment.so.p/Alignment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[205/297] c++ -Isrc/mctree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c ../src/tools/mctree-mean-lengths.cc -[206/297] c++ -o src/builtins/PopGen.so src/builtins/PopGen.so.p/PopGen.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[207/297] c++ -o src/builtins/Range.so src/builtins/Range.so.p/Range.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[208/297] c++ -o src/builtins/Distribution.so src/builtins/Distribution.so.p/Distribution.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[209/297] c++ -o src/builtins/SModel.so src/builtins/SModel.so.p/SModel.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[210/297] c++ -o src/builtins/MCMC.so src/builtins/MCMC.so.p/MCMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[211/297] c++ -o src/builtins/Vector.so src/builtins/Vector.so.p/Vector.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[212/297] c++ -o src/builtins/Environment.so src/builtins/Environment.so.p/Environment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[213/297] c++ -o src/builtins/Real.so src/builtins/Real.so.p/Real.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[214/297] c++ -o src/builtins/Bits.so src/builtins/Bits.so.p/Bits.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[215/297] c++ -o src/builtins/Text.so src/builtins/Text.so.p/Text.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[216/297] c++ -o src/builtins/Foreign.so src/builtins/Foreign.so.p/Foreign.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[217/297] c++ -o src/builtins/Char.so src/builtins/Char.so.p/Char.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[218/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[219/297] c++ -o src/bali-phy/bali-phy src/bali-phy/bali-phy.p/link-partitions.cc.o src/bali-phy/bali-phy.p/bali-phy.cc.o src/bali-phy/bali-phy.p/help.cc.o src/bali-phy/bali-phy.p/A-T-model.cc.o src/bali-phy/bali-phy.p/files.cc.o src/bali-phy/bali-phy.p/loggers.cc.o src/bali-phy/bali-phy.p/system.cc.o src/bali-phy/bali-phy.p/cmd_line.cc.o src/bali-phy/bali-phy.p/paths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-export-dynamic -Wl,--whole-archive -Wl,--start-group src/util/libutil.a src/libcommon.a src/computation/libcomputation.a src/libbaliphy.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -ldl -lm -Wl,--end-group -[220/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[221/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[222/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[223/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[224/297] c++ -Isrc/trees-to-SRQ.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas 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-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 -[270/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[271/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[272/297] c++ -Isrc/bali-subsample.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-subsample.p/tools_subsample.cc.o -MF src/bali-subsample.p/tools_subsample.cc.o.d -o src/bali-subsample.p/tools_subsample.cc.o -c ../src/tools/subsample.cc -[273/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[274/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-distances.p/tools_trees-distances.cc.o -MF src/trees-distances.p/tools_trees-distances.cc.o.d -o src/trees-distances.p/tools_trees-distances.cc.o -c ../src/tools/trees-distances.cc -[275/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[276/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc -[277/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[278/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-cat.p/tools_alignment-cat.cc.o -MF src/alignment-cat.p/tools_alignment-cat.cc.o.d -o src/alignment-cat.p/tools_alignment-cat.cc.o -c ../src/tools/alignment-cat.cc -[279/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[280/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc -[281/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-tool.p/tools_tree-tool.cc.o -MF src/tree-tool.p/tools_tree-tool.cc.o.d -o src/tree-tool.p/tools_tree-tool.cc.o -c ../src/tools/tree-tool.cc -[282/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[283/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-thin.p/tools_alignment-thin.cc.o -MF src/alignment-thin.p/tools_alignment-thin.cc.o.d -o src/alignment-thin.p/tools_alignment-thin.cc.o -c ../src/tools/alignment-thin.cc -[284/297] c++ -o src/alignment-thin src/alignment-thin.p/tools_alignment-thin.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[285/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[286/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc -[287/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[288/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc -[289/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[290/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc -[291/297] c++ -o src/trees-bootstrap src/trees-bootstrap.p/tools_trees-bootstrap.cc.o src/trees-bootstrap.p/tools_bootstrap.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[292/297] 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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/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 -[293/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc -[294/297] c++ -o src/builtins/SMC.so src/builtins/SMC.so.p/SMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group -[295/297] c++ -o src/summarize-ancestors src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group -[296/297] c++ -Isrc/draw-tree.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc +[259/297] c++ -Isrc/statreport.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/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 +[260/297] c++ -Isrc/trees-to-SRQ.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-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 +[261/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[262/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-tool.p/tools_tree-tool.cc.o -MF src/tree-tool.p/tools_tree-tool.cc.o.d -o src/tree-tool.p/tools_tree-tool.cc.o -c ../src/tools/tree-tool.cc +[263/297] c++ -o src/trees-to-SRQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[264/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[265/297] c++ -Isrc/bali-subsample.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-subsample.p/tools_subsample.cc.o -MF src/bali-subsample.p/tools_subsample.cc.o.d -o src/bali-subsample.p/tools_subsample.cc.o -c ../src/tools/subsample.cc +[266/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[267/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc +[268/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc +[269/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[270/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc +[271/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[272/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-distances.p/tools_trees-distances.cc.o -MF src/trees-distances.p/tools_trees-distances.cc.o.d -o src/trees-distances.p/tools_trees-distances.cc.o -c ../src/tools/trees-distances.cc +[273/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[274/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-thin.p/tools_alignment-thin.cc.o -MF src/alignment-thin.p/tools_alignment-thin.cc.o.d -o src/alignment-thin.p/tools_alignment-thin.cc.o -c ../src/tools/alignment-thin.cc +[275/297] c++ -Isrc/alignment-max.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-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 +[276/297] c++ -o src/alignment-thin src/alignment-thin.p/tools_alignment-thin.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[277/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[278/297] c++ -Isrc/trees-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-consensus.p/tools_trees-consensus.cc.o -MF src/trees-consensus.p/tools_trees-consensus.cc.o.d -o src/trees-consensus.p/tools_trees-consensus.cc.o -c ../src/tools/trees-consensus.cc +[279/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc +[280/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc +[281/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[282/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[283/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[284/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/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 +[285/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc +[286/297] c++ -o src/trees-bootstrap src/trees-bootstrap.p/tools_trees-bootstrap.cc.o src/trees-bootstrap.p/tools_bootstrap.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[287/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc +[288/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-cat.p/tools_alignment-cat.cc.o -MF src/alignment-cat.p/tools_alignment-cat.cc.o.d -o src/alignment-cat.p/tools_alignment-cat.cc.o -c ../src/tools/alignment-cat.cc +[289/297] c++ -o src/summarize-ancestors src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[290/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm -Wl,--end-group +[291/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc +[292/297] rm -f src/libbaliphy.a && gcc-ar csrDT src/libbaliphy.a src/libbaliphy.a.p/dp_dp_hmm.cc.o src/libbaliphy.a.p/dp_hmm.cc.o src/libbaliphy.a.p/dp_dp-engine.cc.o src/libbaliphy.a.p/dp_dp-array.cc.o src/libbaliphy.a.p/dp_dp-matrix.cc.o src/libbaliphy.a.p/dp_dp-cube.cc.o src/libbaliphy.a.p/dp_2way.cc.o src/libbaliphy.a.p/dp_3way.cc.o src/libbaliphy.a.p/dp_5way.cc.o src/libbaliphy.a.p/dp_alignment-sums.cc.o src/libbaliphy.a.p/mcmc_mcmc.cc.o src/libbaliphy.a.p/mcmc_proposals.cc.o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o src/libbaliphy.a.p/mcmc_AIS.cc.o src/libbaliphy.a.p/mcmc_logger.cc.o src/libbaliphy.a.p/mcmc_moves.cc.o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o src/libbaliphy.a.p/mcmc_sample-node.cc.o src/libbaliphy.a.p/mcmc_sample-cube.cc.o src/libbaliphy.a.p/mcmc_sample-tri.cc.o src/libbaliphy.a.p/mcmc_setup.cc.o src/libbaliphy.a.p/substitution_substitution.cc.o src/libbaliphy.a.p/substitution_parsimony.cc.o src/libbaliphy.a.p/math_exponential.cc.o src/libbaliphy.a.p/math_eigenvalue.cc.o src/libbaliphy.a.p/math_pow2.cc.o src/libbaliphy.a.p/models_parameters.cc.o src/libbaliphy.a.p/models_site-compression.cc.o src/libbaliphy.a.p/models_TreeInterface.cc.o src/libbaliphy.a.p/models_setup.cc.o src/libbaliphy.a.p/models_rules.cc.o src/libbaliphy.a.p/models_parse.cc.o src/libbaliphy.a.p/models_typecheck.cc.o src/libbaliphy.a.p/models_unification.cc.o src/libbaliphy.a.p/models_model.cc.o src/libbaliphy.a.p/tree-align_link2.cc.o src/libbaliphy.a.p/probability_choose.cc.o src/libbaliphy.a.p/probability_probability.cc.o src/libbaliphy.a.p/imodel_imodel.cc.o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o src/libbaliphy.a.p/alignment_alignment-util2.cc.o src/libbaliphy.a.p/tree-align_n_indels2.cc.o src/libbaliphy.a.p/tools_parsimony2.cc.o src/libbaliphy.a.p/version.cc.o +[293/297] c++ -o src/bali-phy/bali-phy src/bali-phy/bali-phy.p/link-partitions.cc.o src/bali-phy/bali-phy.p/bali-phy.cc.o src/bali-phy/bali-phy.p/help.cc.o src/bali-phy/bali-phy.p/A-T-model.cc.o src/bali-phy/bali-phy.p/files.cc.o src/bali-phy/bali-phy.p/loggers.cc.o src/bali-phy/bali-phy.p/system.cc.o src/bali-phy/bali-phy.p/cmd_line.cc.o src/bali-phy/bali-phy.p/paths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-export-dynamic -Wl,--whole-archive -Wl,--start-group src/util/libutil.a src/libcommon.a src/computation/libcomputation.a src/libbaliphy.a -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -ldl -lm -Wl,--end-group +[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/libpng16 -I/usr/include/freetype2 -I/usr/include/pixman-1 -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc ../src/tools/draw-tree.cc: In function ‘MC_tree_with_lengths collapse_MC_tree(const MC_tree_with_lengths&)’: ../src/tools/draw-tree.cc:3351:17: warning: unused variable ‘right1’ [-Wunused-variable] 3351 | int right1 = MC1.mapping[b1]; | ^~~~~~ -[297/297] c++ -o src/draw-tree src/draw-tree.p/tools_draw-tree.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm /usr/lib/x86_64-linux-gnu/libcairo.so -Wl,--end-group +[295/297] c++ -o src/draw-tree src/draw-tree.p/tools_draw-tree.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -lm /usr/lib/x86_64-linux-gnu/libcairo.so -Wl,--end-group +[296/297] 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 -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -funroll-loops -fno-math-errno -fno-signed-zeros -DNDEBUG_DP -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/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 +[297/297] c++ -o src/builtins/SMC.so src/builtins/SMC.so.p/SMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/bali-phy-3.6.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 -Wl,--end-group dh_auto_test -O--buildsystem=meson - cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=20 meson test --verbose + cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=42 meson test --verbose ninja: Entering directory `/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu' [1/4] Generating src/git-version.h with a custom command 1/36 bali-phy version RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=55 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --version +>>> MALLOC_PERTURB_=138 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --version 2/36 bali-phy help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=23 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --help +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=116 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --help 3/36 bali-phy 5d test RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=110 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --test --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=100 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --test --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg 4/36 bali-phy 5d +A 50 RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MALLOC_PERTURB_=210 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=50 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=41 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=50 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg 5/36 bali-phy 48 +A 3 RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=248 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/48-muscle.fasta --iter=3 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=145 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/48-muscle.fasta --iter=3 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg 6/36 bali-phy 5d -A 200 RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=13 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=200 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg -Inone +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=25 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=200 --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg -Inone 7/36 model_P --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=121 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/model_P --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=178 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/model_P --help 8/36 statreport --help RUNNING ->>> MALLOC_PERTURB_=244 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/statreport --help +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=229 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/statreport --help 9/36 stats-select --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=138 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/stats-select --help +>>> MALLOC_PERTURB_=242 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/stats-select --help 10/36 alignment-gild --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=89 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-gild --help +>>> MALLOC_PERTURB_=168 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-gild --help 11/36 alignment-consensus --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=177 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-consensus --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=200 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-consensus --help 12/36 alignment-max --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=87 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-max --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=252 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-max --help 13/36 alignment-chop-internal --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=60 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-chop-internal --help +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=205 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-chop-internal --help 14/36 alignment-indices --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=75 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-indices --help +>>> MALLOC_PERTURB_=108 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-indices --help 15/36 alignment-info --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=13 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-info --help +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=61 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-info --help 16/36 alignment-cat --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=149 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-cat --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=78 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-cat --help 17/36 alignment-translate --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=5 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-translate --help +>>> MALLOC_PERTURB_=250 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-translate --help 18/36 alignment-find --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=228 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-find --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=124 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-find --help 19/36 trees-consensus --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=189 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-consensus --help +>>> MALLOC_PERTURB_=254 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-consensus --help 20/36 tree-mean-lengths --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=207 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/tree-mean-lengths --help +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=8 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/tree-mean-lengths --help + +21/36 mctree-mean-lengths --help RUNNING +>>> MALLOC_PERTURB_=86 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/mctree-mean-lengths --help + +22/36 trees-to-SRQ --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=141 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-to-SRQ --help + +23/36 pickout --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=17 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/pickout --help + +24/36 cut-range --help RUNNING +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=190 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/cut-range --help - 1/36 bali-phy version OK 0.71s +25/36 trees-distances --help RUNNING +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=202 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-distances --help + +26/36 alignment-thin --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=178 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-thin --help + +27/36 alignments-diff --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=141 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignments-diff --help + +28/36 tree-tool --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=189 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/tree-tool --help + +29/36 alignment-distances --help RUNNING +>>> MALLOC_PERTURB_=138 MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-distances --help + +30/36 alignment-draw --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=165 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-draw --help + +31/36 trees-bootstrap --help RUNNING +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=92 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-bootstrap --help + +32/36 draw-tree --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=165 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/draw-tree --help + +33/36 extract-ancestors --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=78 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/extract-ancestors --help + +34/36 summarize-ancestors --help RUNNING +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=121 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/summarize-ancestors --help + +35/36 subsample --help RUNNING +>>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=204 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-subsample --help + +36/36 bali-phy testsuite RUNNING +>>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=136 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/tests/run-tests.py /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg + + 1/36 bali-phy version OK 0.17s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― VERSION: 3.6.1 [3.6.1] BUILD: Aug 25 2024 20:42:16 @@ -2758,7 +2842,7 @@ COMPILER: gcc 14.2.0 x86_64 ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 2/36 bali-phy help OK 0.68s + 2/36 bali-phy help OK 0.17s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Bayesian Inference of Alignment and Phylogeny Usage: bali-phy [ ...] [OPTIONS] @@ -2799,7 +2883,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 7/36 model_P --help OK 0.53s + 7/36 model_P --help OK 0.15s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute marginal likelihoods using stabilized harmonic mean estimator Usage: model_P < in-file @@ -2810,7 +2894,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 8/36 statreport --help OK 0.50s + 8/36 statreport --help OK 0.14s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute summary statistics for tab-delimited data files. @@ -2841,7 +2925,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 9/36 stats-select --help OK 0.47s + 9/36 stats-select --help OK 0.14s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Select columns from a Tracer-format data file. @@ -2855,7 +2939,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -10/36 alignment-gild --help OK 0.43s +10/36 alignment-gild --help OK 0.13s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column. @@ -2873,7 +2957,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -11/36 alignment-consensus --help OK 0.40s +11/36 alignment-consensus --help OK 0.13s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Construct a consensus alignment to summarize an alignment sample. @@ -2893,7 +2977,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -12/36 alignment-max --help OK 0.38s +12/36 alignment-max --help OK 0.13s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Construct a posterior decoding alignment to summarize an alignment sample. @@ -2914,7 +2998,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -13/36 alignment-chop-internal --help OK 0.34s +13/36 alignment-chop-internal --help OK 0.12s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Remove ancestral sequences from an alignment. @@ -2929,7 +3013,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -14/36 alignment-indices --help OK 0.29s +14/36 alignment-indices --help OK 0.12s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Show the alignment in terms of the index of each character in its sequence. @@ -2949,7 +3033,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -15/36 alignment-info --help OK 0.26s +15/36 alignment-info --help OK 0.11s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Show useful statistics about the alignment. @@ -2966,7 +3050,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -16/36 alignment-cat --help OK 0.23s +16/36 alignment-cat --help OK 0.11s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Concatenate several alignments (with the same sequence names) end-to-end. @@ -3000,7 +3084,7 @@ % alignment-cat filename1.fasta filename2.fasta > all.fasta ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -17/36 alignment-translate --help OK 0.21s +17/36 alignment-translate --help OK 0.10s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Translate a DNA/RNA alignment into amino acids. @@ -3026,7 +3110,7 @@ % alignment-translate -rc --frame=2 < dna.fasta > aa2.fasta ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -18/36 alignment-find --help OK 0.16s +18/36 alignment-find --help OK 0.10s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Find the last (or first) FASTA alignment in a file. (Alignments are ended by blank lines.) @@ -3042,7 +3126,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -19/36 trees-consensus --help OK 0.12s +19/36 trees-consensus --help OK 0.10s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Find consensus trees and supported splits. @@ -3100,7 +3184,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -20/36 tree-mean-lengths --help OK 0.10s +20/36 tree-mean-lengths --help OK 0.09s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute the mean lengths for branches in the given topology. @@ -3124,55 +3208,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -21/36 mctree-mean-lengths --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=232 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/mctree-mean-lengths --help - -22/36 trees-to-SRQ --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=77 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-to-SRQ --help - -23/36 pickout --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=223 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/pickout --help - -24/36 cut-range --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MALLOC_PERTURB_=210 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/cut-range --help - -25/36 trees-distances --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=141 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-distances --help - -26/36 alignment-thin --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=64 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-thin --help - -27/36 alignments-diff --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=160 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignments-diff --help - -28/36 tree-tool --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=26 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/tree-tool --help - -29/36 alignment-distances --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=47 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-distances --help - -30/36 alignment-draw --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=106 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/alignment-draw --help - -31/36 trees-bootstrap --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=90 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/trees-bootstrap --help - -32/36 draw-tree --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=190 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/draw-tree --help - -33/36 extract-ancestors --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=10 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/extract-ancestors --help - -34/36 summarize-ancestors --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=79 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/summarize-ancestors --help - -35/36 subsample --help RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=209 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-subsample --help - -36/36 bali-phy testsuite RUNNING ->>> MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=212 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /build/reproducible-path/bali-phy-3.6.1+dfsg/tests/run-tests.py /build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --package-path=/build/reproducible-path/bali-phy-3.6.1+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/reproducible-path/bali-phy-3.6.1+dfsg - -21/36 mctree-mean-lengths --help OK 0.62s +21/36 mctree-mean-lengths --help OK 0.09s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute the mean lengths for branches in the given topology. @@ -3195,7 +3231,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -22/36 trees-to-SRQ --help OK 0.61s +22/36 trees-to-SRQ --help OK 0.09s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Generate Scaled Regeneration Quantile (SRQ) plot Usage: tree-to-srq [ ...] @@ -3215,7 +3251,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -23/36 pickout --help OK 0.57s +23/36 pickout --help OK 0.08s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Generate table from key = value lines in file. @@ -3229,7 +3265,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -24/36 cut-range --help OK 0.56s +24/36 cut-range --help OK 0.08s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Select lines between certain values of a key. (e.g. iterations) @@ -3250,7 +3286,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -25/36 trees-distances --help OK 0.52s +25/36 trees-distances --help OK 0.07s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute autocorrelations or other functions of tree distances. @@ -3286,7 +3322,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -26/36 alignment-thin --help OK 0.48s +26/36 alignment-thin --help OK 0.07s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Remove sequences or columns from an alignment. @@ -3352,7 +3388,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -27/36 alignments-diff --help OK 0.46s +27/36 alignments-diff --help OK 0.07s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Align two alignments for comparison. @@ -3375,7 +3411,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -28/36 tree-tool --help OK 0.43s +28/36 tree-tool --help OK 0.06s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Perform various operations on Newick trees. @@ -3402,7 +3438,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -29/36 alignment-distances --help OK 0.40s +29/36 alignment-distances --help OK 0.06s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compute distances between alignments. @@ -3455,7 +3491,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -30/36 alignment-draw --help OK 0.36s +30/36 alignment-draw --help OK 0.05s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Draw an alignment to HTML, optionally coloring residues by AU. @@ -3496,7 +3532,7 @@ AA+contrast+fade+fade+fade+fade ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -31/36 trees-bootstrap --help OK 0.33s +31/36 trees-bootstrap --help OK 0.05s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Compare support for partitions between different files. @@ -3530,7 +3566,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -32/36 draw-tree --help OK 0.30s +32/36 draw-tree --help OK 0.05s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Draw NEWICK (and some other) formatted files. @@ -3570,7 +3606,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -33/36 extract-ancestors --help OK 0.26s +33/36 extract-ancestors --help OK 0.04s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Extract and name ancestral sequences according to node- and branch- queries. @@ -3599,7 +3635,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -34/36 summarize-ancestors --help OK 0.25s +34/36 summarize-ancestors --help OK 0.04s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Construct alignments with internal sequences for labeled nodes in query tree. @@ -3630,7 +3666,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -35/36 subsample --help OK 0.20s +35/36 subsample --help OK 0.04s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Subsample lines in a file. @@ -3645,7 +3681,7 @@ ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 3/36 bali-phy 5d test OK 13.04s + 3/36 bali-phy 5d test OK 2.06s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― T:topology ~ uniform on tree topologies T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] @@ -3666,17 +3702,10 @@ rs07:log_rate ~ laplace[-4,0.707] rs07:mean_length ~ shifted_exponential[10,1] - iter = 0 prior = -50.425398427534269 likelihood = -1247.756447478856217 posterior = -1298.181845906390436 prior_A = -37.707775836944393 |A| = 126 #indels = 4 |indels| = 9 #substs = 252 P1/likelihood = -1247.756447478856217 P1/prior_A = -37.707775836944393 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 9 P1/#substs = 252 Scale[1]*|T| = 1.600753651270678 |T| = 1.884669726105896 rs07:log_rate = -4.011035470970905 rs07:mean_length = 26.431410046376786 tn93:kappaPur = 2.586122365255272 tn93:kappaPyr = 2.0077993981133364 tn93:pi[A] = 0.19111111484142912 tn93:pi[C] = 0.569301611182322 tn93:pi[G] = 0.008265143062162318 tn93:pi[T] = 0.23132213091408663 scale[1] = 0.8493549979062672 scale1 = 0.8493549979062672 - -start time: Fri Mar 14 06:21:04 2025 - - end time: Fri Mar 14 06:21:15 2025 - -total (elapsed) time: 11 seconds -total (CPU) time: 4 seconds + iter = 0 prior = -33.801135674594306 likelihood = -1160.212786483853961 posterior = -1194.013922158448167 prior_A = -29.280978317995441 |A| = 126 #indels = 3 |indels| = 6 #substs = 245 P1/likelihood = -1160.212786483853961 P1/prior_A = -29.280978317995441 P1/|A| = 126 P1/#indels = 3 P1/|indels| = 6 P1/#substs = 245 Scale[1]*|T| = 1.199872485014583 |T| = 0.791245081220141 rs07:log_rate = -3.6395566827141512 rs07:mean_length = 4.739405328277083 tn93:kappaPur = 2.4161516442714275 tn93:kappaPyr = 2.9623099969284183 tn93:pi[A] = 0.4143132782332432 tn93:pi[C] = 0.09424152146597427 tn93:pi[G] = 0.1477217397665254 tn93:pi[T] = 0.3437234605342571 scale[1] = 1.5164359482201366 scale1 = 1.5164359482201366 ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 6/36 bali-phy 5d -A 200 OK 22.39s + 6/36 bali-phy 5d -A 200 OK 4.16s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: T:topology ~ uniform on tree topologies @@ -3695,32 +3724,32 @@ tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] Beginning pre-burnin: 3 iterations. - Start #1 prior = 9.92292 likelihood = -1596.77 |T| = 0.197671 Scale1*|T| = 0.247499 + Start #1 prior = -1.62745 likelihood = -1085.87 |T| = 1.21789 Scale1*|T| = 2.11615 - Tree (S)ize #1 prior = -5.52492 likelihood = -1204.87 |T| = 0.382394 Scale1*|T| = 8.91423 - Tree (S)ize #2 prior = -3.66775 likelihood = -1204.44 |T| = 0.913303 Scale1*|T| = 9.6599 - Tree (S)ize #3 prior = -3.09327 likelihood = -1204.9 |T| = 0.810074 Scale1*|T| = 8.87435 + Tree (S)ize #1 prior = -17.3057 likelihood = -850.034 |T| = 1.21789 Scale1*|T| = 36.8259 + Tree (S)ize #2 prior = -22.2483 likelihood = -840.784 |T| = 1.21789 Scale1*|T| = 48.529 + Tree (S)ize #3 prior = -27.3815 likelihood = -827.139 |T| = 3.68848 Scale1*|T| = 94.0873 - (S)+Branch (L)engths #1 prior = -14.9758 likelihood = -1111.35 |T| = 4.0736 Scale1*|T| = 47.292 - (S)+Branch (L)engths #2 prior = -5.95183 likelihood = -1090.74 |T| = 2.25335 Scale1*|T| = 9.54184 - (S)+Branch (L)engths #3 prior = 1.05664 likelihood = -1078.96 |T| = 0.425427 Scale1*|T| = 2.29709 + (S)+Branch (L)engths #1 prior = -18.8683 likelihood = -825.898 |T| = 1.47939 Scale1*|T| = 39.2142 + (S)+Branch (L)engths #2 prior = -13.5672 likelihood = -830.771 |T| = 2.02689 Scale1*|T| = 25.7238 + (S)+Branch (L)engths #3 prior = -10.5224 likelihood = -826.792 |T| = 0.89731 Scale1*|T| = 15.5019 - (S)+(L)+(P)arameters #1 prior = -10.2557 likelihood = -887.646 |T| = 1.87302 Scale1*|T| = 4.6191 - (S)+(L)+(P)arameters #2 prior = -8.9002 likelihood = -838.008 |T| = 1.00935 Scale1*|T| = 5.93341 - (S)+(L)+(P)arameters #3 prior = -5.41885 likelihood = -804.444 |T| = 1.05572 Scale1*|T| = 7.11923 + (S)+(L)+(P)arameters #1 prior = -8.08989 likelihood = -816.277 |T| = 1.42835 Scale1*|T| = 16.3993 + (S)+(L)+(P)arameters #2 prior = -7.97469 likelihood = -806.893 |T| = 1.62499 Scale1*|T| = 9.20891 + (S)+(L)+(P)arameters #3 prior = -5.28312 likelihood = -797.007 |T| = 0.783632 Scale1*|T| = 6.17332 - (S)+(L)+(P)+NNI #1 prior = -3.68892 likelihood = -807.45 |T| = 1.57207 Scale1*|T| = 7.36017 - (S)+(L)+(P)+NNI #2 prior = -8.04023 likelihood = -799.357 |T| = 1.88979 Scale1*|T| = 5.60275 - (S)+(L)+(P)+NNI #3 prior = -6.36679 likelihood = -798.609 |T| = 1.24229 Scale1*|T| = 6.5149 - (S)+(L)+(P)+NNI #4 prior = -6.89587 likelihood = -799.61 |T| = 1.70524 Scale1*|T| = 6.48394 + (S)+(L)+(P)+NNI #1 prior = -11.9139 likelihood = -797.114 |T| = 2.09771 Scale1*|T| = 5.19576 + (S)+(L)+(P)+NNI #2 prior = -10.3494 likelihood = -794.628 |T| = 1.75584 Scale1*|T| = 5.37134 + (S)+(L)+(P)+NNI #3 prior = -8.8226 likelihood = -793.363 |T| = 1.48231 Scale1*|T| = 5.29243 + (S)+(L)+(P)+NNI #4 prior = -13.7425 likelihood = -795.979 |T| = 2.65779 Scale1*|T| = 5.85065 - SPR #1 prior = -6.30811 likelihood = -799.928 |T| = 1.06275 Scale1*|T| = 7.02602 + SPR #1 prior = -12.7151 likelihood = -789.792 |T| = 2.68962 Scale1*|T| = 5.79855 - (S)+(L)+(P)+NNI #1 prior = -8.26126 likelihood = -798.636 |T| = 1.76901 Scale1*|T| = 5.23933 - (S)+(L)+(P)+NNI #2 prior = -8.36661 likelihood = -789.555 |T| = 1.09472 Scale1*|T| = 6.30706 - (S)+(L)+(P)+NNI #3 prior = -5.55502 likelihood = -792.607 |T| = 1.15118 Scale1*|T| = 5.53351 + (S)+(L)+(P)+NNI #1 prior = -8.85249 likelihood = -791.505 |T| = 1.92444 Scale1*|T| = 5.47042 + (S)+(L)+(P)+NNI #2 prior = -6.84307 likelihood = -793.918 |T| = 1.33638 Scale1*|T| = 6.33199 + (S)+(L)+(P)+NNI #3 prior = -9.62693 likelihood = -794.571 |T| = 1.90091 Scale1*|T| = 4.77938 -Finished pre-burnin in 0.24 seconds. +Finished pre-burnin in 0.08 seconds. BAli-Phy does NOT detect how many iterations is sufficient: @@ -3742,7 +3771,7 @@ Partition #1: 126 columns -> 110 unique patterns. ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 4/36 bali-phy 5d +A 50 OK 39.77s + 4/36 bali-phy 5d +A 50 OK 5.52s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: T:topology ~ uniform on tree topologies @@ -3765,32 +3794,32 @@ rs07:mean_length ~ shifted_exponential[10,1] Beginning pre-burnin: 3 iterations. - Start #1 prior = -41.7589 likelihood = -1311 |T| = 0.721996 Scale1*|T| = 0.436976 + Start #1 prior = -36.0809 likelihood = -1373.19 |T| = 0.567121 Scale1*|T| = 0.40482 - Tree (S)ize #1 prior = -15.4576 likelihood = -1025.04 |T| = 0.775523 Scale1*|T| = 9.4489 - Tree (S)ize #2 prior = -12.5869 likelihood = -1018.92 |T| = 0.694194 Scale1*|T| = 5.68203 - Tree (S)ize #3 prior = -14.1147 likelihood = -1018.88 |T| = 1.1557 Scale1*|T| = 5.71607 + Tree (S)ize #1 prior = -17.7904 likelihood = -1101.17 |T| = 0.961269 Scale1*|T| = 20.0093 + Tree (S)ize #2 prior = -11.3027 likelihood = -1089.39 |T| = 1.31921 Scale1*|T| = 6.09901 + Tree (S)ize #3 prior = -14.8304 likelihood = -1083.88 |T| = 2.31051 Scale1*|T| = 4.09942 - (S)+Branch (L)engths #1 prior = -18.8191 likelihood = -989.394 |T| = 1.26604 Scale1*|T| = 7.93053 - (S)+Branch (L)engths #2 prior = -17.2072 likelihood = -983.103 |T| = 1.23607 Scale1*|T| = 10.1911 - (S)+Branch (L)engths #3 prior = -14.2469 likelihood = -972.155 |T| = 0.430592 Scale1*|T| = 4.44756 + (S)+Branch (L)engths #1 prior = -16.3173 likelihood = -1008.81 |T| = 2.14961 Scale1*|T| = 4.05605 + (S)+Branch (L)engths #2 prior = -17.2733 likelihood = -1003.03 |T| = 2.35921 Scale1*|T| = 3.42251 + (S)+Branch (L)engths #3 prior = -18.3515 likelihood = -1000.77 |T| = 2.4163 Scale1*|T| = 3.07711 - (S)+(L)+(P)arameters #1 prior = -13.9203 likelihood = -864.31 |T| = 0.883958 Scale1*|T| = 5.24606 - (S)+(L)+(P)arameters #2 prior = -13.1464 likelihood = -815.276 |T| = 1.91101 Scale1*|T| = 7.44475 - (S)+(L)+(P)arameters #3 prior = -13.4097 likelihood = -802.032 |T| = 1.42104 Scale1*|T| = 6.40735 + (S)+(L)+(P)arameters #1 prior = -47.3667 likelihood = -911.477 |T| = 2.41842 Scale1*|T| = 4.23041 + (S)+(L)+(P)arameters #2 prior = -64.5815 likelihood = -821.445 |T| = 1.30003 Scale1*|T| = 5.18737 + (S)+(L)+(P)arameters #3 prior = -38.9363 likelihood = -804.669 |T| = 1.07531 Scale1*|T| = 6.51574 - (S)+(L)+(P)+NNI #1 prior = -13.3372 likelihood = -802.263 |T| = 1.02102 Scale1*|T| = 8.03928 - (S)+(L)+(P)+NNI #2 prior = -20.2817 likelihood = -793.416 |T| = 1.96642 Scale1*|T| = 9.79669 - (S)+(L)+(P)+NNI #3 prior = -15.5595 likelihood = -791.425 |T| = 2.02776 Scale1*|T| = 13.645 - (S)+(L)+(P)+NNI #4 prior = -13.8229 likelihood = -788.643 |T| = 1.70484 Scale1*|T| = 12.9523 + (S)+(L)+(P)+NNI #1 prior = -46.3828 likelihood = -799.698 |T| = 4.02664 Scale1*|T| = 11.358 + (S)+(L)+(P)+NNI #2 prior = -34.1718 likelihood = -792.602 |T| = 1.6138 Scale1*|T| = 17.0299 + (S)+(L)+(P)+NNI #3 prior = -32.9467 likelihood = -789.213 |T| = 1.43267 Scale1*|T| = 12.6415 + (S)+(L)+(P)+NNI #4 prior = -34.5164 likelihood = -791.414 |T| = 1.30715 Scale1*|T| = 17.5283 - SPR #1 prior = -13.9652 likelihood = -791.495 |T| = 2.06543 Scale1*|T| = 8.62335 + SPR #1 prior = -32.608 likelihood = -791.011 |T| = 1.57127 Scale1*|T| = 13.8463 - (S)+(L)+(P)+NNI #1 prior = -14.1093 likelihood = -791.826 |T| = 1.38883 Scale1*|T| = 6.47794 - (S)+(L)+(P)+NNI #2 prior = -14.7739 likelihood = -796.83 |T| = 2.10595 Scale1*|T| = 5.2791 - (S)+(L)+(P)+NNI #3 prior = -16.9211 likelihood = -792.582 |T| = 1.80382 Scale1*|T| = 5.6634 + (S)+(L)+(P)+NNI #1 prior = -38.3131 likelihood = -789.668 |T| = 2.93837 Scale1*|T| = 15.6121 + (S)+(L)+(P)+NNI #2 prior = -39.2199 likelihood = -793.763 |T| = 3.4153 Scale1*|T| = 11.8483 + (S)+(L)+(P)+NNI #3 prior = -33.5216 likelihood = -795.976 |T| = 2.01053 Scale1*|T| = 8.00822 -Finished pre-burnin in 0.19 seconds. +Finished pre-burnin in 0.08 seconds. BAli-Phy does NOT detect how many iterations is sufficient: @@ -3811,7 +3840,7 @@ Created directory '5d-1/' for output files. ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― - 5/36 bali-phy 48 +A 3 OK 70.80s + 5/36 bali-phy 48 +A 3 OK 9.74s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: T:topology ~ uniform on tree topologies @@ -3834,34 +3863,34 @@ rs07:mean_length ~ shifted_exponential[10,1] Beginning pre-burnin: 3 iterations. - Start #1 prior = -1468.16 likelihood = -9650.03 |T| = 0.762253 Scale1*|T| = 3.87642 + Start #1 prior = -2175.33 likelihood = -12263.8 |T| = 0.785165 Scale1*|T| = 0.304374 - Tree (S)ize #1 prior = 200.989 likelihood = -9338.67 |T| = 0.756028 Scale1*|T| = 10.4543 - Tree (S)ize #2 prior = 201.847 likelihood = -9304.2 |T| = 0.756028 Scale1*|T| = 9.24981 - Tree (S)ize #3 prior = 164.476 likelihood = -9295.38 |T| = 1.17588 Scale1*|T| = 8.65679 - - (S)+Branch (L)engths #1 prior = 74.0485 likelihood = -7882.51 |T| = 2.19011 Scale1*|T| = 10.164 - (S)+Branch (L)engths #2 prior = 67.8584 likelihood = -7574.1 |T| = 2.14152 Scale1*|T| = 12.0799 - (S)+Branch (L)engths #3 prior = 82.6332 likelihood = -7485.96 |T| = 1.9278 Scale1*|T| = 9.49742 - - (S)+(L)+(P)arameters #1 prior = 149.614 likelihood = -6449.16 |T| = 0.757053 Scale1*|T| = 22.183 - (S)+(L)+(P)arameters #2 prior = 165.185 likelihood = -5923.15 |T| = 0.953454 Scale1*|T| = 21.6381 - (S)+(L)+(P)arameters #3 prior = 144.82 likelihood = -5820.46 |T| = 1.1885 Scale1*|T| = 19.1775 - - (S)+(L)+(P)+NNI #1 prior = 153.546 likelihood = -5721.22 |T| = 1.05129 Scale1*|T| = 17.9502 - (S)+(L)+(P)+NNI #2 prior = 129.726 likelihood = -5504.47 |T| = 1.28719 Scale1*|T| = 18.7408 - (S)+(L)+(P)+NNI #3 prior = 138.961 likelihood = -5250.34 |T| = 1.14924 Scale1*|T| = 15.4173 - (S)+(L)+(P)+NNI #4 prior = 134.224 likelihood = -5034.19 |T| = 1.30897 Scale1*|T| = 13.8299 - (S)+(L)+(P)+NNI #5 prior = 161.298 likelihood = -4933.12 |T| = 0.928555 Scale1*|T| = 14.0554 - (S)+(L)+(P)+NNI #6 prior = 117.511 likelihood = -4811.32 |T| = 1.38326 Scale1*|T| = 13.3925 - - SPR #1 prior = 125.054 likelihood = -4508.33 |T| = 1.27945 Scale1*|T| = 12.1644 - - (S)+(L)+(P)+NNI #1 prior = 145.877 likelihood = -4496.03 |T| = 1.01285 Scale1*|T| = 10.8971 - (S)+(L)+(P)+NNI #2 prior = 148.3 likelihood = -4500.9 |T| = 0.995307 Scale1*|T| = 11.915 - (S)+(L)+(P)+NNI #3 prior = 145.154 likelihood = -4490.89 |T| = 0.996593 Scale1*|T| = 11.5196 + Tree (S)ize #1 prior = 170.63 likelihood = -7923.46 |T| = 0.862066 Scale1*|T| = 10.0155 + Tree (S)ize #2 prior = 166.182 likelihood = -7921.75 |T| = 0.904285 Scale1*|T| = 10.9422 + Tree (S)ize #3 prior = 167.965 likelihood = -7921.12 |T| = 0.887569 Scale1*|T| = 10.5139 + + (S)+Branch (L)engths #1 prior = 115.967 likelihood = -6864.48 |T| = 1.34065 Scale1*|T| = 16.2742 + (S)+Branch (L)engths #2 prior = 130.621 likelihood = -6606.87 |T| = 1.2911 Scale1*|T| = 13.3541 + (S)+Branch (L)engths #3 prior = 145.732 likelihood = -6530.21 |T| = 1.03798 Scale1*|T| = 9.80206 + + (S)+(L)+(P)arameters #1 prior = 138.628 likelihood = -5789.92 |T| = 1.14503 Scale1*|T| = 17.997 + (S)+(L)+(P)arameters #2 prior = 130.788 likelihood = -5749.16 |T| = 1.24892 Scale1*|T| = 18.5512 + (S)+(L)+(P)arameters #3 prior = 160.138 likelihood = -5736.34 |T| = 0.876475 Scale1*|T| = 19.9965 + + (S)+(L)+(P)+NNI #1 prior = 136.92 likelihood = -5626.54 |T| = 1.11097 Scale1*|T| = 17.5427 + (S)+(L)+(P)+NNI #2 prior = 141.054 likelihood = -5335.36 |T| = 1.11565 Scale1*|T| = 15.1793 + (S)+(L)+(P)+NNI #3 prior = 122.595 likelihood = -5186.11 |T| = 1.22694 Scale1*|T| = 16.2697 + (S)+(L)+(P)+NNI #4 prior = 141.975 likelihood = -5085.78 |T| = 0.975235 Scale1*|T| = 15.3916 + (S)+(L)+(P)+NNI #5 prior = 131.116 likelihood = -4908.19 |T| = 1.12212 Scale1*|T| = 14.2445 + (S)+(L)+(P)+NNI #6 prior = 113.639 likelihood = -4827.86 |T| = 1.32722 Scale1*|T| = 12.578 + + SPR #1 prior = 118.423 likelihood = -4528.45 |T| = 1.1884 Scale1*|T| = 11.5835 + + (S)+(L)+(P)+NNI #1 prior = 157.339 likelihood = -4531.82 |T| = 0.820603 Scale1*|T| = 11.7528 + (S)+(L)+(P)+NNI #2 prior = 142.916 likelihood = -4531.8 |T| = 0.953989 Scale1*|T| = 11.7594 + (S)+(L)+(P)+NNI #3 prior = 114.281 likelihood = -4536.17 |T| = 1.31052 Scale1*|T| = 11.6829 -Finished pre-burnin in 6.59 seconds. +Finished pre-burnin in 1.99 seconds. BAli-Phy does NOT detect how many iterations is sufficient: @@ -3882,142 +3911,142 @@ Created directory '48-muscle-1/' for output files. ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -36/36 bali-phy testsuite OK 728.12s +36/36 bali-phy testsuite OK 156.58s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― Running tests for 'bali-phy': -Running test: mcmc/one-sequence/1 ... ok -Running test: mcmc/two-sequences/1 ... ok -Running test: mcmc/fixed-scale ... ok -Running test: mcmc/with-imodel ... ok -Running test: mcmc/no-imodel ... ok -Running test: optimizer/12 ... FAIL! ['error'] (expected) -Running test: optimizer/10 ... ok -Running test: optimizer/8 ... ok -Running test: optimizer/13 ... ok -Running test: optimizer/7 ... ok -Running test: optimizer/15 ... ok -Running test: optimizer/6 ... ok -Running test: optimizer/4 ... ok -Running test: optimizer/3 ... ok -Running test: optimizer/9 ... ok -Running test: optimizer/11 ... FAIL! ['error'] (expected) -Running test: optimizer/16 ... FAIL! ['error'] (expected) -Running test: optimizer/5 ... ok -Running test: optimizer/pat-bind ... ok -Running test: optimizer/1 ... ok -Running test: optimizer/eta-reduction ... ok -Running test: optimizer/14 ... ok -Running test: optimizer/2 ... ok -Running test: print/1 ... ok -Running test: print/2 ... ok -Running test: IO/errors/Triplets/AUTGC ... ok -Running test: IO/errors/Triplets/1 ... ok -Running test: IO/errors/Triplets/2 ... ok +Running test: IO/errors/DNA-RNA/3 ... ok +Running test: IO/errors/DNA-RNA/1 ... ok +Running test: IO/errors/DNA-RNA/2 ... ok Running test: IO/errors/Codons/3 ... ok -Running test: IO/errors/Codons/AUTGC ... ok -Running test: IO/errors/Codons/1 ... ok Running test: IO/errors/Codons/stop/1 ... ok Running test: IO/errors/Codons/stop/2 ... ok +Running test: IO/errors/Codons/1 ... ok Running test: IO/errors/Codons/2 ... ok -Running test: IO/errors/DNA-RNA/3 ... ok -Running test: IO/errors/DNA-RNA/1 ... ok -Running test: IO/errors/DNA-RNA/2 ... ok -Running test: parse/18 ... ok -Running test: parse/12 ... ok -Running test: parse/partitions/link/8 ... ok -Running test: parse/partitions/link/7 ... ok -Running test: parse/partitions/link/6 ... ok -Running test: parse/partitions/link/4 ... ok -Running test: parse/partitions/link/3 ... ok -Running test: parse/partitions/link/9 ... ok -Running test: parse/partitions/link/5 ... ok -Running test: parse/partitions/link/1 ... ok -Running test: parse/partitions/link/2 ... ok -Running test: parse/partitions/4 ... ok -Running test: parse/partitions/3 ... ok -Running test: parse/partitions/1 ... ok -Running test: parse/partitions/2 ... ok +Running test: IO/errors/Codons/AUTGC ... ok +Running test: IO/errors/Triplets/1 ... ok +Running test: IO/errors/Triplets/2 ... ok +Running test: IO/errors/Triplets/AUTGC ... ok +Running test: print/1 ... ok +Running test: print/2 ... ok +Running test: prob_prog/lazy_sample/3 ... ok +Running test: prob_prog/lazy_sample/1 ... ok +Running test: prob_prog/lazy_sample/2 ... ok +Running test: prob_prog/regression ... ok +Running test: prob_prog/functions/1 ... ok +Running test: prob_prog/observe/1 ... ok +Running test: prob_prog/categorical ... ok +Running test: prob_prog/infer_tree/1 ... ok +Running test: prob_prog/demos/3 ... ok +Running test: prob_prog/demos/airline ... ok +Running test: prob_prog/demos/6 ... ok +Running test: prob_prog/demos/1 ... ok +Running test: prob_prog/demos/2 ... ok +Running test: prob_prog/demos/coalmine ... ok +Running test: prob_prog/demos/5 ... ok +Running test: prob_prog/demos/4 ... ok +Running test: prob_prog/sample_tree/3 ... ok +Running test: prob_prog/sample_tree/1 ... ok +Running test: prob_prog/sample_tree/2 ... ok +Running test: prob_prog/sample_crp ... ok +Running test: prob_prog/popgen/li_stephens ... ok +Running test: prob_prog/order-two ... ok +Running test: prob_prog/if-then-else/1 ... ok +Running test: mcmc/with-imodel ... ok +Running test: mcmc/one-sequence/1 ... ok +Running test: mcmc/no-imodel ... ok +Running test: mcmc/fixed-scale ... ok +Running test: mcmc/two-sequences/1 ... ok +Running test: parse/constraints/1 ... FAIL! ['exit'] (expected) + evaluating reg # 8552: case <8553> of {SModel.ReversibleMarkov.ReversibleMarkov h i j k l m n -> h; SModel.F81 h i j k -> h; SModel.MixtureModel h -> SModel.getAlphabet (SModel.baseModel (SModel.MixtureModel h) SModel.#365); SModel.MixtureModels h i -> case i of {j:k -> SModel.getAlphabet j; _ -> SModel.#348}; _ -> SModel.#348} + + evaluating reg # 8662: Prelude:add <8689> <12923> + + Add: object 'SModel.ReversibleMarkov.ReversibleMarkov %5 %3 %2 %4 %1 %6 %0' is not double, int, log_double, or char' + Running test: parse/10 ... ok -Running test: parse/8 ... ok -Running test: parse/13 ... ok -Running test: parse/7 ... ok -Running test: parse/6 ... ok -Running test: parse/M3/1 ... ok -Running test: parse/M3/2 ... ok -Running test: parse/let/1 ... ok -Running test: parse/4 ... ok Running test: parse/24 ... ok +Running test: parse/21 ... ok Running test: parse/3 ... ok +Running test: parse/functions/1 ... ok +Running test: parse/16 ... ok +Running test: parse/6 ... ok Running test: parse/int-to-double/3 ... ok Running test: parse/int-to-double/1 ... ok Running test: parse/int-to-double/2 ... ok -Running test: parse/22 ... ok -Running test: parse/25 ... ok -Running test: parse/x3/4 ... ok +Running test: parse/13 ... ok +Running test: parse/8 ... ok +Running test: parse/23 ... ok +Running test: parse/11 ... ok +Running test: parse/12 ... ok +Running test: parse/18 ... ok +Running test: parse/26 ... ok +Running test: parse/19 ... ok +Running test: parse/17 ... ok Running test: parse/x3/3 ... ok -Running test: parse/x3/5 ... ok Running test: parse/x3/1 ... ok Running test: parse/x3/2 ... ok -Running test: parse/functions/1 ... ok -Running test: parse/26 ... ok +Running test: parse/x3/5 ... ok +Running test: parse/x3/4 ... ok Running test: parse/9 ... ok -Running test: parse/11 ... ok -Running test: parse/constraints/1 ... FAIL! ['exit'] (expected) - evaluating reg # 8552: case <8553> of {SModel.ReversibleMarkov.ReversibleMarkov h i j k l m n -> h; SModel.F81 h i j k -> h; SModel.MixtureModel h -> SModel.getAlphabet (SModel.baseModel (SModel.MixtureModel h) SModel.#365); SModel.MixtureModels h i -> case i of {j:k -> SModel.getAlphabet j; _ -> SModel.#348}; _ -> SModel.#348} - - evaluating reg # 8662: Prelude:add <8689> <12861> - - Add: object 'SModel.ReversibleMarkov.ReversibleMarkov %5 %3 %2 %4 %1 %6 %0' is not double, int, log_double, or char' - -Running test: parse/21 ... ok -Running test: parse/16 ... ok -Running test: parse/17 ... ok +Running test: parse/22 ... ok Running test: parse/5 ... ok -Running test: parse/error/4 ... ok -Running test: parse/error/3 ... ok -Running test: parse/error/1 ... ok -Running test: parse/error/2 ... ok +Running test: parse/25 ... ok Running test: parse/guess-alphabet/rna ... ok -Running test: parse/guess-alphabet/Triplets/rna ... ok -Running test: parse/guess-alphabet/Triplets/dna ... ok Running test: parse/guess-alphabet/Codons/rna ... ok Running test: parse/guess-alphabet/Codons/dna ... ok -Running test: parse/guess-alphabet/dna ... ok +Running test: parse/guess-alphabet/Triplets/rna ... ok +Running test: parse/guess-alphabet/Triplets/dna ... ok Running test: parse/guess-alphabet/aa ... ok -Running test: parse/23 ... ok -Running test: parse/19 ... ok +Running test: parse/guess-alphabet/dna ... ok +Running test: parse/error/3 ... ok +Running test: parse/error/1 ... ok +Running test: parse/error/2 ... ok +Running test: parse/error/4 ... ok Running test: parse/14 ... ok -Running test: prob_prog/if-then-else/1 ... ok -Running test: prob_prog/order-two ... ok -Running test: prob_prog/regression ... ok -Running test: prob_prog/lazy_sample/3 ... ok -Running test: prob_prog/lazy_sample/1 ... ok -Running test: prob_prog/lazy_sample/2 ... ok -Running test: prob_prog/functions/1 ... ok -Running test: prob_prog/observe/1 ... ok -Running test: prob_prog/popgen/li_stephens ... ok -Running test: prob_prog/sample_tree/3 ... ok -Running test: prob_prog/sample_tree/1 ... ok -Running test: prob_prog/sample_tree/2 ... ok -Running test: prob_prog/infer_tree/1 ... ok -Running test: prob_prog/categorical ... ok -Running test: prob_prog/sample_crp ... ok -Running test: prob_prog/demos/coalmine ... ok -Running test: prob_prog/demos/airline ... ok -Running test: prob_prog/demos/6 ... ok -Running test: prob_prog/demos/4 ... ok -Running test: prob_prog/demos/3 ... ok -Running test: prob_prog/demos/5 ... ok -Running test: prob_prog/demos/1 ... ok -Running test: prob_prog/demos/2 ... ok -Running test: haskell/Data/Map ... ok +Running test: parse/M3/1 ... ok +Running test: parse/M3/2 ... ok +Running test: parse/4 ... ok +Running test: parse/let/1 ... ok +Running test: parse/partitions/3 ... ok +Running test: parse/partitions/1 ... ok +Running test: parse/partitions/2 ... ok +Running test: parse/partitions/link/3 ... ok +Running test: parse/partitions/link/6 ... ok +Running test: parse/partitions/link/8 ... ok +Running test: parse/partitions/link/1 ... ok +Running test: parse/partitions/link/2 ... ok +Running test: parse/partitions/link/9 ... ok +Running test: parse/partitions/link/5 ... ok +Running test: parse/partitions/link/4 ... ok +Running test: parse/partitions/link/7 ... ok +Running test: parse/partitions/4 ... ok +Running test: parse/7 ... ok Running test: haskell/IO/3 ... ok Running test: haskell/IO/1 ... ok -Running test: haskell/parse/1 ... ok Running test: haskell/Ord/3 ... ok Running test: haskell/Ord/1 ... ok Running test: haskell/Ord/2 ... ok +Running test: haskell/parse/1 ... ok +Running test: haskell/Data/Map ... ok +Running test: optimizer/10 ... ok +Running test: optimizer/pat-bind ... ok +Running test: optimizer/3 ... ok +Running test: optimizer/16 ... FAIL! ['error'] (expected) +Running test: optimizer/6 ... ok +Running test: optimizer/13 ... ok +Running test: optimizer/8 ... ok +Running test: optimizer/1 ... ok +Running test: optimizer/11 ... FAIL! ['error'] (expected) +Running test: optimizer/12 ... FAIL! ['error'] (expected) +Running test: optimizer/2 ... ok +Running test: optimizer/9 ... ok +Running test: optimizer/5 ... ok +Running test: optimizer/14 ... ok +Running test: optimizer/eta-reduction ... ok +Running test: optimizer/4 ... ok +Running test: optimizer/15 ... ok +Running test: optimizer/7 ... ok SUCCESS! (0 unexpected failures, 4 expected failures, 126 tests total) ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― @@ -4038,424 +4067,424 @@ [1/5] Generating src/git-version.h with a custom command [1/2] Installing files Installing subdir /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Tree.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/PopGen.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Range.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/MCMC.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Prelude.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Parameters.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SMC.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Parse.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Range.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/PopGen.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Prelude.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Tree.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/IModel.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Parse.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SMC.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/MCMC.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Set.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Either.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Tuple.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Map.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/BitVector.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/ReadFile.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Char.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Eq.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Ix.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Ord.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Text.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Array.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Matrix.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Maybe.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/List.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/JSON.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Function.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Bool.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/System/Environment.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/System +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Control/DeepSeq.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Control/Monad.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Frequency.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Doublets.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Nucleotides.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Codons.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/ReversibleMarkov.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Likelihood.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Random.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Bernoulli.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Tree.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/ExpTransform.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Categorical.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Normal.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Poisson.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Gamma.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Dirichlet.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Geometric.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/FakeDist.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Uniform.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/DirichletProcess.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/ExpTransform.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Beta.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Exponential.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/RandomAlignment.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/List.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Uniform.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Discrete.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Cauchy.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Gamma.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Geometric.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Mixture.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Beta.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Binomial.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Laplace.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Vector.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Introspection.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Pair.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/String.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Cauchy.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Categorical.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Tree.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/List.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/RandomAlignment.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Binomial.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/FakeDist.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Poisson.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Normal.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Discrete.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Probability/Distribution/Bernoulli.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Probability/Distribution +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Num.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Real.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/ST.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Base.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/IO.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Num.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Enum.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/ST.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Compiler/Base.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Compiler Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Tree/Newick.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Tree -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/ReversibleMarkov.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Nucleotides.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Frequency.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Likelihood.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Codons.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/SModel/Doublets.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/SModel -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Control/Monad.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Control/DeepSeq.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Control -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/BAliPhy/ATModel.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/BAliPhy/ATModel/DataPartition.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy/ATModel Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Alignment.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Alphabet.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Sequence.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Alphabet.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Alignment/Matrix.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio/Alignment Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Bio/Alignment/Pairwise.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Bio/Alignment -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/System/Environment.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/System -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Matrix.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Maybe.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Either.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/JSON.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Map.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/ReadFile.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Array.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Tuple.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/List.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Function.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Text.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Set.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Eq.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/BitVector.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Ix.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Ord.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Char.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Data/Bool.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Data +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Introspection.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/String.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Vector.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/Foreign/Pair.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/Foreign +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/BAliPhy/ATModel.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/haskell/BAliPhy/ATModel/DataPartition.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/haskell/BAliPhy/ATModel Installing subdir /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/shifted_gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/symmetric_dirichlet_on.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/laplace.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/exponential.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/bernoulli.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/symmetric_dirichlet.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/laplace.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/binomial.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/uniform_int.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/cauchy.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/shifted_gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/poisson.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/uniform.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/beta.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/shifted_exponential.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_laplace.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/uniform.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/binomial.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/iid.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/symmetric_dirichlet_on.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/cauchy.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/log_laplace.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/geometric.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f61.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/hky85.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/density.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gy94.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94k.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8a_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/tn93_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/scaled_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m2a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fe.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/wag_freq.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/multiMixtureModel.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/lg08_freq.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/tn93.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f3x4.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/distributions/symmetric_dirichlet.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/distributions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/unit_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/zip.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/intToDouble.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/log.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/div.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/add.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/tan.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/zipWith.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/cos.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/rna.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sub.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/aa.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/codons.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/uniform_discretize.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/exp.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/replicate.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/num_branches.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/quantile.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/map.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/dna.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sin.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/mul.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/length.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/getAminoAcids.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/standard_code.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/take.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/letters.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sqrt.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/getNucleotides.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/letter_pairs.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/constructors/Nil.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/constructors/Cons.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m3_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/jc69.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m7.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rs07_relaxed_rates.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/hky85_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/markov_modulate_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fMutSel0.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/tn93.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gwF.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/sample.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gy94_ext.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m2a_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/multiMixtureModel.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rna_16a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m1a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x2.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/wag.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/empirical.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rs07_relaxed_rates.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/equ.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8a_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94k.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/lg08.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/multi_rate.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x3x3.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/wag_freq.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gtr.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/density.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/wag.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/parameter_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mut_sel_aa.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f1x4.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rs05.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/get_q.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/hky85_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rs07.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m3_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x3_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gtr.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x2_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f3x4.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/jtt.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/branch_site.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/lg08_freq.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/tn93_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mut_sel_aa.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mut_sel.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/dNdS.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m3.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/pam.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/rs07.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f1x4.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fMutSel.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m1a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fe.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94_ext.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/branch_site.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f81.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gtr_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gy94.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x3_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/hky85.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/equ.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f61.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x3.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/jc69.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gwF.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fMutSel0.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m7.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m8.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/k80.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/mg94_ext.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/lg08.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/gy94_ext.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/fMutSel.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x2_sym.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/scaled_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/inv.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x3x3.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m3.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x2.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/x2x2.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m2a_test.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/pam.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/sample.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/m2a.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/f.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/empirical.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/get_q.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Rates/free.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Rates/log_normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Rates/gamma.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Rates/log_normal.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Rates Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Frequencies/uniform.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Frequencies -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/huelsenbeck02.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/ts98.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/wang07.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/galtier01.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/div.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/num_branches.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/tan.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/quantile.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/add.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/replicate.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/letters.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/mul.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sqrt.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/log.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/unit_mixture.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/length.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/map.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/zip.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/cos.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sin.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/sub.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/aa.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/dna.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/exp.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/take.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/uniform_discretize.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/getNucleotides.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/zipWith.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/codons.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/letter_pairs.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/getAminoAcids.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/standard_code.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/intToDouble.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/rna.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/constructors/Nil.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/functions/constructors/Cons.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/functions/constructors +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/wang07.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/ts98.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/bindings/models/Covarion/huelsenbeck02.json to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/bindings/models/Covarion Installing subdir /build/reproducible-path/bali-phy-3.6.1+dfsg/help to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/parameters.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/parameters/priors.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/parameters +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/name.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/enable.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/tree.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/align.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/version.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/disable.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/imodel.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/print.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/alphabet.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/seed.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/model.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/config.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/enable.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/test.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/smodel.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/align.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/set.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/branch-lengths.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/seed.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/link.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/version.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/iterations.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/verbose.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/scale.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/Rao-Blackwellize.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/pre-burnin.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/verbose.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/link.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/package-path.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/smodel.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/model.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/unalign.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/disable.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/branch-lengths.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/subsample.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/test.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/iterations.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/print.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/name.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/scale.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/commands/unalign.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/commands Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets/Triplets.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets/Doublets.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets/Codons.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets/genetic-code.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/help/alphabets/Codons.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/lib/bali-phy/help/alphabets Installing subdir /build/reproducible-path/bali-phy-3.6.1+dfsg/examples to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisF.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/tyr.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp-tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/orig.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/cleaned.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/README.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/orig.nex to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/config.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/config2.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/subtilase.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/lysozyme.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/papain.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/lectin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/haloperoxidase.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/legume_lectin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/Starch_binding_domain.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/annexin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/lectin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/xylose_isomerase.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/parvalbumin-like.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/annexin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/lysozyme.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/rr_receiver.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/legume_lectin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/haloperoxidase.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/Src_homology_2_domains.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/subtilase.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-fsa.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-tcoffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-c10.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-fsa.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-WPD.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.command to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-WPD.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-consensus.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-tcoffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.trees to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Miklos-2008/rr_receiver.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Miklos-2008 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4-c50.PP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.1.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4.MAP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-bali-phy-C20-gamma4.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-bali-phy-C20-gamma4.MAP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.rna.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.gb to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/NOTES.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc12.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/keep.pl to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/25-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/globins-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Feng-Doolittle-1987/v-src-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/paper.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/other.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/table1.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.aln to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/additional.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/ITS1-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/5.8S.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/ITS2-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/HIVSIV.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env-clustal.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env-common.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/pol-common.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env-clustal-codons.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/pol-clustal.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/pol.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/some.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/globins.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/many-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/pol-common.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env-clustal-codons.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/HIV/chain-2005/env-common.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/HIV/chain-2005 +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/trp-tyr-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/trp-tyr/tyr.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/trp-tyr +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA-hisF-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisF-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Duplications/hisA-hisF/hisF.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Duplications/hisA-hisF Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/many.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/bglobin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/10-globins-Lunter.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/10-globins.xml to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/ITS1-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/5.8S.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ITS/ITS2-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ITS -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/other.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.aln to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/paper.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/additional.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/table1.accessions to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/30-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-clustalw.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/37-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/microbotryum/76-muscle.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/microbotryum +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/10-globins-Lunter.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/few-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/globins.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/bglobin.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/some.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Globins/many-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Globins +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.rna.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc.gb to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/NOTES.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/keep.pl to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/lrRNA/mollusc12.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/lrRNA Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Enolase/enolase-38-trimmed.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/Enolase/enolase-38.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/Enolase -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo6.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/12d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/25-mafft.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/48b.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/EF-Tu/5d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/EF-Tu +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/config2.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/cleaned.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/config.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/orig.nex to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/orig.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/ferns/README.txt to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/ferns +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.command to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-WPD.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-WPD.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-consensus.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-muscle.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-tcoffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA-trained.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-c10.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-tcoffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-t-coffee.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-poy.trees to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-GTR-LN8-c50.tree to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-t-coffee.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-fsa.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-GTR-DP6-MAP.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-clustalw.dnd to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-probcons-RNA.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-dialign2-2.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25-fsa.ph to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/25.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/5d.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-fsa.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/sequences/5S-rRNA/48-clustalw.fasta to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/sequences/5S-rRNA +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo5.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or false to copy the link. -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo5.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo2.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or false to copy the link. -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo1.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo3.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or false to copy the link. -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo2.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo6.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or false to copy the link. -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo3.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Coalmine.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or @@ -4465,7 +4494,7 @@ the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or false to copy the link. -Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Coalmine.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models +Installing /build/reproducible-path/bali-phy-3.6.1+dfsg/examples/models/Demo1.hs to /build/reproducible-path/bali-phy-3.6.1+dfsg/debian/bali-phy/usr/share/doc/bali-phy/examples/models Warning: trying to copy a symlink that points to a file. This currently copies the file by default, but will be changed in a future version of Meson to copy the link instead. Set follow_symlinks to true to preserve current behavior, or @@ -4582,8 +4611,8 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'bali-phy-dbgsym' in '../bali-phy-dbgsym_3.6.1+dfsg-3_amd64.deb'. dpkg-deb: building package 'bali-phy' in '../bali-phy_3.6.1+dfsg-3_amd64.deb'. +dpkg-deb: building package 'bali-phy-dbgsym' in '../bali-phy-dbgsym_3.6.1+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bali-phy_3.6.1+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../bali-phy_3.6.1+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4591,12 +4620,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1247855/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1247855/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/1833660 and its subdirectories -I: Current time: Fri Mar 14 06:42:41 -12 2025 -I: pbuilder-time-stamp: 1741977761 +I: removing directory /srv/workspace/pbuilder/1247855 and its subdirectories +I: Current time: Fri Apr 17 15:11:42 +14 2026 +I: pbuilder-time-stamp: 1776388302