Diff of the two buildlogs: -- --- b1/build.log 2025-09-27 12:19:20.159114416 +0000 +++ b2/build.log 2025-09-27 12:30:38.295962274 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 27 00:08:48 -12 2025 -I: pbuilder-time-stamp: 1758974928 +I: Current time: Sat Oct 31 08:42:23 +14 2026 +I: pbuilder-time-stamp: 1793385743 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4009427/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1815774/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 30 18:42 /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/1815774/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1815774/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='6e444124ecd54110aa837a5e3bc23d5f' - 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='4009427' - PS1='# ' - PS2='> ' + INVOCATION_ID=c492b8e881974570a2a406c27fc792d9 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1815774 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.P36Z021I/pbuilderrc_fF9o --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P36Z021I/b1 --logfile b1/build.log libbpp-phyl_2.4.1-12.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.P36Z021I/pbuilderrc_wpGU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P36Z021I/b2 --logfile b2/build.log libbpp-phyl_2.4.1-12.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4009427/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1815774/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -179,7 +211,7 @@ Get: 62 http://deb.debian.org/debian unstable/main arm64 libbpp-core-dev arm64 2.4.1-14 [922 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbpp-seq12t64 arm64 2.4.1-13 [452 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libbpp-seq-dev arm64 2.4.1-13 [724 kB] -Fetched 31.7 MB in 0s (137 MB/s) +Fetched 31.7 MB in 0s (79.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20001 files and directories currently installed.) @@ -455,7 +487,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && 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 > ../libbpp-phyl_2.4.1-12_source.changes +I: user script /srv/workspace/pbuilder/1815774/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1815774/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && 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 > ../libbpp-phyl_2.4.1-12_source.changes dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-12 dpkg-buildpackage: info: source distribution unstable @@ -486,8 +522,8 @@ -- shared lib: /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (0.5s) --- Generating done (0.1s) +-- Configuring done (0.7s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -507,681 +543,681 @@ make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/depend make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o [ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp +[ 9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o +cd 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CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp -[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp -[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o +[ 32%] Building 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp [ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ 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"CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o" +/usr/bin/ranlib libbpp-phyl.a +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +[ 92%] Built target bpp-phyl-static +ed.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o" /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl.so.12.0.0 libbpp-phyl.so.12 libbpp-phyl.so make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' [ 92%] Built target bpp-phyl-shared make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/depend make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/depend -make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" -make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend -make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_likelihood.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_mapping.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_likelihood_clock.dir/DependInfo.cmake "--color=" -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend +make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_mapping.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_mapping_codon.dir/DependInfo.cmake "--color=" -make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_models.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_nhx.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_tree.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_simulations.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build -make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' [ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -[ 93%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build +make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build +[ 93%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build +[ 93%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF 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CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood.cpp -[ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp -[ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp -[ 95%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_parsimony.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 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/build/reproducible-path/libbpp-phyl-2.4.1/test/test_nhx.cpp [ 95%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree.cpp -[ 96%] Linking CXX executable test_nhx -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_nhx.dir/link.d CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[ 96%] Built target test_nhx -make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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cmake_link_script CMakeFiles/test_tree_getpath.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable test_tree -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable test_models -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_tree_getpath.dir/link.d CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -o test_tree_getpath -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 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CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_tree.dir/link.d CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +[ 97%] Linking CXX executable test_nhx +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong 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"CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o" -/usr/bin/ranlib libbpp-phyl.a -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[ 97%] Built target bpp-phyl-static -[ 98%] Linking CXX executable test_likelihood_clock -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[ 98%] Built target test_bowker +[ 98%] Built target test_tree [ 98%] Linking CXX executable test_likelihood cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable test_tree_rootat -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_rootat.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable test_simulations -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_likelihood_clock.dir/link.d CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[ 99%] Built target test_simulations -[ 99%] Linking CXX executable test_detailed_simulations -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 +[ 99%] Built target test_likelihood_clock [100%] Linking CXX executable test_mapping_codon cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1 +[100%] Linking CXX executable test_detailed_simulations +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_mapping_codon.dir/link.d CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +[100%] Built target test_mapping_codon /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_detailed_simulations.dir/link.d CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' [100%] Built target test_detailed_simulations -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_mapping_codon.dir/link.d CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +[100%] Linking CXX executable test_bowker +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -[100%] Built target test_mapping_codon +[100%] Built target test_bowker +[100%] Linking CXX executable test_simulations +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_simulations.dir/link.d CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +[100%] Built target test_simulations [100%] Linking CXX executable test_mapping cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_mapping.dir/link.d CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 @@ -1464,62 +1500,12 @@ 12: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/test_tree_getpath 12: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test 12: Test timeout computed to be: 60000 -4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. -2: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -2: 4 -10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -12: Id node1 0 -12: Id node2 1 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 1 -12: Id node1 0 -12: Id node3 2 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 2 -6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 1: / 1 - 2 \ 3 nodes loaded. 1: ..:: Testing with homogeneous model ::.. -5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -5: 4x4 -5: [ -5: [-1.37306, 0.362694, 0.906736, 0.103627] -5: [0.103627, -0.984456, 0.362694, 0.518135] -5: [0.259067, 0.362694, -0.777202, 0.15544] -5: [0.0518135, 0.906736, 0.272021, -1.23057] -5: ] - 1/13 Test #8: test_nhx ......................... Passed 0.05 sec -test 13 - Start 13: test_tree_rootat - -13: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/test_tree_rootat -13: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test -13: Test timeout computed to be: 60000 +2: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +2: 4 3: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.206767 -10: Theta1 set to 0.24869 -10: Theta2 set to 0.497465 -10: Theta3 set to 0.813006 -10: Theta4 set to 0.456828 -10: Fast check: - 2/13 Test #12: test_tree_getpath ................ Passed 0.05 sec 3: Testing Single Tree Traversal likelihood class... -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 94.395699097704181213 -4: * initial likelihood...................: 94.3957 -4: Log-likelihood after adding clock......: 94.3957 -9: Initializing data structure............: Done. -9: Number of distinct sites...............: 9 -9: Parsimony score: 9 - 3/13 Test #9: test_parsimony ................... Passed 0.07 sec 3: Initializing data structure............: Done. 3: Number of distinct sites...............: 12 3: Test model.............................: T92 @@ -1535,7 +1521,55 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -13: Total length...........................: 97.1023 +4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +4: Test model.............................: T92 +4: 94.395699097704181213 +4: * initial likelihood...................: 94.3957 +4: Log-likelihood after adding clock......: 94.3957 +5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +5: 4x4 +5: [ +5: [-1.37306, 0.362694, 0.906736, 0.103627] +5: [0.103627, -0.984456, 0.362694, 0.518135] +5: [0.259067, 0.362694, -0.777202, 0.15544] +5: [0.0518135, 0.906736, 0.272021, -1.23057] +5: ] +6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +9: Initializing data structure............: Done. +9: Number of distinct sites...............: 9 +9: Parsimony score: 9 + 1/13 Test #9: test_parsimony ................... Passed 0.03 sec + 2/13 Test #8: test_nhx ......................... Passed 0.04 sec +test 13 + Start 13: test_tree_rootat + +13: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test/test_tree_rootat +13: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test +13: Test timeout computed to be: 60000 +10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +10: Theta0 set to 0.935209 +10: Theta1 set to 0.248668 +10: Theta2 set to 0.798877 +10: Theta3 set to 0.404213 +10: Theta4 set to 0.596775 +10: Fast check: +12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +12: Id node1 0 +12: Id node2 1 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 1 +12: Id node1 0 +12: Id node3 2 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 2 4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 4: 4: 71.265799586338530958 @@ -1555,10 +1589,8 @@ 4: Test model.............................: T92 4: 92.32951163340790401435 4: * initial likelihood...................: 92.3295 -3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 -3: -3: 65.72293577215030779826 -3: * likelihood after full optimization...: 65.7229 +13: Total length...........................: 99.9629 + 3/13 Test #12: test_tree_getpath ................ Passed 0.04 sec 4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 4: 4: 71.26579406918833115014 @@ -1570,13 +1602,18 @@ 4: HeightP2 0.819072 [ 0; 1] 4: T92.kappa 0.996398 ]0; +inf[ 4: T92.theta 0.579960 ]1e-06; 0.999999[ - 4/13 Test #4: test_likelihood_clock ............ Passed 0.13 sec + 4/13 Test #4: test_likelihood_clock ............ Passed 0.10 sec +3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 +3: +3: 65.72293577215030779826 +3: * likelihood after full optimization...: 65.7229 3: Testing Double Tree Traversal likelihood class... 3: Initializing data structure............: Done. 3: Number of distinct sites...............: 12 3: Test model.............................: T92 3: 85.03094203195020384101 3: * initial likelihood...................: 85.0309 + 5/13 Test #7: test_models ...................... Passed 0.10 sec 3: Initial bracketing: 3: A: x = 0.5, f = 80.2872 3: B: x = 2.11803, f = 71.6905 @@ -1587,7 +1624,6 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 - 5/13 Test #7: test_models ...................... Passed 0.14 sec 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215042148509 @@ -1601,14 +1637,12 @@ 3: BrLen2 3.41183634475886687909 3.41183634475886687909 3: BrLen3 -187.23500312027670133830 -187.23500312027670133830 3: BrLen4 -56.02595035004603118978 -56.02595035004603829520 - 6/13 Test #3: test_likelihood .................. Passed 0.22 sec - 7/13 Test #13: test_tree_rootat ................. Passed 0.18 sec -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 183 + 6/13 Test #3: test_likelihood .................. Passed 0.25 sec + 7/13 Test #13: test_tree_rootat ................. Passed 0.22 sec 5: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 78% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 5: Initializing data structure............: Done. -5: Number of distinct sites...............: 76 -5: 77086.8 +5: Number of distinct sites...............: 73 +5: 76821.3 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1628,47 +1662,6 @@ 5: [1, 1, 1, 0] 5: ] 5: Compute joint node-pairs likelihood....: -2: Br0 BrLen = 0.001 counts = 0.00088 -2: 4x4 -2: [ -2: [0, 1e-05, 7e-05, 1e-05] -2: [2e-05, 0, 4e-05, 0.00023] -2: [0.00012, 0.00015, 0, 3e-05] -2: [0, 0.00019, 1e-05, 0] -2: ] -2: Br1 BrLen = 0.002 counts = 0.00199 -2: 4x4 -2: [ -2: [0, 9e-05, 0.00018, 4e-05] -2: [6e-05, 0, 0.00029, 0.00037] -2: [0.00018, 0.00019, 0, 9e-05] -2: [1e-05, 0.0004, 9e-05, 0] -2: ] -2: Br2 BrLen = 0.003 counts = 0.00321 -2: 4x4 -2: [ -2: [0, 7e-05, 0.00031, 4e-05] -2: [9e-05, 0, 0.00042, 0.0006] -2: [0.00032, 0.00038, 0, 0.00014] -2: [2e-05, 0.00054, 0.00028, 0] -2: ] -2: Br3 BrLen = 0.01 counts = 0.01003 -2: 4x4 -2: [ -2: [0, 0.00033, 0.0011, 0.00014] -2: [0.00032, 0, 0.00123, 0.00187] -2: [0.00096, 0.00133, 0, 0.0004] -2: [0.00011, 0.00171, 0.00053, 0] -2: ] -2: Br4 BrLen = 0.1 counts = 0.09967 -2: 4x4 -2: [ -2: [0, 0.00356, 0.00925, 0.00103] -2: [0.0035, 0, 0.01228, 0.01775] -2: [0.00941, 0.01259, 0, 0.00559] -2: [0.00093, 0.01836, 0.00542, 0] -2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 0.73 sec 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, type 1: 5: 4x4 @@ -1698,6 +1691,8 @@ 5: [6.26537e-09, 0.000129478, 5.67996e-12, 5.21646e-08] 5: [6.26139e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12] 5: ] +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 187 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Total count, uniformization method: @@ -1793,14 +1788,58 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 51 50.5007 50.4634 50.4634 50.5007 50.5007 50.5007 50.5007 -5: B 0.002 116 115.802 115.639 115.639 115.802 115.802 115.802 115.802 -5: 0.008 396 391.516 389.139 389.139 391.516 391.516 391.516 391.516 -5: C 0.01 479 478.61 474.758 474.758 478.61 478.61 478.61 478.61 -5: D 0.02 1013 1011.43 996.208 996.208 1011.43 1011.43 1011.43 1011.43 -5: A 0.001 1.00861/1 1.01036/1 1.01036/1 4.0231/4 4.02683/4 4.02683/4 0.000475608/0 0.000812686/0 0.000812686/0 2.98304/3 2.9828/3 2.9828/3 -5: B 0.002 1.01856/1 1.02326/1 1.02326/1 13.6028/14 13.6178/14 13.6178/14 7.17513e-05/0 0.00344401/0 0.00344401/0 5.99303/5 5.996/5 5.996/5 -5: 0.008 15.6894/16 15.7421/16 15.7421/16 28.7961/29 29.0738/29 29.0738/29 2.01993/2 2.03678/2 2.03678/2 6.29317/6 6.39597/6 6.39597/6 +5: A 0.001 45 46.0844 46.0469 46.0469 46.0844 46.0844 46.0844 46.0844 +2: Br0 BrLen = 0.001 counts = 0.00103 +2: 4x4 +2: [ +2: [0, 5e-05, 0.00013, 0] +2: [3e-05, 0, 0.0001, 0.00016] +2: [0.00012, 0.00012, 0, 8e-05] +2: [0, 0.00017, 7e-05, 0] +2: ] +2: Br1 BrLen = 0.002 counts = 0.00203 +2: 4x4 +2: [ +2: [0, 4e-05, 0.00025, 0] +2: [6e-05, 0, 0.00024, 0.00031] +2: [0.00018, 0.00026, 0, 0.00014] +2: [2e-05, 0.00039, 0.00014, 0] +2: ] +2: Br2 BrLen = 0.003 counts = 0.00294 +2: 4x4 +2: [ +2: [0, 7e-05, 0.00023, 6e-05] +2: [0.0001, 0, 0.00044, 0.00059] +2: [0.00027, 0.00039, 0, 0.00012] +2: [1e-05, 0.00046, 0.0002, 0] +2: ] +2: Br3 BrLen = 0.01 counts = 0.0101 +2: 4x4 +2: [ +2: [0, 0.00035, 0.00095, 0.0001] +2: [0.00028, 0, 0.00127, 0.00193] +2: [0.00099, 0.00108, 0, 0.00062] +2: [7e-05, 0.00188, 0.00058, 0] +2: ] +2: Br4 BrLen = 0.1 counts = 0.09896 +2: 4x4 +2: [ +2: [0, 0.00343, 0.00957, 0.00087] +2: [0.00342, 0, 0.01269, 0.0179] +2: [0.00838, 0.01268, 0, 0.00553] +2: [0.00105, 0.01804, 0.0054, 0] +2: ] + 8/13 Test #2: test_detailed_simulations ........ Passed 1.11 sec +5: B 0.002 98 97.2688 97.1235 97.1235 97.2688 97.2688 97.2688 97.2688 +5: 0.008 377 377.486 375.081 375.081 377.486 377.486 377.486 377.486 +5: C 0.01 468 473.286 469.446 469.446 473.286 473.286 473.286 473.286 +5: D 0.02 1021 1015.36 999.852 999.852 1015.36 1015.36 1015.36 1015.36 +5: A 0.001 0.99997/1 1.00078/1 1.00078/1 3.02537/3 3.02964/3 3.02964/3 0.000533664/0 0.00106969/0 0.00106969/0 2.98367/3 2.98386/3 2.98386/3 +5: B 0.002 1.01816/1 1.02331/1 1.02331/1 9.05735/9 9.07091/9 9.07091/9 0.000118499/0 0.00261982/0 0.00261982/0 0.00205579/0 0.0096579/0 0.0096579/0 +5: 0.008 17.3127/18 17.362/18 17.362/18 36.6633/38 36.9556/38 36.9556/38 4.00967/4 4.004/4 4.004/4 14.3201/15 14.3613/15 14.3613/15 +5: C 0.01 24.2919/24 24.3425/24 24.3425/24 41.1682/41 41.6457/41 41.6457/41 3.19241/3 3.22026/3 3.22026/3 10.9986/11 11.1432/11 11.1432/11 +5: D 0.02 40.1778/41 40.5622/41 40.5622/41 104.304/109 106.118/109 106.118/109 11.0096/11 10.9683/11 10.9683/11 29.2968/30 29.8278/30 29.8278/30 + 9/13 Test #5: test_mapping ..................... Passed 1.93 sec 11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 11: ((A:1,B:2):3,C:4); 11: @@ -1829,10 +1868,7 @@ 11: Node 3: 11: Node 4: 11: B: ESS=2 -5: C 0.01 19.645/19 19.7917/19 19.7917/19 52.3816/54 52.8574/54 52.8574/54 9.55104/10 9.46602/10 9.46602/10 12.7191/13 12.9039/13 12.9039/13 11: Newick I/O ok. -5: D 0.02 39.621/39 39.9498/39 39.9498/39 90.4558/93 92.1973/93 92.1973/93 7.1454/7 7.2057/7 7.2057/7 27.5371/29 28.1118/29 28.1118/29 - 9/13 Test #5: test_mapping ..................... Passed 1.54 sec 11: Newick multiple I/O ok. 11: Testing parsing a directory... 11: Ok, reading on directory throws exception! @@ -1862,21 +1898,23 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 3.19 sec -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 +10/13 Test #11: test_tree ........................ Passed 5.64 sec +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 10: -10: 0.206767 0.187447 -10: 0.24869 0.227244 -10: 0.497465 0.498226 -10: 0.813006 0.832888 -10: 0.456828 0.454003 +10: 0.935209 0.94075 +10: 0.248668 0.248769 +10: 0.798877 0.799237 +10: 0.404213 0.397212 +10: 0.596775 0.589733 10: Detailed check: 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 195 +10: Number of distinct sites...............: 187 6: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 79% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 6: Initializing data structure............: Done. -6: Number of distinct sites...............: 973 -6: 96041.5 +6: Number of distinct sites...............: 970 +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0395 0.0047 +1: ..:: Testing with homogeneous, non-stationary model ::.. +6: 95686.6 6: Analytical total count: 6: 64x64 6: [ @@ -1946,8 +1984,6 @@ 6: [3.00249, 3.00221, 3.00125, 2.00023, 3.00172, 3.00192, 3.00098, 2.00023, 3.00167, 3.00282, 3.00133, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00192, 3.00222, 3.0018, 2.00023, 3.00248, 3.00094, 3.00167, 2.00023, 3.0026, 3.00164, 3.00171, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.0016, 3.0021, 3.00221, 2.00023, 3.00191, 3.00171, 3.00175, 2.00023, 3.00254, 3.00135, 3.00175, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, nan, 2.00015, nan, 1.00012, 2.00015, 2.00023, 2.00019, 1.00012, nan, 2.00019, 2.00015, 1.00012, 1.00012, 1.00012, 1.00012, 1.21058e-07] 6: ] 6: Compute joint node-pairs likelihood....: -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.042 0.0061 -1: ..:: Testing with homogeneous, non-stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: 6: 64x64 @@ -2228,26 +2264,26 @@ 6: [2.75108, 2.00072, 2.99986, 2.00023, 2.33358, 2.00046, 2.4996, 2.00023, 2.75027, 2.00115, 2.99976, 2.00023, 1.50015, 1.00029, 2.00008, 1.00012, 2.50055, 2.00069, 2.50049, 2.00023, 2.16746, 1.99977, 2.16689, 2.00023, 2.00098, 2.00026, 2.33356, 2.00023, 1.00015, 1.00019, 1.00017, 1.00012, 2.75022, 2.00063, 2.75081, 2.00023, 2.33369, 2.0003, 2.33359, 2.00023, 2.25098, 2.00008, 2.50025, 2.00023, 1.5001, 1.00023, 1.50011, 1.00012, 0, 1.00019, 0, 1.00012, 1.50004, 1.00023, 1.50009, 1.00012, 0, 1.00027, 2.00006, 1.00012, 1, 0.000232033, 1, 1.07607e-07] 6: ] 6: Compute joint node-pairs likelihood....: -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 -10: -10: 0.206767 0.227024 -10: 0.24869 0.260364 -10: 0.497465 0.503208 -10: 0.813006 0.803123 -10: 0.456828 0.443309 -11/13 Test #10: test_simulations ................. Passed 8.06 sec 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -12/13 Test #6: test_mapping_codon ............... Passed 8.39 sec -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0429 0.0063 +11/13 Test #6: test_mapping_codon ............... Passed 17.77 sec +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 +10: +10: 0.935209 0.934765 +10: 0.248668 0.234638 +10: 0.798877 0.804168 +10: 0.404213 0.400906 +10: 0.596775 0.60235 +12/13 Test #10: test_simulations ................. Passed 20.68 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0441 0.0066 1: ..:: Testing with non-homogeneous, non-stationary model ::.. -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9347 0.8067 +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9349 0.8024 1: ..:: Testing with non-homogeneous, stationary model ::.. -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0395 0.0054 -13/13 Test #1: test_bowker ...................... Passed 28.43 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0418 0.0066 +13/13 Test #1: test_bowker ...................... Passed 67.68 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 28.46 sec +Total Test time (real) = 67.70 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -2553,9 +2589,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-12_arm64.deb'. dpkg-deb: building package 'libbpp-phyl12t64' in '../libbpp-phyl12t64_2.4.1-12_arm64.deb'. dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-12_arm64.deb'. +dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-12_arm64.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2563,12 +2599,14 @@ 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/1815774/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1815774/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/4009427 and its subdirectories -I: Current time: Sat Sep 27 00:19:19 -12 2025 -I: pbuilder-time-stamp: 1758975559 +I: removing directory /srv/workspace/pbuilder/1815774 and its subdirectories +I: Current time: Sat Oct 31 08:53:37 +14 2026 +I: pbuilder-time-stamp: 1793386417