Diff of the two buildlogs: -- --- b1/build.log 2024-11-19 22:15:41.000786482 +0000 +++ b2/build.log 2024-11-19 22:20:11.832619037 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 22 16:33:50 -12 2025 -I: pbuilder-time-stamp: 1766464430 +I: Current time: Wed Nov 20 12:15:46 +14 2024 +I: pbuilder-time-stamp: 1732054546 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying remove_test_likelihood_nh.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3636918/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4123576/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 19 22:15 /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/4123576/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4123576/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='438a4e3004a04df99a679d2f15aabe12' - 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='3636918' - PS1='# ' - PS2='> ' + INVOCATION_ID=4e82968966ae47a2abc0f9b580378dd5 + 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=4123576 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.FyS3H0cl/pbuilderrc_cM0N --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.FyS3H0cl/b1 --logfile b1/build.log libbpp-phyl_2.4.1-11.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FyS3H0cl/pbuilderrc_6mgC --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.FyS3H0cl/b2 --logfile b2/build.log libbpp-phyl_2.4.1-11.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3636918/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4123576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -175,7 +207,7 @@ Get: 56 http://deb.debian.org/debian unstable/main arm64 libbpp-core-dev arm64 2.4.1-13+b1 [941 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libbpp-seq12t64 arm64 2.4.1-13 [452 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libbpp-seq-dev arm64 2.4.1-13 [724 kB] -Fetched 37.8 MB in 0s (151 MB/s) +Fetched 37.8 MB in 0s (133 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) @@ -422,7 +454,11 @@ Building tag database... -> Finished parsing the build-deps 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_2.4.1-11_source.changes +I: user script /srv/workspace/pbuilder/4123576/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4123576/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_2.4.1-11_source.changes dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-11 dpkg-buildpackage: info: source distribution unstable @@ -461,7 +497,7 @@ -- 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 (0.4s) +-- Configuring done (0.7s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -486,215 +522,217 @@ 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-shared.dir/DependInfo.cmake "--color=" 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]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' 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 -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.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 CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o 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/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 -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.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 +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.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/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 -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.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 -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 +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 +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.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 -[ 2%] 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++ -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/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o +[ 2%] 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++ -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 +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.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 CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.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/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 -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o +[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.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/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.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/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o 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 +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o +cd 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.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/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.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/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.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/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.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/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp -[ 6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.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/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp +[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o +cd 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-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/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.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 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, @@ -721,78 +759,54 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.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 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-Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp +[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.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/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, @@ -819,405 +833,420 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/src 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp +[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.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/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp [ 92%] Linking CXX shared library libbpp-phyl.so cd 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test/CMakeFiles/test_models.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.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_models.dir/DependInfo.cmake "--color=" -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' 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_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build -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/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 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'/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' -make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.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_tree.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_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_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[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]: 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_bowker.dir/build.make test/CMakeFiles/test_bowker.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 -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build +make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.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 -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build -[ 93%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.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_likelihood.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c 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test/CMakeFiles/test_bowker.dir/test_bowker.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 CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp +[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.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_likelihood.dir/test_likelihood.cpp.o -MF 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 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_models.dir/build.make test/CMakeFiles/test_models.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_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build +[ 94%] 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 +[ 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' make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build -[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -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_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' 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test/CMakeFiles/test_tree.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/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_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping_codon.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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"CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o" "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-stati[ 97%] Linking CXX executable test_parsimony cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.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 -rdynamic -Wl,--dependency-file,CMakeFiles/test_parsimony.dir/link.d CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony -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 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'/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' +[ 98%] Built target test_bowker /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 -rdynamic -Wl,--dependency-file,CMakeFiles/test_likelihood.dir/link.d CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -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_likelihood -[ 99%] 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 -rdynamic -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 +[ 98%] Built target test_likelihood +[ 98%] 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%] 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 +/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 -rdynamic -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' -[ 99%] Built target test_bowker +[ 99%] 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 -rdynamic -Wl,--dependency-file,CMakeFiles/test_tree_rootat.dir/link.d CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -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_tree_rootat [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 -rdynamic -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 -rdynamic -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 [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 +[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 -rdynamic -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 -rdynamic -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 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-aarch64-linux-gnu' [100%] Built target test_mapping @@ -1505,26 +1541,6 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -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 -3: Initial bracketing: -3: A: x = 0.5, f = 80.2872 -3: B: x = 2.11803, f = 71.6905 -3: C: x = 2.76139, f = 71.7653 -3: Step scale factor Function Time -3: 0 2.11803 71.690520 0.000000 -3: Optimizing... / 11 2.11803 71.690520 0.000000 -3: Done. -3: Tree scaled by.........................: 8.31477 -3: * likelihood after tree scale..........: 71.6905 4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. 4: Initializing data structure............: Done. 4: Number of distinct sites...............: 14 @@ -1532,6 +1548,33 @@ 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 +10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +10: Theta0 set to 0.419915 +10: Theta1 set to 0.317124 +10: Theta2 set to 0.705476 +10: Theta3 set to 0.0307086 +10: Theta4 set to 0.4362 +10: Fast check: + 1/13 Test #8: test_nhx ......................... Passed 0.04 sec + 2/13 Test #9: test_parsimony ................... Passed 0.03 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 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 @@ -1551,46 +1594,16 @@ 4: Test model.............................: T92 4: 92.32951163340790401435 4: * initial likelihood...................: 92.3295 -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 -4: * likelihood after full optimization...: 71.2658 -4: Name: Value: Constraint: -4: _________________________________________________ -4: TotalHeight 0.448127 [ 0; 10000] -4: HeightP4 0.390916 [ 0; 1] -4: HeightP2 0.819072 [ 0; 1] -4: T92.kappa 0.996398 ]0; +inf[ -4: T92.theta 0.579960 ]1e-06; 0.999999[ -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 #4: test_likelihood_clock ............ Passed 0.07 sec - 2/13 Test #7: test_models ...................... Passed 0.06 sec - 3/13 Test #8: test_nhx ......................... Passed 0.05 sec - 4/13 Test #9: test_parsimony ................... 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 -10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.306746 -10: Theta1 set to 0.823943 -10: Theta2 set to 0.648461 -10: Theta3 set to 0.475169 -10: Theta4 set to 0.287152 -10: Fast check: +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 12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 12: Id node1 0 12: Id node2 1 @@ -1606,8 +1619,31 @@ 12: 4 12: 3 12: 2 - 5/13 Test #12: test_tree_getpath ................ Passed 0.03 sec -13: Total length...........................: 104.815 +3: Initial bracketing: +3: A: x = 0.5, f = 80.2872 +3: B: x = 2.11803, f = 71.6905 +3: C: x = 2.76139, f = 71.7653 +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 +4: * likelihood after full optimization...: 71.2658 +4: Name: Value: Constraint: +4: _________________________________________________ +4: TotalHeight 0.448127 [ 0; 10000] +4: HeightP4 0.390916 [ 0; 1] +4: HeightP2 0.819072 [ 0; 1] +4: T92.kappa 0.996398 ]0; +inf[ +4: T92.theta 0.579960 ]1e-06; 0.999999[ +3: Step scale factor Function Time +3: 0 2.11803 71.690520 0.000000 +3: Optimizing... / 11 2.11803 71.690520 0.000000 +3: Done. +3: Tree scaled by.........................: 8.31477 +3: * likelihood after tree scale..........: 71.6905 + 3/13 Test #4: test_likelihood_clock ............ Passed 0.07 sec + 4/13 Test #12: test_tree_getpath ................ Passed 0.03 sec +13: Total length...........................: 101.795 + 5/13 Test #7: test_models ...................... Passed 0.08 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 @@ -1621,14 +1657,14 @@ 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 0.10 sec - 7/13 Test #13: test_tree_rootat ................. Passed 0.10 sec + 6/13 Test #3: test_likelihood .................. Passed 0.11 sec + 7/13 Test #13: test_tree_rootat ................. Passed 0.11 sec 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 194 +10: Number of distinct sites...............: 196 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...............: 74 -5: 77255.3 +5: Number of distinct sites...............: 79 +5: 77541.7 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1657,58 +1693,58 @@ 5: [0, 0, 0, 0] 5: [0, 0, 0, 0] 5: ] -5: Compute joint node-pairs likelihood....: -5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -5: Total count, decomposition method: -5: 4x4 -5: [ -5: [2.77963e-07, 1.00058, 1.00009, 1.00159] -5: [1.00058, 6.39004e-07, 1.00032, 1.00007] -5: [1.00009, 1.00032, 4.08766e-07, 1.00069] -5: [1.00159, 1.00007, 1.00069, 5.17576e-07] -5: ] -5: Compute joint node-pairs likelihood....: -2: Br0 BrLen = 0.001 counts = 0.00103 +2: Br0 BrLen = 0.001 counts = 0.00109 2: 4x4 2: [ -2: [0, 1e-05, 7e-05, 0] -2: [5e-05, 0, 0.00017, 0.00016] -2: [8e-05, 0.00015, 0, 5e-05] -2: [1e-05, 0.00023, 5e-05, 0] +2: [0, 4e-05, 8e-05, 1e-05] +2: [3e-05, 0, 0.00015, 0.00021] +2: [9e-05, 0.00013, 0, 7e-05] +2: [3e-05, 0.00021, 4e-05, 0] 2: ] -2: Br1 BrLen = 0.002 counts = 0.00203 +2: Br1 BrLen = 0.002 counts = 0.00204 2: 4x4 2: [ -2: [0, 0.00012, 0.00019, 4e-05] -2: [7e-05, 0, 0.00022, 0.00041] -2: [0.00021, 0.00015, 0, 0.00012] -2: [1e-05, 0.00036, 0.00013, 0] +2: [0, 8e-05, 0.00018, 3e-05] +2: [0.0001, 0, 0.00024, 0.00037] +2: [0.00022, 0.00029, 0, 0.00014] +2: [1e-05, 0.00032, 6e-05, 0] 2: ] -2: Br2 BrLen = 0.003 counts = 0.00281 +2: Br2 BrLen = 0.003 counts = 0.00309 2: 4x4 2: [ -2: [0, 0.00012, 0.00022, 3e-05] -2: [6e-05, 0, 0.00032, 0.00049] -2: [0.00024, 0.00038, 0, 0.00014] -2: [4e-05, 0.00056, 0.00021, 0] +2: [0, 0.00011, 0.00033, 5e-05] +2: [0.00014, 0, 0.00054, 0.00059] +2: [0.00015, 0.00039, 0, 0.00011] +2: [2e-05, 0.0005, 0.00016, 0] 2: ] -2: Br3 BrLen = 0.01 counts = 0.01029 +2: Br3 BrLen = 0.01 counts = 0.01019 2: 4x4 2: [ -2: [0, 0.00048, 0.001, 0.00011] -2: [0.00031, 0, 0.00133, 0.00162] -2: [0.00096, 0.00127, 0, 0.00062] -2: [6e-05, 0.00196, 0.00057, 0] +2: [0, 0.00042, 0.00073, 0.0001] +2: [0.00029, 0, 0.00126, 0.00187] +2: [0.00092, 0.0014, 0, 0.00059] +2: [0.00015, 0.0019, 0.00056, 0] 2: ] -2: Br4 BrLen = 0.1 counts = 0.10075 +2: Br4 BrLen = 0.1 counts = 0.10014 2: 4x4 2: [ -2: [0, 0.0036, 0.00933, 0.00098] -2: [0.00374, 0, 0.01202, 0.01858] -2: [0.00903, 0.01246, 0, 0.00553] -2: [0.00111, 0.01848, 0.00589, 0] +2: [0, 0.00343, 0.0094, 0.00108] +2: [0.00336, 0, 0.01259, 0.0186] +2: [0.00864, 0.01278, 0, 0.00527] +2: [0.00089, 0.01846, 0.00564, 0] 2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 0.57 sec + 8/13 Test #2: test_detailed_simulations ........ Passed 0.56 sec +5: Compute joint node-pairs likelihood....: +5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. +5: Total count, decomposition method: +5: 4x4 +5: [ +5: [2.77963e-07, 1.00058, 1.00009, 1.00159] +5: [1.00058, 6.39004e-07, 1.00032, 1.00007] +5: [1.00009, 1.00032, 4.08766e-07, 1.00069] +5: [1.00159, 1.00007, 1.00069, 5.17576e-07] +5: ] +5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, decomposition method, type 1: 5: 4x4 @@ -1813,9 +1849,7 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 51 52.4931 52.4526 52.4526 52.4931 52.4931 52.4931 52.4931 -5: B 0.002 122 120.918 120.748 120.748 120.918 120.918 120.918 120.918 -5: 0.008 375 376.646 374.237 374.237 376.646 376.646 376.646 376.646 +5: A 0.001 52 52.1611 52.1224 52.1224 52.1611 52.1611 52.1611 52.1611 11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 11: ((A:1,B:2):3,C:4); 11: @@ -1844,15 +1878,17 @@ 11: Node 3: 11: Node 4: 11: B: ESS=2 +5: B 0.002 116 114.16 114 114 114.16 114.16 114.16 114.16 11: Newick I/O ok. -5: C 0.01 485 480.035 476.25 476.25 480.035 480.035 480.035 480.035 -5: D 0.02 1039 1039.52 1024.32 1024.32 1039.52 1039.52 1039.52 1039.52 -5: A 0.001 1.00798/1 1.00964/1 1.00964/1 6.0411/6 6.04468/6 6.04468/6 0.106583/0 0.107025/0 0.107025/0 2.98404/3 2.98467/3 2.98467/3 -5: B 0.002 3.01762/3 3.0225/3 3.0225/3 10.1767/10 10.1947/10 10.1947/10 1.00151/1 1.00135/1 1.00135/1 2.99459/3 3.00448/3 3.00448/3 -5: 0.008 14.6045/15 14.6484/15 14.6484/15 31.859/33 32.134/33 32.134/33 1.26393/2 1.29007/2 1.29007/2 12.0397/13 12.1295/13 12.1295/13 -5: C 0.01 17.1262/16 17.2721/16 17.2721/16 46.9215/48 47.3763/48 47.3763/48 8.01258/8 7.94755/8 7.94755/8 17.0179/16 17.1022/16 17.1022/16 -5: D 0.02 39.1202/40 39.4485/40 39.4485/40 98.3706/100 100.122/100 100.122/100 9.01559/9 9.02892/9 9.02892/9 29.5278/31 30.0328/31 30.0328/31 - 9/13 Test #5: test_mapping ..................... Passed 1.22 sec +5: 0.008 417 418.256 415.773 415.773 418.256 418.256 418.256 418.256 +5: C 0.01 524 520.869 517.002 517.002 520.869 520.869 520.869 520.869 +5: D 0.02 1004 1010.04 994.928 994.928 1010.04 1010.04 1010.04 1010.04 +5: A 0.001 0.00587231/0 0.0075341/0 0.0075341/0 5.27057/5 5.27387/5 5.27387/5 0.000892557/0 0.001466/0 0.001466/0 1.99189/2 1.99343/2 1.99343/2 +5: B 0.002 4.01091/4 4.01453/4 4.01453/4 6.08995/6 6.10831/6 6.10831/6 0.00426918/0 0.00711642/0 0.00711642/0 2.99642/3 3.00492/3 3.00492/3 +5: 0.008 15.3756/15 15.4351/15 15.4351/15 38.1252/38 38.4088/38 38.4088/38 1.53788/1 1.56278/1 1.56278/1 17.1346/16 17.1962/16 17.1962/16 +5: C 0.01 17.1357/19 17.2671/19 17.2671/19 45.1927/43 45.6233/43 45.6233/43 5.00911/5 4.99506/5 4.99506/5 20.1848/20 20.2893/20 20.2893/20 +5: D 0.02 31.473/30 32.0102/30 32.0102/30 93.7464/94 95.5064/94 95.5064/94 13.1874/14 13.0423/14 13.0423/14 32.8435/36 33.2594/36 33.2594/36 + 9/13 Test #5: test_mapping ..................... Passed 1.31 sec 11: Newick multiple I/O ok. 11: Testing parsing a directory... 11: Ok, reading on directory throws exception! @@ -1882,21 +1918,11 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 2.71 sec -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 -10: -10: 0.306746 0.321123 -10: 0.823943 0.828104 -10: 0.648461 0.644609 -10: 0.475169 0.472535 -10: 0.287152 0.292358 -10: Detailed check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 193 +10/13 Test #11: test_tree ........................ Passed 2.76 sec 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...............: 1018 -6: 96567 +6: Number of distinct sites...............: 1012 +6: 96291.1 6: Analytical total count: 6: 64x64 6: [ @@ -1966,15 +1992,7 @@ 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....: -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: 0.306746 0.306016 -10: 0.823943 0.809866 -10: 0.648461 0.643177 -10: 0.475169 0.467639 -10: 0.287152 0.290926 -11/13 Test #10: test_simulations ................. Passed 6.83 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%0.0398 0.0052 +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 0.0063 1: ..:: Testing with homogeneous, non-stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: @@ -2257,17 +2275,35 @@ 6: ] 6: Compute joint node-pairs likelihood....: 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -12/13 Test #6: test_mapping_codon ............... Passed 8.15 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%0.0449 0.008 +11/13 Test #6: test_mapping_codon ............... Passed 8.18 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%0.0433 0.0061 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%0.9331 0.8048 +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 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 +10: +10: 0.419915 0.404289 +10: 0.317124 0.298407 +10: 0.705476 0.697946 +10: 0.0307086 0.0236168 +10: 0.4362 0.437161 +10: Detailed check: +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 195 +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%0.936 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%0.0435 0.0063 -13/13 Test #1: test_bowker ...................... Passed 33.60 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%0.038 0.0059 +12/13 Test #1: test_bowker ...................... Passed 32.80 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 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 Optimizing... - 56 Optimizing... / 57 Optimizing... - 58 Optimizing... \ 59 Optimizing... - 60 Optimizing... / 61 +10: +10: 0.419915 0.441194 +10: 0.317124 0.308263 +10: 0.705476 0.705024 +10: 0.0307086 0.0194259 +10: 0.4362 0.434098 +13/13 Test #10: test_simulations ................. Passed 39.16 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 33.61 sec +Total Test time (real) = 39.19 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 @@ -2573,9 +2609,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-11_arm64.deb'. dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-11_arm64.deb'. dpkg-deb: building package 'libbpp-phyl12t64' in '../libbpp-phyl12t64_2.4.1-11_arm64.deb'. +dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-11_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-11_arm64.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2583,12 +2619,14 @@ 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/4123576/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4123576/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/3636918 and its subdirectories -I: Current time: Mon Dec 22 16:38:37 -12 2025 -I: pbuilder-time-stamp: 1766464718 +I: removing directory /srv/workspace/pbuilder/4123576 and its subdirectories +I: Current time: Wed Nov 20 12:20:10 +14 2024 +I: pbuilder-time-stamp: 1732054810