Diff of the two buildlogs: -- --- b1/build.log 2025-09-08 19:27:26.415891317 +0000 +++ b2/build.log 2025-09-08 19:29:47.116076384 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 8 07:23:13 -12 2025 -I: pbuilder-time-stamp: 1757359393 +I: Current time: Mon Oct 12 15:50:27 +14 2026 +I: pbuilder-time-stamp: 1791769827 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ 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/2675403/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3768367/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 12 01:50 /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/3768367/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3768367/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='573f617b89f04d4ab56c0255a6ff771d' - 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='2675403' - PS1='# ' - PS2='> ' + INVOCATION_ID=346f6fc97ac74a4fb0ebeb0f78d9b1b5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3768367 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.BpI4oxbY/pbuilderrc_I5nU --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BpI4oxbY/b1 --logfile b1/build.log libbpp-phyl_2.4.1-11.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.BpI4oxbY/pbuilderrc_P8yR --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BpI4oxbY/b2 --logfile b2/build.log libbpp-phyl_2.4.1-11.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2675403/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3768367/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -178,7 +210,7 @@ Get: 62 http://deb.debian.org/debian forky/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libbpp-seq12t64 amd64 2.4.1-13 [510 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libbpp-seq-dev amd64 2.4.1-13 [745 kB] -Fetched 34.3 MB in 13s (2628 kB/s) +Fetched 34.3 MB in 2s (15.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -449,7 +481,11 @@ 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/3768367/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3768367/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 @@ -501,7 +537,7 @@ -- Build files have been written to: /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -514,267 +550,267 @@ make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 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/AbstractAgglomerativeDistanceMethod.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.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-static.dir/Bpp/Phyl/BipartitionList.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o +[ 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-x86_64-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 -fcf-protection -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/BipartitionTools.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/BipartitionList.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-static.dir/Bpp/Phyl/BipartitionList.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/AbstractAgglomerativeDistanceMethod.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o +[ 2%] 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-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.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-x86_64-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 -fcf-protection -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 -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT 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object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o +[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp -[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -cd 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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 -[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp In file included from /usr/include/x86_64-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, @@ -801,8 +837,16 @@ /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))); | ^ -[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp +[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF 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CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp [ 53%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o @@ -965,279 +999,281 @@ cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c 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-o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp [ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp -[ 55%] Building CXX object 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp -[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o [ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp -[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o +[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp +[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp +[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp +[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.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-shared.dir/Bpp/Phyl/TreeTools.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp [ 92%] Linking CXX static library libbpp-phyl.a cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bpp-phyl-static.dir/cmake_clean_target.cmake @@ -1253,11 +1289,11 @@ 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-x86_64-linux-gnu' -make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend +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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake "--color=" +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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_likelihood.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend @@ -1266,19 +1302,19 @@ 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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_mapping.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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_models.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend +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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_simulations.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' @@ -1289,69 +1325,69 @@ cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-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-x86_64-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]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu' make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build -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-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 92%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o [ 92%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +[ 93%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 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/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 +[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_nhx.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_models.dir/test_models.cpp.o -MF CMakeFiles/test_models.dir/test_models.cpp.o.d -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_models.cpp -[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -[ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 +[ 95%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o [ 95%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o -[ 95%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 +[ 96%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 +[ 96%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_simulations.cpp -[ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -MF CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o.d -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp [ 96%] Linking CXX executable test_tree_getpath cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_getpath.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 @@ -1367,13 +1403,13 @@ /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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_tree_rootat -[ 98%] Linking CXX executable test_parsimony [ 98%] Linking CXX executable test_models cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_models.dir/link.d CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_models +[ 98%] Linking CXX executable test_parsimony +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_parsimony @@ -1394,19 +1430,23 @@ [ 99%] Built target test_likelihood [100%] Linking CXX executable test_mapping_codon cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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-x86_64-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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[100%] Linking CXX executable test_detailed_simulations [100%] Linking CXX executable test_bowker cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 -[100%] Built target test_detailed_simulations +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 +c.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-x86_64-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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[100%] Built target test_detailed_simulations [100%] Built target test_bowker -[100%] Built target test_mapping_codon +[100%] Built target bpp-phyl-static [100%] Linking CXX executable test_simulations cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 @@ -1417,18 +1457,14 @@ /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 -fcf-protection -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-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_mapping -c.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-x86_64-linux-gnu' -[100%] Built target bpp-phyl-static make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j40 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -1540,39 +1576,6 @@ 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: 65.72293577215015147885 -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 -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: 65.72293577215069149133 -3: * likelihood after full optimization...: 65.7229 -3: Initializing data structure............: Done. -3: Number of distinct sites...............: 12 -3: Initializing data structure............: Done. -3: Number of distinct sites...............: 12 -3: BrLen0 -212.54368339472844695592 -212.54368339472844695592 -3: BrLen1 -107.42239645667785907790 -107.42239645667787328875 -3: BrLen2 3.41183634475365238359 3.41183634475364838679 -3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 -3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. 4: Initializing data structure............: Done. 4: Number of distinct sites...............: 14 @@ -1589,19 +1592,17 @@ 5: [0.0518135, 0.906736, 0.272021, -1.23057] 5: ] 6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. + 1/13 Test #8: test_nhx ......................... Passed 0.01 sec 9: Initializing data structure............: Done. 9: Number of distinct sites...............: 9 9: Parsimony score: 9 - 1/13 Test #3: test_likelihood .................. Passed 0.09 sec - 2/13 Test #7: test_models ...................... Passed 0.09 sec - 3/13 Test #8: test_nhx ......................... Passed 0.09 sec - 4/13 Test #9: test_parsimony ................... Passed 0.09 sec + 2/13 Test #9: test_parsimony ................... Passed 0.01 sec 10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.752282 -10: Theta1 set to 0.172484 -10: Theta2 set to 0.648525 -10: Theta3 set to 0.824042 -10: Theta4 set to 0.866869 +10: Theta0 set to 0.405151 +10: Theta1 set to 0.718785 +10: Theta2 set to 0.0807994 +10: Theta3 set to 0.280022 +10: Theta4 set to 0.96411 10: Fast check: 12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 12: Id node1 0 @@ -1618,6 +1619,7 @@ 12: 4 12: 3 12: 2 + 3/13 Test #12: test_tree_getpath ................ Passed 0.01 sec 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: 71.26579958637299228 @@ -1632,16 +1634,32 @@ 4: BrLen5 0.448312 [ 1e-06; 10000] 4: T92.kappa 0.996464 ]0; +inf[ 4: T92.theta 0.579955 ]1e-06; 0.999999[ - 5/13 Test #12: test_tree_getpath ................ Passed 0.01 sec -13: Total length...........................: 105.311 4: Initializing data structure............: Done. 4: Number of distinct sites...............: 14 4: Test model.............................: T92 4: 92.32951163315719611546 4: * initial likelihood...................: 92.3295 - 6/13 Test #13: test_tree_rootat ................. Passed 0.07 sec -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 186 +13: Total length...........................: 105.332 +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: 65.72293577215015147885 +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: 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: 71.26579406919438497425 @@ -1653,11 +1671,29 @@ 4: HeightP2 0.819072 [ 0; 1] 4: T92.kappa 0.996398 ]0; +inf[ 4: T92.theta 0.579960 ]1e-06; 0.999999[ - 7/13 Test #4: test_likelihood_clock ............ Passed 0.36 sec + 4/13 Test #4: test_likelihood_clock ............ Passed 0.03 sec + 5/13 Test #7: test_models ...................... Passed 0.04 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: 65.72293577215069149133 +3: * likelihood after full optimization...: 65.7229 +3: Initializing data structure............: Done. +3: Number of distinct sites...............: 12 +3: Initializing data structure............: Done. +3: Number of distinct sites...............: 12 +3: BrLen0 -212.54368339472844695592 -212.54368339472844695592 +3: BrLen1 -107.42239645667785907790 -107.42239645667787328875 +3: BrLen2 3.41183634475365238359 3.41183634475364838679 +3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 +3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 + 6/13 Test #3: test_likelihood .................. Passed 0.05 sec + 7/13 Test #13: test_tree_rootat ................. Passed 0.07 sec +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 179 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...............: 73 -5: 76862.6 +5: Number of distinct sites...............: 71 +5: 77169.2 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1687,47 +1723,47 @@ 5: [0, 0, 0, 0] 5: ] 5: Compute joint node-pairs likelihood....: -2: Br0 BrLen = 0.001 counts = 0.00087 +2: Br0 BrLen = 0.001 counts = 0.00078 2: 4x4 2: [ -2: [0, 2e-05, 6e-05, 1e-05] -2: [3e-05, 0, 8e-05, 0.00011] -2: [0.00015, 0.00012, 0, 7e-05] -2: [0, 0.00018, 4e-05, 0] +2: [0, 2e-05, 7e-05, 2e-05] +2: [4e-05, 0, 0.00011, 0.00018] +2: [6e-05, 9e-05, 0, 3e-05] +2: [3e-05, 0.0001, 3e-05, 0] 2: ] -2: Br1 BrLen = 0.002 counts = 0.00208 +2: Br1 BrLen = 0.002 counts = 0.00226 2: 4x4 2: [ -2: [0, 0.0001, 0.00026, 1e-05] -2: [6e-05, 0, 0.00024, 0.0004] -2: [0.00011, 0.00022, 0, 0.00013] -2: [3e-05, 0.00047, 5e-05, 0] +2: [0, 9e-05, 0.00016, 2e-05] +2: [6e-05, 0, 0.00023, 0.00057] +2: [0.0002, 0.00025, 0, 0.0001] +2: [2e-05, 0.00049, 7e-05, 0] 2: ] -2: Br2 BrLen = 0.003 counts = 0.0031 +2: Br2 BrLen = 0.003 counts = 0.00317 2: 4x4 2: [ -2: [0, 0.00015, 0.00039, 3e-05] -2: [0.0001, 0, 0.00036, 0.00055] -2: [0.00025, 0.00031, 0, 0.00017] -2: [4e-05, 0.00056, 0.00019, 0] +2: [0, 0.00012, 0.00035, 3e-05] +2: [9e-05, 0, 0.00037, 0.00048] +2: [0.00034, 0.00039, 0, 0.00015] +2: [3e-05, 0.00059, 0.00023, 0] 2: ] -2: Br3 BrLen = 0.01 counts = 0.00974 +2: Br3 BrLen = 0.01 counts = 0.01009 2: 4x4 2: [ -2: [0, 0.00053, 0.00098, 8e-05] -2: [0.00028, 0, 0.00126, 0.00186] -2: [0.00075, 0.0012, 0, 0.00054] -2: [0.00011, 0.00163, 0.00052, 0] +2: [0, 0.00031, 0.00096, 0.00018] +2: [0.00036, 0, 0.0013, 0.00177] +2: [0.001, 0.00132, 0, 0.00051] +2: [8e-05, 0.00171, 0.00059, 0] 2: ] -2: Br4 BrLen = 0.1 counts = 0.10026 +2: Br4 BrLen = 0.1 counts = 0.09852 2: 4x4 2: [ -2: [0, 0.00356, 0.0093, 0.00095] -2: [0.00333, 0, 0.01318, 0.01773] -2: [0.00874, 0.01234, 0, 0.00572] -2: [0.00103, 0.01895, 0.00543, 0] +2: [0, 0.00363, 0.00854, 0.00109] +2: [0.00316, 0, 0.01238, 0.01832] +2: [0.00888, 0.013, 0, 0.00506] +2: [0.00107, 0.0178, 0.00559, 0] 2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 0.52 sec + 8/13 Test #2: test_detailed_simulations ........ Passed 0.51 sec 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Total count, decomposition method: 5: 4x4 @@ -1842,12 +1878,8 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 54 53.2643 53.2247 53.2247 53.2643 53.2643 53.2643 53.2643 -5: B 0.002 83 84.0627 83.9271 83.9271 84.0627 84.0627 84.0627 84.0627 -5: 0.008 412 408.007 405.552 405.552 408.007 408.007 408.007 408.007 -5: C 0.01 509 508.487 504.682 504.682 508.487 508.487 508.487 508.487 -5: D 0.02 966 959.26 944.242 944.242 959.26 959.26 959.26 959.26 -5: A 0.001 0.999656/1 1.0013/1 1.0013/1 2.02976/2 2.03318/2 2.03318/2 0.000173579/0 0.000849325/0 0.000849325/0 4.97248/5 4.97051/5 4.97051/5 +5: A 0.001 47 45.8999 45.8643 45.8643 45.8999 45.8999 45.8999 45.8999 +5: B 0.002 106 105.391 105.233 105.233 105.391 105.391 105.391 105.391 11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 11: ((A:1,B:2):3,C:4); 11: @@ -1876,13 +1908,17 @@ 11: Node 3: 11: Node 4: 11: B: ESS=2 -5: B 0.002 2.02962/2 2.03365/2 2.03365/2 5.57801/6 5.59341/6 5.59341/6 0.999991/1 0.998943/1 0.998943/1 0.00215354/0 0.00721886/0 0.00721886/0 -5: 0.008 13.6088/15 13.7005/15 13.7005/15 37.7358/37 38.0151/37 38.0151/37 6.15918/6 6.12488/6 6.12488/6 18.3933/19 18.4264/19 18.4264/19 -5: C 0.01 21.1735/22 21.27/22 21.27/22 41.3892/42 41.8562/42 41.8562/42 5.21127/5 5.19102/5 5.19102/5 17.5766/18 17.7017/18 17.7017/18 -5: D 0.02 34.1148/36 34.5015/36 34.5015/36 86.8846/90 88.5638/90 88.5638/90 6.01532/6 6.07906/6 6.07906/6 29.0287/29 29.5879/29 29.5879/29 - 9/13 Test #5: test_mapping ..................... Passed 1.10 sec 11: Newick I/O ok. -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%0.0365 0.0051 +5: 0.008 368 367.538 365.174 365.174 367.538 367.538 367.538 367.538 +5: C 0.01 535 532.581 528.615 528.615 532.581 532.581 532.581 532.581 +5: D 0.02 1000 1010.9 995.53 995.53 1010.9 1010.9 1010.9 1010.9 +5: A 0.001 0.00876016/0 0.0107211/0 0.0107211/0 4.03994/5 4.0431/5 4.0431/5 0.000531729/0 0.00093068/0 0.00093068/0 0.996501/1 0.997055/1 0.997055/1 +5: B 0.002 5.00466/5 5.00936/5 5.00936/5 4.02256/4 4.04367/4 4.04367/4 1.99968/2 1.99611/2 1.99611/2 2.99586/3 3.00118/3 3.00118/3 +5: 0.008 9.67163/10 9.74999/10 9.74999/10 38.0774/38 38.3349/38 38.3349/38 4.01348/4 4.00091/4 4.00091/4 9.76755/10 9.8535/10 9.8535/10 +5: C 0.01 17.5741/17 17.6895/17 17.6895/17 43.4788/45 43.9256/45 43.9256/45 4.41782/5 4.41742/5 4.41742/5 22.0802/21 22.1857/21 22.1857/21 +5: D 0.02 37.4152/39 37.7831/39 37.7831/39 90.4275/90 92.1673/90 92.1673/90 7.02235/7 7.06928/7 7.06928/7 39.8745/41 40.3174/41 40.3174/41 + 9/13 Test #5: test_mapping ..................... Passed 1.22 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%0.0386 0.006 1: ..:: Testing with homogeneous, non-stationary model ::.. 11: Newick multiple I/O ok. 11: Testing parsing a directory... @@ -1913,13 +1949,23 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 3.38 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%0.0411 0.0056 +10/13 Test #11: test_tree ........................ Passed 3.17 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: +10: 0.405151 0.391231 +10: 0.718785 0.702117 +10: 0.0807994 0.0818896 +10: 0.280022 0.292329 +10: 0.96411 0.963051 +10: Detailed check: +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 180 +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%0.041 0.0061 1: ..:: Testing with non-homogeneous, non-stationary model ::.. 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...............: 987 -6: 96251.3 +6: Number of distinct sites...............: 975 +6: 96548.3 6: Analytical total count: 6: 64x64 6: [ @@ -1989,16 +2035,6 @@ 6: [3.00169, 3.00145, 3.00139, 2.00023, 3.00149, 3.00181, 3.00139, 2.00023, 3.00136, 3.0016, 3.00152, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00144, 3.0014, 3.00135, 2.00023, 3.00092, 3.00161, 3.00111, 2.00023, 3.00164, 3.00171, 3.0018, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00157, 3.00128, 3.00143, 2.00023, 3.00155, 3.0017, 3.00158, 2.00023, 3.00136, 3.0013, 3.00154, 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 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 -10: -10: 0.752282 0.758249 -10: 0.172484 0.181013 -10: 0.648525 0.652083 -10: 0.824042 0.831329 -10: 0.866869 0.867868 -10: Detailed check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 180 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: 6: 64x64 @@ -2231,6 +2267,8 @@ 6: [1.50017, 1.00029, 2.00008, 1.00012, 1.00021, 1.00017, 1.50012, 1.00012, 1.50017, 1.00029, 2.00008, 1.00012, 0.000116061, 0.000116055, 1, 9.4154e-08, 2.50022, 2.0004, 2.83347, 2.00023, 2.00029, 2.0003, 2.33354, 2.00023, 1.83361, 2.00026, 2.16692, 2.00023, 1.00015, 1.00017, 1.50006, 1.00012, 2.50022, 2.00037, 2.8335, 2.00023, 2.00031, 2.00026, 2.33359, 2.00023, 2.1669, 2.00033, 2.50021, 2.00023, 1.00019, 1.00017, 1.5001, 1.00012, 0, 2.00031, 0, 2.00023, 2.16688, 2.00028, 2.50017, 2.00023, 0, 2.0004, 3.00011, 2.00023, 1.50012, 1.00029, 2.00002, 1.00012] 6: [1.00006, 2.00008, 1.00029, 2.00008, 2.00017, 2.50046, 2.00097, 2.50069, 1.50022, 2.6666, 1.50059, 2.667, 2.00015, 2.49936, 2.33361, 2.49946, 9.41499e-08, 1, 0.000231997, 1, 1.00012, 1.5001, 1.00023, 1.5001, 1.00012, 1.50009, 1.00023, 1.50009, 1.00012, 1.5001, 1.00023, 1.5001, 1.00006, 2.00008, 1.00029, 2.00008, 2.00019, 2.50047, 2.0004, 2.4997, 2.00015, 2.50053, 2.00009, 2.50052, 2.00017, 2.50034, 2.00055, 2.50027, 0, 2.00015, 0, 2.00015, 2.00023, 2.49989, 2.00015, 2.50037, 0, 2.66684, 2.00027, 2.6667, 1.00046, 2.50055, 1.00077, 2.50053] 6: [2.00008, 1.00012, 2.00008, 1.00035, 2.49957, 2.00023, 2.50033, 2.00049, 2.50025, 2.00023, 2.50029, 2.00058, 2.50016, 2.00023, 2.83375, 2.00069, 1, 1.07606e-07, 1, 0.000232029, 1.50011, 1.00012, 1.50011, 1.00023, 1.50011, 1.00012, 1.50011, 1.00023, 1.50011, 1.00012, 1.50011, 1.00023, 2.00008, 1.00012, 2.00008, 1.00035, 2.50037, 2.00023, 2.49999, 2.00043, 2.50034, 2.00023, 2.5001, 2.00039, 2.50033, 2.00023, 2.50027, 2.00031, 0, 1.00012, 0, 1.00019, 2.2504, 2.00023, 2.25042, 2.0003, 0, 2.00023, 2.75038, 2.00027, 2.25045, 2.00023, 2.2504, 2.00056] +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%0.933 0.7978 +1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [1.00029, 2.00008, 1.00006, 2.00008, 2.00049, 2.50051, 2.00017, 2.49959, 1.50055, 2.66677, 1.50026, 2.66696, 2.3339, 2.83463, 2.00015, 2.83394, 0.000231997, 1, 9.41494e-08, 1, 1.00023, 1.5001, 1.00012, 1.5001, 1.00023, 1.5001, 1.00012, 1.5001, 1.00023, 1.5001, 1.00012, 1.5001, 1.00029, 2.00008, 1.00006, 2.00008, 2.00048, 2.49984, 2.00019, 2.5002, 2.00013, 2.49978, 2.00017, 2.49996, 2.0001, 2.50033, 2.00017, 2.49999, 0, 2.00015, 0, 2.00015, 2.0005, 2.50082, 2.00027, 2.5004, 0, 2.75024, 2.00023, 2.75038, 1.00072, 2.50007, 1.00054, 2.50002] 6: [2.00008, 1.00035, 2.00008, 1.00012, 2.50028, 2.0004, 2.5002, 2.00023, 2.50008, 2.0005, 2.5001, 2.00023, 2.50009, 2.00029, 2.83343, 2.00023, 1, 0.000232029, 1, 1.07606e-07, 1.50011, 1.00023, 1.50011, 1.00012, 1.50011, 1.00023, 1.50011, 1.00012, 1.50011, 1.00023, 1.50011, 1.00012, 2.00008, 1.00035, 2.00008, 1.00012, 2.5001, 2.00036, 2.50025, 2.00023, 2.50019, 2.00034, 2.50025, 2.00023, 2.50006, 2.00035, 2.50019, 2.00023, 0, 1.00019, 0, 1.00012, 2.2502, 2.00027, 2.25027, 2.00023, 0, 2.00032, 2.7502, 2.00023, 2.25023, 2.0004, 2.25031, 2.00023] 6: [2.00017, 2.50018, 2.00029, 2.50018, 1.00012, 1.00012, 1.00012, 1.00012, 1.50024, 2.16688, 1.50035, 2.16691, 2.00019, 2.00063, 2.33371, 2.00024, 1.00012, 1.50011, 1.00023, 1.50011, 8.07051e-08, 8.29459e-08, 8.07051e-08, 8.29459e-08, 1.00012, 1.00014, 1.00012, 1.00014, 1.00012, 1.00014, 1.00012, 1.00014, 2.00019, 2.5001, 2.00037, 2.50008, 1.00012, 1.00012, 1.00012, 1.00012, 2.00017, 2.00024, 2.00021, 2.00033, 2.00021, 2.00018, 2.00023, 2.00015, 0, 2.25033, 0, 2.25028, 1.00012, 1.00012, 1.00012, 1.00012, 0, 2.00029, 2.00023, 2.00028, 1.50021, 2.16692, 1.50035, 2.16681] @@ -2279,29 +2317,27 @@ 6: [2.75035, 2.00021, 3, 2.00023, 2.3334, 2.00039, 2.49994, 2.00023, 2.74999, 2.00034, 2.99996, 2.00023, 1.50015, 1.00029, 2.00008, 1.00012, 2.50014, 2.00014, 2.50011, 2.00023, 2.16633, 2.00021, 2.16649, 2.00023, 2.00034, 2.0003, 2.33363, 2.00023, 1.00015, 1.00019, 1.00017, 1.00012, 2.75019, 2.00008, 2.7501, 2.00023, 2.33341, 2.0003, 2.33346, 2.00023, 2.2501, 2.00005, 2.50008, 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....: -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%0.9342 0.8038 -1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -11/13 Test #6: test_mapping_codon ............... Passed 8.73 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%0.0411 0.005 -12/13 Test #1: test_bowker ...................... Passed 11.28 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 +11/13 Test #6: test_mapping_codon ............... Passed 8.72 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 10: -10: 0.752282 0.752828 -10: 0.172484 0.18785 -10: 0.648525 0.633612 -10: 0.824042 0.833591 -10: 0.866869 0.869534 -13/13 Test #10: test_simulations ................. Passed 13.17 sec +10: 0.405151 0.421096 +10: 0.718785 0.741778 +10: 0.0807994 0.0899008 +10: 0.280022 0.26765 +10: 0.96411 0.965941 +12/13 Test #10: test_simulations ................. Passed 10.08 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%0.0397 0.005 +13/13 Test #1: test_bowker ...................... Passed 11.16 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 13.18 sec +Total Test time (real) = 11.16 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2319,237 +2355,237 @@ -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-phyl.so -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RASTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Mapping.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionMethods.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionReward.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Reward.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Tree.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/OptimizationTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNITopologySearch.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/AncestralStateReconstruction.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WrappedModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/InMixedSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWrappedModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h --- Installing: 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/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M2.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h -- Installing: 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/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h +-- Installing: 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/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h --- Installing: 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/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Tree.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets.cmake -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' @@ -2598,9 +2634,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-11_amd64.deb'. dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-11_amd64.deb'. dpkg-deb: building package 'libbpp-phyl12t64' in '../libbpp-phyl12t64_2.4.1-11_amd64.deb'. +dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-11_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-11_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-11_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2608,12 +2644,14 @@ 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/3768367/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3768367/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/2675403 and its subdirectories -I: Current time: Mon Sep 8 07:27:26 -12 2025 -I: pbuilder-time-stamp: 1757359646 +I: removing directory /srv/workspace/pbuilder/3768367 and its subdirectories +I: Current time: Mon Oct 12 15:52:46 +14 2026 +I: pbuilder-time-stamp: 1791769966