Diff of the two buildlogs: -- --- b1/build.log 2025-03-12 09:23:52.969988767 +0000 +++ b2/build.log 2025-03-12 09:26:54.537812823 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Mar 11 20:55:12 -12 2025 -I: pbuilder-time-stamp: 1741769712 +I: Current time: Wed Apr 15 05:46:51 +14 2026 +I: pbuilder-time-stamp: 1776181611 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying remove_test_likelihood_nh.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/972581/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3663368/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 14 15:47 /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/3663368/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3663368/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a55bd3eeb708442db4338f5d1d3fcce9' - 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='972581' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ab110e87fe943e2838ea062e5378f81 + 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=3663368 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.Tod8ISYN/pbuilderrc_6bVz --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Tod8ISYN/b1 --logfile b1/build.log libbpp-phyl_2.4.1-11.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Tod8ISYN/pbuilderrc_Vtpf --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Tod8ISYN/b2 --logfile b2/build.log libbpp-phyl_2.4.1-11.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/972581/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3663368/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: 63 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libbpp-seq12t64 amd64 2.4.1-13 [510 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libbpp-seq-dev amd64 2.4.1-13 [745 kB] -Fetched 43.6 MB in 2s (28.4 MB/s) +Fetched 43.6 MB in 7s (6331 kB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0: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 ... 19783 files and directories currently installed.) @@ -453,7 +485,11 @@ 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/3663368/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3663368/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 @@ -493,8 +529,8 @@ -- shared lib: /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (1.6s) --- Generating done (0.8s) +-- Configuring done (1.9s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -505,7 +541,7 @@ -- 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 -j20 "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 @@ -518,215 +554,253 @@ 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 -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-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 -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build -[ 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 -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 -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 -[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-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/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp 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' +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-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 [ 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/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 -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.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/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o +[ 1%] 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/DistanceEstimation.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/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-static.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-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o +[ 3%] 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/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 +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o +[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-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 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=. 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.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/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp +[ 7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o +cd 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9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o +[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.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/Io/NexusIoTree.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp +[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.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/Io/IoSubstitutionModelFactory.cpp.o -MF 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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 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, @@ -753,118 +827,50 @@ /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))); | ^ -[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.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 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/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_M10.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.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, @@ -891,365 +897,388 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return 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test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend make -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/depend make -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/depend -make[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_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' 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.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 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"--color=" -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.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[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_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build +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[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 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'/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[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 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/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.dir/DependInfo.cmake "--color=" +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_tree_getpath.dir/DependInfo.cmake "--color=" +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_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 -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.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[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_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' -[ 93%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.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.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood.cpp -[ 93%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-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_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-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[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.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.dir/build.make test/CMakeFiles/test_mapping.dir/build make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build make[3]: Entering 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/depend -make[3]: Leaving 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]: 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]: Leaving 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]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 93%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -[ 93%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend -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 -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/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 +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]: 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_parsimony.dir/build.make test/CMakeFiles/test_parsimony.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' -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.dir/DependInfo.cmake "--color=" -[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o 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/depend -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_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.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_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 make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build -[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -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/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 +make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build +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[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_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' -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_getpath.dir/DependInfo.cmake "--color=" 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_tree_rootat.dir/DependInfo.cmake "--color=" -make[3]: Leaving 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 -[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o 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_detailed_simulations.dir/test_detailed_simulations.cpp.o +[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.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 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test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o [ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o +[ 95%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o +[ 95%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o +[ 95%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o +[ 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 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"CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o" "CMakeFiles/bpp-phyl-stati[ 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 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' @@ -1376,17 +1408,17 @@ 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_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 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 /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 +/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' 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 +[ 98%] Built target test_parsimony [ 98%] Linking CXX executable test_tree 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.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 /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.dir/link.d CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-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 @@ -1394,27 +1426,27 @@ cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_likelihood_clock.dir/link.d CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-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' +[ 99%] Linking CXX executable test_likelihood +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.dir/link.txt --verbose=1 [ 99%] Built target test_likelihood_clock -[ 99%] 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_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 +/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_likelihood.dir/link.d CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-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' -[ 99%] Built target test_detailed_simulations +[ 99%] Built target test_likelihood [ 99%] 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 -/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' -[ 99%] Built target test_bowker +[ 99%] 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 [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 +/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_bowker +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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_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 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_mapping_codon -[100%] Linking CXX executable test_likelihood -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.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_likelihood.dir/link.d CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-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_likelihood [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 @@ -1425,14 +1457,18 @@ /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 -j20 test ARGS\+=--verbose ARGS\+=-j20 + 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 -j20 +/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 @@ -1544,9 +1580,30 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 +4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +4: Test model.............................: T92 +4: 94.395699097704181213 +4: * initial likelihood...................: 94.3957 +4: Log-likelihood after adding clock......: 94.3957 +5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +5: 4x4 +5: [ +5: [-1.37306, 0.362694, 0.906736, 0.103627] +5: [0.103627, -0.984456, 0.362694, 0.518135] +5: [0.259067, 0.362694, -0.777202, 0.15544] +5: [0.0518135, 0.906736, 0.272021, -1.23057] +5: ] +6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +9: Initializing data structure............: Done. +9: Number of distinct sites...............: 9 +9: Parsimony score: 9 + 1/13 Test #8: test_nhx ......................... Passed 0.01 sec + 2/13 Test #9: test_parsimony ................... Passed 0.01 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: 65.72293577215039306338 +3: 65.72293577215015147885 3: * likelihood after full optimization...: 65.7229 3: Testing Double Tree Traversal likelihood class... 3: Initializing data structure............: Done. @@ -1558,19 +1615,36 @@ 3: A: x = 0.5, f = 80.2872 3: B: x = 2.11803, f = 71.6905 3: C: x = 2.76139, f = 71.7653 +10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +10: Theta0 set to 0.491553 +10: Theta1 set to 0.0279114 +10: Theta2 set to 0.816803 +10: Theta3 set to 0.732081 +10: Theta4 set to 0.922238 +10: Fast check: 3: Step scale factor Function Time 3: 0 2.11803 71.690520 0.000000 3: Optimizing... / 11 2.11803 71.690520 0.000000 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 94.395699097704181213 -4: * initial likelihood...................: 94.3957 -4: Log-likelihood after adding clock......: 94.3957 +12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +12: Id node1 0 +12: Id node2 1 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 1 +12: Id node1 0 +12: Id node3 2 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 2 + 3/13 Test #12: test_tree_getpath ................ Passed 0.01 sec +13: Total length...........................: 94.4248 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 @@ -1592,7 +1666,7 @@ 4: * initial likelihood...................: 92.3295 4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 4: -4: 71.26579406919543657750 +4: 71.26579406919438497425 4: * likelihood after full optimization...: 71.2658 4: Name: Value: Constraint: 4: _________________________________________________ @@ -1601,46 +1675,7 @@ 4: HeightP2 0.819072 [ 0; 1] 4: T92.kappa 0.996398 ]0; +inf[ 4: T92.theta 0.579960 ]1e-06; 0.999999[ -5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -5: 4x4 -5: [ -5: [-1.37306, 0.362694, 0.906736, 0.103627] -5: [0.103627, -0.984456, 0.362694, 0.518135] -5: [0.259067, 0.362694, -0.777202, 0.15544] -5: [0.0518135, 0.906736, 0.272021, -1.23057] -5: ] -6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -9: Initializing data structure............: Done. -9: Number of distinct sites...............: 9 -9: Parsimony score: 9 - 1/13 Test #8: test_nhx ......................... Passed 0.14 sec - 2/13 Test #9: test_parsimony ................... Passed 0.13 sec - 3/13 Test #4: test_likelihood_clock ............ Passed 0.24 sec -10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.975371 -10: Theta1 set to 0.854676 -10: Theta2 set to 0.833838 -10: Theta3 set to 0.96089 -10: Theta4 set to 0.682296 -10: Fast check: -12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -12: Id node1 0 -12: Id node2 1 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 1 -12: Id node1 0 -12: Id node3 2 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 2 - 4/13 Test #12: test_tree_getpath ................ Passed 0.10 sec -13: Total length...........................: 100.561 - 5/13 Test #7: test_models ...................... Passed 0.27 sec + 4/13 Test #4: test_likelihood_clock ............ Passed 0.03 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 @@ -1654,55 +1689,15 @@ 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 0.43 sec - 7/13 Test #13: test_tree_rootat ................. Passed 0.73 sec + 5/13 Test #3: test_likelihood .................. Passed 0.05 sec + 6/13 Test #7: test_models ...................... Passed 0.04 sec + 7/13 Test #13: test_tree_rootat ................. Passed 0.07 sec 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 177 +10: Number of distinct sites...............: 182 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. -2: Br0 BrLen = 0.001 counts = 0.00097 -2: 4x4 -2: [ -2: [0, 4e-05, 5e-05, 1e-05] -2: [6e-05, 0, 0.00012, 0.00014] -2: [7e-05, 0.00014, 0, 5e-05] -2: [0, 0.00023, 6e-05, 0] -2: ] -2: Br1 BrLen = 0.002 counts = 0.00201 -2: 4x4 -2: [ -2: [0, 2e-05, 0.00017, 0] -2: [9e-05, 0, 0.00015, 0.00041] -2: [0.00022, 0.00031, 0, 0.00011] -2: [1e-05, 0.00044, 8e-05, 0] -2: ] -2: Br2 BrLen = 0.003 counts = 0.00316 -2: 4x4 -2: [ -2: [0, 0.00014, 0.00028, 4e-05] -2: [0.00013, 0, 0.00036, 0.00051] -2: [0.0003, 0.00038, 0, 0.00017] -2: [2e-05, 0.00061, 0.00022, 0] -2: ] -2: Br3 BrLen = 0.01 counts = 0.00988 -2: 4x4 -2: [ -2: [0, 0.00034, 0.00096, 8e-05] -2: [0.00025, 0, 0.00122, 0.00199] -2: [0.00062, 0.00135, 0, 0.0007] -2: [6e-05, 0.00189, 0.00042, 0] -2: ] -2: Br4 BrLen = 0.1 counts = 0.10027 -2: 4x4 -2: [ -2: [0, 0.00371, 0.00909, 0.00112] -2: [0.00356, 0, 0.01296, 0.01813] -2: [0.00956, 0.01267, 0, 0.00519] -2: [0.00106, 0.01796, 0.00526, 0] -2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 4.10 sec 5: Initializing data structure............: Done. -5: Number of distinct sites...............: 73 -5: 77037.5 +5: Number of distinct sites...............: 74 +5: 76568.3 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1722,6 +1717,47 @@ 5: [1, 1, 1, 0] 5: ] 5: Compute joint node-pairs likelihood....: +2: Br0 BrLen = 0.001 counts = 0.00095 +2: 4x4 +2: [ +2: [0, 1e-05, 6e-05, 1e-05] +2: [4e-05, 0, 0.00016, 0.00022] +2: [7e-05, 9e-05, 0, 5e-05] +2: [3e-05, 0.00017, 4e-05, 0] +2: ] +2: Br1 BrLen = 0.002 counts = 0.00186 +2: 4x4 +2: [ +2: [0, 4e-05, 0.00014, 4e-05] +2: [0.0001, 0, 0.00019, 0.00031] +2: [0.00019, 0.00028, 0, 0.0001] +2: [2e-05, 0.00038, 7e-05, 0] +2: ] +2: Br2 BrLen = 0.003 counts = 0.00274 +2: 4x4 +2: [ +2: [0, 0.00011, 0.00023, 5e-05] +2: [9e-05, 0, 0.00037, 0.00061] +2: [0.00019, 0.0003, 0, 7e-05] +2: [0, 0.00057, 0.00015, 0] +2: ] +2: Br3 BrLen = 0.01 counts = 0.00985 +2: 4x4 +2: [ +2: [0, 0.0003, 0.00075, 0.00015] +2: [0.00041, 0, 0.00121, 0.0019] +2: [0.00093, 0.00131, 0, 0.00059] +2: [0.00012, 0.00171, 0.00047, 0] +2: ] +2: Br4 BrLen = 0.1 counts = 0.09973 +2: 4x4 +2: [ +2: [0, 0.00339, 0.00919, 0.00109] +2: [0.00375, 0, 0.01304, 0.01822] +2: [0.00905, 0.01277, 0, 0.00508] +2: [0.00108, 0.01791, 0.00516, 0] +2: ] + 8/13 Test #2: test_detailed_simulations ........ Passed 0.50 sec 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, type 1: 5: 4x4 @@ -1771,36 +1807,7 @@ 5: [6.26538e-09, 0.000129478, 5.67996e-12, 5.21646e-08] 5: [6.2614e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12] 5: ] -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4); -11: -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A,B),C); -11: -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A:1,B:2)80:3,C:4):5; -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: N: BOOTSTRAP=80 -11: Node 3: -11: Node 4: -11: N: BOOTSTRAP=2 -11: ((A,B),C); -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: B: ESS=aa -11: Node 3: -11: Node 4: -11: B: ESS=2 5: Compute joint node-pairs likelihood....: -11: Newick I/O ok. 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: checking saturation... 5: Total count, uniformization method for 0.001 @@ -1875,18 +1882,47 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 46 46.1933 46.1569 46.1569 46.1933 46.1933 46.1933 46.1933 -5: B 0.002 108 108.101 107.939 107.939 108.101 108.101 108.101 108.101 -5: 0.008 381 380.422 377.988 377.988 380.422 380.422 380.422 380.422 -5: C 0.01 518 513.854 510.005 510.005 513.854 513.854 513.854 513.854 -5: D 0.02 965 974.923 959.973 959.973 974.923 974.923 974.923 974.923 -5: A 0.001 0.00446903/0 0.0068874/0 0.0068874/0 3.02433/3 3.02865/3 3.02865/3 1.00049/1 0.999227/1 0.999227/1 1.99135/2 1.99234/2 1.99234/2 -5: B 0.002 6.01068/6 6.01138/6 6.01138/6 10.1185/11 10.1371/11 10.1371/11 0.000117596/0 0.00341986/0 0.00341986/0 1.99748/2 2.00696/2 2.00696/2 -5: 0.008 16.1447/16 16.1926/16 16.1926/16 31.9845/32 32.2812/32 32.2812/32 2.83714/2 2.84184/2 2.84184/2 15.0885/15 15.1481/15 15.1481/15 -5: C 0.01 17.3913/17 17.498/17 17.498/17 57.0638/58 57.496/58 57.496/58 4.01067/4 4.01852/4 4.01852/4 23.302/23 23.3704/23 23.3704/23 -5: D 0.02 38.4444/40 38.7976/40 38.7976/40 89.6876/90 91.369/90 91.369/90 7.01262/7 7.05971/7 7.05971/7 34.2099/35 34.6554/35 34.6554/35 - 9/13 Test #5: test_mapping ..................... Passed 10.19 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 0.0067 +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4); +11: +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A,B),C); +11: +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A:1,B:2)80:3,C:4):5; +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: N: BOOTSTRAP=80 +11: Node 3: +11: Node 4: +11: N: BOOTSTRAP=2 +11: ((A,B),C); +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: B: ESS=aa +11: Node 3: +11: Node 4: +11: B: ESS=2 +11: Newick I/O ok. +5: A 0.001 50 49.5167 49.4757 49.4757 49.5167 49.5167 49.5167 49.5167 +5: B 0.002 99 99.7982 99.6501 99.6501 99.7982 99.7982 99.7982 99.7982 +5: 0.008 361 361.406 359.047 359.047 361.406 361.406 361.406 361.406 +5: C 0.01 477 482.866 479.022 479.022 482.866 482.866 482.866 482.866 +5: D 0.02 972 971.447 956.655 956.655 971.447 971.447 971.447 971.447 +5: A 0.001 2.00193/2 2.0026/2 2.0026/2 2.37961/2 2.38434/2 2.38434/2 0.000510616/0 0.00124148/0 0.00124148/0 3.97911/4 3.9799/4 3.9799/4 +5: B 0.002 5.02215/5 5.02303/5 5.02303/5 9.03687/9 9.05403/9 9.05403/9 0.00176608/0 0.00435083/0 0.00435083/0 3.03112/3 3.03638/3 3.03638/3 +5: 0.008 9.22078/8 9.29456/8 9.29456/8 28.6419/32 28.9049/32 28.9049/32 3.00811/3 3.00494/3 3.00494/3 10.3049/10 10.3913/10 10.3913/10 +5: C 0.01 21.1165/21 21.2049/21 21.2049/21 43.2177/44 43.6785/44 43.6785/44 7.06574/7 7.03038/7 7.03038/7 22.0664/22 22.14/22 22.14/22 +5: D 0.02 18.0497/21 18.7092/21 18.7092/21 98.1273/101 99.7358/101 99.7358/101 10.4518/10 10.3315/10 10.3315/10 38.6761/39 39.0393/39 39.0393/39 + 9/13 Test #5: test_mapping ..................... Passed 1.30 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0398 0.0054 1: ..:: Testing with homogeneous, non-stationary model ::.. 11: Newick multiple I/O ok. 11: Testing parsing a directory... @@ -1917,13 +1953,23 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 17.12 sec +10/13 Test #11: test_tree ........................ Passed 3.20 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 +10: +10: 0.491553 0.524388 +10: 0.0279114 0.0264781 +10: 0.816803 0.814042 +10: 0.732081 0.771217 +10: 0.922238 0.921548 +10: Detailed check: +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%0.0402 0.0055 +1: ..:: Testing with non-homogeneous, non-stationary model ::.. +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 184 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...............: 991 -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%0.04 0.0064 -1: ..:: Testing with non-homogeneous, non-stationary model ::.. -6: 96284.9 +6: Number of distinct sites...............: 988 +6: 96131.2 6: Analytical total count: 6: 64x64 6: [ @@ -1993,6 +2039,8 @@ 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....: +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%0.9335 0.8044 +1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: 6: 64x64 @@ -2273,39 +2321,27 @@ 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%0.9291 0.801 -1: ..:: Testing with non-homogeneous, stationary model ::.. 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -11/13 Test #6: test_mapping_codon ............... Passed 41.58 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%0.0404 0.0054 -12/13 Test #1: test_bowker ...................... Passed 52.83 sec -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 -10: -10: 0.975371 0.984931 -10: 0.854676 0.849746 -10: 0.833838 0.824692 -10: 0.96089 0.952649 -10: 0.682296 0.675444 -10: Detailed check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 185 -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 Optimizing... - 56 Optimizing... / 57 Optimizing... - 58 Optimizing... \ 59 Optimizing... - 60 Optimizing... / 61 Optimizing... - 62 Optimizing... \ 63 Optimizing... - 64 Optimizing... / 65 Optimizing... - 66 Optimizing... \ 67 Optimizing... - 68 Optimizing... / 69 Optimizing... - 70 Optimizing... \ 71 Optimizing... - 72 Optimizing... / 73 Optimizing... - 74 Optimizing... \ 75 Optimizing... - 76 Optimizing... / 77 Optimizing... - 78 Optimizing... \ 79 Optimizing... - 80 Optimizing... / 81 Optimizing... - 82 Optimizing... \ 83 Optimizing... - 84 Optimizing... / 85 Optimizing... - 86 Optimizing... \ 87 Optimizing... - 88 Optimizing... / 89 Optimizing... - 90 Optimizing... \ 91 Optimizing... - 92 Optimizing... / 93 Optimizing... - 94 Optimizing... \ 95 Optimizing... - 96 Optimizing... / 97 Optimizing... - 98 Optimizing... \ 99 Optimizing... - 100 Optimizing... / 101 Optimizing... - 102 Optimizing... \ 103 Optimizing... - 104 Optimizing... / 105 Optimizing... - 106 Optimizing... \ 107 Optimizing... - 108 Optimizing... / 109 Optimizing... - 110 Optimizing... \ 111 Optimizing... - 112 Optimizing... / 113 Optimizing... - 114 Optimizing... \ 115 Optimizing... - 116 Optimizing... / 117 Optimizing... - 118 Optimizing... \ 119 Optimizing... - 120 Optimizing... / 121 Optimizing... - 122 Optimizing... \ 123 Optimizing... - 124 Optimizing... / 125 Optimizing... - 126 Optimizing... \ 127 Optimizing... - 128 Optimizing... / 129 Optimizing... - 130 Optimizing... \ 131 Optimizing... - 132 +11/13 Test #6: test_mapping_codon ............... Passed 9.94 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: 0.975371 0.977883 -10: 0.854676 0.861461 -10: 0.833838 0.833045 -10: 0.96089 0.966872 -10: 0.682296 0.687076 -13/13 Test #10: test_simulations ................. Passed 299.45 sec +10: 0.491553 0.489731 +10: 0.0279114 0.0298902 +10: 0.816803 0.824497 +10: 0.732081 0.712797 +10: 0.922238 0.924049 +12/13 Test #10: test_simulations ................. Passed 10.68 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0417 0.0059 +13/13 Test #1: test_bowker ...................... Passed 11.17 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 299.66 sec +Total Test time (real) = 11.29 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 -j20 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 @@ -2323,237 +2359,237 @@ -- 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/AncestralStateReconstruction.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/Io --- 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/BppOSubstitutionModelFormat.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/IoSubstitutionModelFactory.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/IoTreeFactory.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/BppOTreeWriterFormat.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/BppOFrequenciesSetFormat.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/NexusIoTree.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/IoPairedSiteLikelihoods.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/BppOMultiTreeWriterFormat.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/IoSubstitutionModel.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/BppOMultiTreeReaderFormat.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/Mapping --- 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/Mapping/ProbabilisticRewardMapping.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/Mapping.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/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/Reward.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/SubstitutionCount.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/NaiveSubstitutionCount.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/ProbabilisticSubstitutionMapping.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/RewardMappingTools.h --- 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/DecompositionReward.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/SitePatterns.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/BipartitionTools.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/TreeTemplate.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/NonHomogeneousSequenceSimulator.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/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/SequenceSimulationTools.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/TreeParsimonyData.h --- Installing: 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/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/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/BipartitionList.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/Distance --- 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/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/PGMA.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/HierarchicalClustering.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/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/NNISearchable.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/OptimizationTools.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/Model --- 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/AbstractWordSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.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/GaussianDiscreteRateDistribution.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/RateDistribution/ConstantRateDistribution.h +-- 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/MixedSubstitutionModel.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/WordSubstitutionModel.h +-- Installing: /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/AbstractBiblioSubstitutionModel.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/TS98.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeTransitionModel.h +-- Installing: 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/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/ProteinFrequenciesSet.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/SubstitutionModel.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/AbstractMixedSubstitutionModel.h -- Installing: 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/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/TN93.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/gBGC.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/Nucleotide/HKY85.h --- 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/RN95.h --- Installing: 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/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/NucleotideSubstitutionModel.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/JCnuc.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/RegisterRatesSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.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/MixedSubstitutionModel.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/F84.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/WrappedModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.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/RE08.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/InMixedSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FromMixtureSubstitutionModel.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/Codon --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.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/KroneckerCodonDistanceFrequenciesSubstitutionModel.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/AbstractCodonFitnessSubstitutionModel.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/AbstractCodonAAFitnessSubstitutionModel.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/KCM.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/YNGP_M.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/AbstractCodonPhaseFrequenciesSubstitutionModel.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/TripletSubstitutionModel.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/CodonAdHocSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.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/CodonDistanceFrequenciesSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.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/GY94.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.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/CodonDistancePhaseFrequenciesSubstitutionModel.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/CodonSubstitutionModel.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/KroneckerCodonDistanceFrequenciesSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.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/AbstractCodonDistanceSubstitutionModel.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/AbstractCodonFitnessSubstitutionModel.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/AbstractCodonSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/MG94.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.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/MG94.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/YNGP_M8.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/CodonDistanceSubstitutionModel.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/YNGP_M.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/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/AbstractCodonAARateSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.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/RateDistribution --- 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/GammaDiscreteRateDistribution.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/RateDistribution/ConstantRateDistribution.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/FromMixtureSubstitutionModel.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/OneChangeRegisterTransitionModel.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/AbstractWrappedModel.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/FrequenciesSet --- 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/ProteinFrequenciesSet.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/MvaFrequenciesSet.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/FrequenciesSet/FrequenciesSet.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/TS98.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/SubstitutionModelSet.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/MixtureOfSubstitutionModels.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/MixtureOfASubstitutionModel.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/Codon/YNGP_M7.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/Protein +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JCprot.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/CoalaCore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.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/PhyloStatistics.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/BppOMultiTreeWriterFormat.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/IoTree.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/PhylipDistanceMatrixFormat.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/IoDistanceMatrixFactory.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/BppOTreeWriterFormat.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/Newick.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/IoTreeFactory.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/NexusIoTree.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/Nhx.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/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/IoSubstitutionModel.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/Likelihood --- 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/DRHomogeneousTreeLikelihood.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/HomogeneousTreeLikelihood.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/ClockTreeLikelihood.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/DRTreeLikelihood.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/DiscreteRatesAcrossSitesTreeLikelihood.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/AbstractNonHomogeneousTreeLikelihood.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/DRTreeLikelihoodTools.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/DRHomogeneousTreeLikelihood.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/RNonHomogeneousMixedTreeLikelihood.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/RHomogeneousClockTreeLikelihood.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/DRASDRTreeLikelihoodData.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/Likelihood/AbstractHomogeneousTreeLikelihood.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/DRNonHomogeneousTreeLikelihood.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/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.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/AbstractDiscreteRatesAcrossSitesTreeLikelihood.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/NNIHomogeneousTreeLikelihood.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/HomogeneousTreeLikelihood.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/RHomogeneousTreeLikelihood.h -- 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/TreeLikelihoodData.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/RHomogeneousTreeLikelihood.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/DRASDRTreeLikelihoodData.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/TreeLikelihood.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/GlobalClockTreeLikelihoodFunctionWrapper.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/AbstractTreeLikelihood.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/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/ClockTreeLikelihood.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/DRTreeLikelihood.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/Tree.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/Node.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/NNISearchable.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/DistanceEstimation.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/AbstractAgglomerativeDistanceMethod.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/Distance/PGMA.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/TreeTools.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/Mapping +-- 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/SubstitutionRegister.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/NaiveSubstitutionCount.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/RewardMappingTools.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/Mapping.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/CategorySubstitutionRegister.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/DecompositionMethods.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/Reward.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/DecompositionSubstitutionCount.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/RewardMapping.h +-- 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/TreeTemplateTools.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/DRTreeParsimonyData.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/TreeParsimonyData.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/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/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' @@ -2603,8 +2639,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-11_amd64.deb'. -dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_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) @@ -2612,12 +2648,14 @@ 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/3663368/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3663368/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/972581 and its subdirectories -I: Current time: Tue Mar 11 21:23:52 -12 2025 -I: pbuilder-time-stamp: 1741771432 +I: removing directory /srv/workspace/pbuilder/3663368 and its subdirectories +I: Current time: Wed Apr 15 05:49:50 +14 2026 +I: pbuilder-time-stamp: 1776181790