Diff of the two buildlogs: -- --- b1/build.log 2025-09-27 12:12:40.322614693 +0000 +++ b2/build.log 2025-09-27 12:18:02.483017323 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 27 00:09:15 -12 2025 -I: pbuilder-time-stamp: 1758974955 +I: Current time: Sat Oct 31 08:35:41 +14 2026 +I: pbuilder-time-stamp: 1793385341 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3634674/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2530739/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 Oct 30 18:36 /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/2530739/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2530739/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=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='34fb913c8fff4e21961bcb229240d6bc' - 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='3634674' - PS1='# ' - PS2='> ' + INVOCATION_ID=d1d85c1d098c4a73938f6b119b3a9c06 + 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=2530739 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.mpvO1TQo/pbuilderrc_0iSr --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.mpvO1TQo/b1 --logfile b1/build.log libbpp-phyl_2.4.1-12.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - 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.mpvO1TQo/pbuilderrc_0v7l --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.mpvO1TQo/b2 --logfile b2/build.log libbpp-phyl_2.4.1-12.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3634674/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2530739/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -179,7 +211,7 @@ Get: 62 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-14 [964 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libbpp-seq12t64 amd64 2.4.1-13 [510 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libbpp-seq-dev amd64 2.4.1-13 [745 kB] -Fetched 34.6 MB in 1s (46.4 MB/s) +Fetched 34.6 MB in 1s (37.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -455,7 +487,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-phyl_2.4.1-12_source.changes +I: user script /srv/workspace/pbuilder/2530739/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2530739/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbpp-phyl_2.4.1-12_source.changes dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-12 dpkg-buildpackage: info: source distribution unstable @@ -498,7 +534,7 @@ -- Build files have been written to: /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -516,680 +552,680 @@ make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -[ 3%] 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/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 -[ 3%] 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/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.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 -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp -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 -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -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 -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-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/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 -[ 3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -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 +[ 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/Distance/DistanceEstimation.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp +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 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.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/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.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/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.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/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.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/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -cd 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp +[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.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/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.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/Likelihood/PseudoNewtonOptimizer.cpp.o -MF 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp +[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.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 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90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -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/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.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 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/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_models.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_nhx.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend -make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake "--color=" +make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_simulations.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' @@ -1235,67 +1271,67 @@ 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[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 -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_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 -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_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.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 test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: 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]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build +make -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' +make -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_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' -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' 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 -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[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' -[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -[ 94%] 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_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp -[ 94%] Building CXX object test/CMakeFiles/test_likelihood_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_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_likelihood.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o 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/build/reproducible-path/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp [ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp -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_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 +[ 95%] 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_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 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 [ 95%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood.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 +[ 95%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.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_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_simulations.cpp -[ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -MF CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o.d -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree.cpp +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -MF CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o.d -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp +[ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_nhx.cpp cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp [ 96%] Linking CXX executable test_tree_getpath cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_getpath.dir/link.txt --verbose=1 @@ -1309,19 +1345,19 @@ [ 97%] Built target test_nhx [ 98%] Linking CXX executable test_tree_rootat 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_rootat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_tree_rootat.dir/link.d CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[ 98%] Linking CXX executable test_models +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 [ 98%] Linking CXX executable test_parsimony cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_tree_rootat.dir/link.d CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_tree_rootat +/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 -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 -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 -[ 98%] Linking CXX executable test_models -cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 -/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 -Wl,--dependency-file=CMakeFiles/test_models.dir/link.d CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_models +[ 98%] 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 -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 @@ -1334,46 +1370,46 @@ [ 99%] Built target test_likelihood_clock [ 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%] 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 -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_likelihood -/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 -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 -/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 -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' -[ 99%] Built target test_detailed_simulations -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%] Linking CXX executable test_mapping_codon cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1 -[100%] Built target bpp-phyl-static +[100%] Linking CXX executable test_detailed_simulations +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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' +/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 -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' +[100%] Built target test_detailed_simulations +[100%] Linking CXX executable test_bowker +cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 [100%] Built target test_mapping_codon [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 -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' /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 -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 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_simulations +[100%] Built target test_bowker [100%] Linking CXX executable test_mapping 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.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 -Wl,--dependency-file=CMakeFiles/test_mapping.dir/link.d CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_mapping +c.dir/Bpp/Phyl/OptimizationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o" +/usr/bin/ranlib libbpp-phyl.a +make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[100%] Built target bpp-phyl-static make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j40 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -1507,12 +1543,26 @@ 9: Parsimony score: 9 2/13 Test #9: test_parsimony ................... Passed 0.01 sec 10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.871083 -10: Theta1 set to 0.85242 -10: Theta2 set to 0.989091 -10: Theta3 set to 0.155469 -10: Theta4 set to 0.00886209 +10: Theta0 set to 0.811468 +10: Theta1 set to 0.686792 +10: Theta2 set to 0.844446 +10: Theta3 set to 0.726813 +10: Theta4 set to 0.385578 10: Fast check: +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 +4: * likelihood after full optimization...: 71.2658 +4: Name: Value: Constraint: +4: _________________________________________________ +4: BrLen0 0.143684 [ 1e-06; 10000] +4: BrLen1 0.143684 [ 1e-06; 10000] +4: BrLen2 0.031698 [ 1e-06; 10000] +4: BrLen3 0.175382 [ 1e-06; 10000] +4: BrLen4 0.272930 [ 1e-06; 10000] +4: BrLen5 0.448312 [ 1e-06; 10000] +4: T92.kappa 0.996464 ]0; +inf[ +4: T92.theta 0.579955 ]1e-06; 0.999999[ 12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 12: Id node1 0 12: Id node2 1 @@ -1528,27 +1578,7 @@ 12: 4 12: 3 12: 2 -4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 -4: -4: 71.26579958637299228 -4: * likelihood after full optimization...: 71.2658 -4: Name: Value: Constraint: -4: _________________________________________________ -4: BrLen0 0.143684 [ 1e-06; 10000] -4: BrLen1 0.143684 [ 1e-06; 10000] -4: BrLen2 0.031698 [ 1e-06; 10000] -4: BrLen3 0.175382 [ 1e-06; 10000] -4: BrLen4 0.272930 [ 1e-06; 10000] -4: BrLen5 0.448312 [ 1e-06; 10000] -4: T92.kappa 0.996464 ]0; +inf[ -4: T92.theta 0.579955 ]1e-06; 0.999999[ 3/13 Test #12: test_tree_getpath ................ Passed 0.01 sec -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 92.32951163315719611546 -4: * initial likelihood...................: 92.3295 -13: Total length...........................: 91.8641 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215015147885 @@ -1556,6 +1586,7 @@ 3: Testing Double Tree Traversal likelihood class... 3: Initializing data structure............: Done. 3: Number of distinct sites...............: 12 +13: Total length...........................: 100.091 3: Test model.............................: T92 3: 85.03094203195020384101 3: * initial likelihood...................: 85.0309 @@ -1569,18 +1600,7 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 -4: -4: 71.26579406919438497425 -4: * likelihood after full optimization...: 71.2658 -4: Name: Value: Constraint: -4: _________________________________________________ -4: TotalHeight 0.448127 [ 0; 10000] -4: HeightP4 0.390916 [ 0; 1] -4: HeightP2 0.819072 [ 0; 1] -4: T92.kappa 0.996398 ]0; +inf[ -4: T92.theta 0.579960 ]1e-06; 0.999999[ - 4/13 Test #4: test_likelihood_clock ............ Passed 0.03 sec + 4/13 Test #7: test_models ...................... Passed 0.04 sec 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215069149133 @@ -1595,14 +1615,18 @@ 3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 5/13 Test #3: test_likelihood .................. Passed 0.05 sec - 6/13 Test #7: test_models ...................... Passed 0.05 sec - 7/13 Test #13: test_tree_rootat ................. Passed 0.07 sec + 6/13 Test #13: test_tree_rootat ................. Passed 0.07 sec +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +4: Test model.............................: T92 +4: 92.32951163315719611546 +4: * initial likelihood...................: 92.3295 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 166 +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. 5: Initializing data structure............: Done. -5: Number of distinct sites...............: 77 -5: 76811.4 +5: Number of distinct sites...............: 70 +5: 76995.5 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1621,6 +1645,17 @@ 5: [1, 1, 0, 1] 5: [1, 1, 1, 0] 5: ] +4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 +4: +4: 71.26579406919438497425 +4: * likelihood after full optimization...: 71.2658 +4: Name: Value: Constraint: +4: _________________________________________________ +4: TotalHeight 0.448127 [ 0; 10000] +4: HeightP4 0.390916 [ 0; 1] +4: HeightP2 0.819072 [ 0; 1] +4: T92.kappa 0.996398 ]0; +inf[ +4: T92.theta 0.579960 ]1e-06; 0.999999[ 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, type 1: @@ -1631,48 +1666,48 @@ 5: [0, 0, 0, 0] 5: [0, 0, 0, 0] 5: ] -2: Br0 BrLen = 0.001 counts = 0.00109 +5: Compute joint node-pairs likelihood....: +2: Br0 BrLen = 0.001 counts = 0.00108 2: 4x4 2: [ -2: [0, 3e-05, 9e-05, 2e-05] -2: [4e-05, 0, 0.00016, 0.00023] -2: [8e-05, 0.00017, 0, 8e-05] -2: [1e-05, 0.00016, 2e-05, 0] +2: [0, 4e-05, 0.00012, 2e-05] +2: [2e-05, 0, 0.00014, 0.00019] +2: [8e-05, 0.00016, 0, 4e-05] +2: [3e-05, 0.00019, 5e-05, 0] 2: ] -2: Br1 BrLen = 0.002 counts = 0.00187 +2: Br1 BrLen = 0.002 counts = 0.00204 2: 4x4 2: [ -2: [0, 7e-05, 0.00021, 3e-05] -2: [8e-05, 0, 0.00022, 0.00032] -2: [0.00015, 0.00021, 0, 0.00013] -2: [1e-05, 0.00038, 6e-05, 0] +2: [0, 0.0001, 0.00013, 1e-05] +2: [8e-05, 0, 0.0003, 0.00032] +2: [0.00019, 0.00028, 0, 0.00011] +2: [2e-05, 0.00037, 0.00013, 0] 2: ] -2: Br2 BrLen = 0.003 counts = 0.00271 +2: Br2 BrLen = 0.003 counts = 0.0032 2: 4x4 2: [ -2: [0, 0.00011, 0.00029, 5e-05] -2: [0.0001, 0, 0.0004, 0.00047] -2: [0.00029, 0.00033, 0, 0.00016] -2: [2e-05, 0.0004, 9e-05, 0] +2: [0, 0.00013, 0.00028, 4e-05] +2: [0.00011, 0, 0.00047, 0.00061] +2: [0.00027, 0.00034, 0, 0.00019] +2: [6e-05, 0.00056, 0.00014, 0] 2: ] -2: Br3 BrLen = 0.01 counts = 0.00977 +2: Br3 BrLen = 0.01 counts = 0.0099 2: 4x4 2: [ -2: [0, 0.0004, 0.00097, 0.00014] -2: [0.00037, 0, 0.00134, 0.00158] -2: [0.00106, 0.00113, 0, 0.00054] -2: [6e-05, 0.00181, 0.00037, 0] +2: [0, 0.00036, 0.00081, 8e-05] +2: [0.00033, 0, 0.00131, 0.00189] +2: [0.00094, 0.00126, 0, 0.00055] +2: [0.00015, 0.00184, 0.00038, 0] 2: ] -2: Br4 BrLen = 0.1 counts = 0.09988 +2: Br4 BrLen = 0.1 counts = 0.09975 2: 4x4 2: [ -2: [0, 0.00338, 0.00896, 0.00095] -2: [0.00359, 0, 0.01301, 0.01816] -2: [0.00898, 0.01278, 0, 0.00538] -2: [0.00106, 0.01818, 0.00545, 0] +2: [0, 0.00359, 0.00931, 0.00099] +2: [0.00339, 0, 0.0125, 0.0183] +2: [0.00899, 0.01262, 0, 0.00562] +2: [0.00093, 0.01777, 0.00574, 0] 2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 0.49 sec -5: Compute joint node-pairs likelihood....: + 7/13 Test #2: test_detailed_simulations ........ Passed 0.52 sec 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Total count, decomposition method: 5: 4x4 @@ -1682,6 +1717,7 @@ 5: [1.00009, 1.00032, 4.08766e-07, 1.00069] 5: [1.00159, 1.00007, 1.00069, 5.17576e-07] 5: ] + 8/13 Test #4: test_likelihood_clock ............ Passed 0.56 sec 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, decomposition method, type 1: @@ -1787,6 +1823,7 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 +5: A 0.001 52 52.9082 52.8688 52.8688 52.9082 52.9082 52.9082 52.9082 11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. 11: ((A:1,B:2):3,C:4); 11: @@ -1815,19 +1852,18 @@ 11: Node 3: 11: Node 4: 11: B: ESS=2 -5: A 0.001 51 51.7705 51.7289 51.7289 51.7705 51.7705 51.7705 51.7705 +5: B 0.002 107 104.376 104.227 104.227 104.376 104.376 104.376 104.376 +5: 0.008 391 394.539 392.026 392.026 394.539 394.539 394.539 394.539 +5: C 0.01 497 498.577 494.699 494.699 498.577 498.577 498.577 498.577 +5: D 0.02 990 979.546 964.53 964.53 979.546 979.546 979.546 979.546 +5: A 0.001 1.00386/1 1.00515/1 1.00515/1 4.02034/4 4.02463/4 4.02463/4 0.000150621/0 0.00070277/0 0.00070277/0 0.996304/1 0.998617/1 0.998617/1 +5: B 0.002 4.00588/4 4.01181/4 4.01181/4 16.0354/16 16.0525/16 16.0525/16 2.00141/2 1.99867/2 1.99867/2 1.9992/2 2.00283/2 2.00283/2 +5: 0.008 18.5397/18 18.599/18 18.599/18 32.8668/32 33.1679/32 33.1679/32 5.4738/6 5.45029/6 5.45029/6 17.5562/17 17.6252/17 17.6252/17 +5: C 0.01 15.3626/16 15.4814/16 15.4814/16 36.3562/36 36.803/36 36.803/36 6.01742/6 5.98861/6 5.98861/6 26.6448/27 26.7076/27 26.7076/27 11: Newick I/O ok. -5: B 0.002 113 111.816 111.657 111.657 111.816 111.816 111.816 111.816 -5: 0.008 381 379.787 377.377 377.377 379.787 379.787 379.787 379.787 -5: C 0.01 485 488.483 484.775 484.775 488.483 488.483 488.483 488.483 -5: D 0.02 964 963.675 948.597 948.597 963.675 963.675 963.675 963.675 -5: A 0.001 6.48472/6 6.48412/6 6.48412/6 6.78845/7 6.79468/7 6.79468/7 1.13686/1 1.13631/1 1.13631/1 2.98448/3 2.98477/3 2.98477/3 -5: B 0.002 4.01756/4 4.02407/4 4.02407/4 13.037/13 13.0564/13 13.0564/13 2.00147/2 1.99823/2 1.99823/2 2.56586/3 2.5741/3 2.5741/3 -5: 0.008 13.6204/13 13.7069/13 13.7069/13 29.6532/30 29.9549/30 29.9549/30 7.99796/7 7.93569/7 7.93569/7 12.8604/14 12.925/14 12.925/14 -5: C 0.01 16.7539/16 16.8242/16 16.8242/16 37.8164/36 38.2376/36 38.2376/36 0.214517/0 0.274301/0 0.274301/0 17.0307/17 17.1235/17 17.1235/17 -5: D 0.02 32.8079/30 33.3406/30 33.3406/30 92.1768/94 93.9212/94 93.9212/94 13.4411/13 13.2853/13 13.2853/13 32.8924/32 33.3154/32 33.3154/32 - 9/13 Test #5: test_mapping ..................... Passed 1.29 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%0.0375 0.0038 +5: D 0.02 32.2956/37 32.7269/37 32.7269/37 87.9499/90 89.6976/90 89.6976/90 9.31563/8 9.26958/8 9.26958/8 42.2667/42 42.6238/42 42.6238/42 + 9/13 Test #5: test_mapping ..................... Passed 1.19 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%0.0412 0.0048 1: ..:: Testing with homogeneous, non-stationary model ::.. 11: Newick multiple I/O ok. 11: Testing parsing a directory... @@ -1858,23 +1894,23 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 3.07 sec -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 +10/13 Test #11: test_tree ........................ Passed 3.94 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 10: -10: 0.871083 0.869897 -10: 0.85242 0.855212 -10: 0.989091 0.989447 -10: 0.155469 0.17311 -10: 0.00886209 0.0094797 +10: 0.811468 0.809265 +10: 0.686792 0.68092 +10: 0.844446 0.842985 +10: 0.726813 0.735047 +10: 0.385578 0.379834 10: Detailed check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 165 -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%0.044 0.008 +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%0.0393 0.006 1: ..:: Testing with non-homogeneous, non-stationary model ::.. +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 185 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...............: 1040 -6: 96707.9 +6: Number of distinct sites...............: 1025 +6: 96639 6: Analytical total count: 6: 64x64 6: [ @@ -2225,28 +2261,28 @@ 6: ] 6: Compute joint node-pairs likelihood....: 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -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%0.9314 0.7954 +11/13 Test #6: test_mapping_codon ............... Passed 8.46 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%0.9331 0.7963 1: ..:: Testing with non-homogeneous, stationary model ::.. -11/13 Test #6: test_mapping_codon ............... Passed 8.45 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 +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 10: -10: 0.871083 0.86551 -10: 0.85242 0.849622 -10: 0.989091 0.991162 -10: 0.155469 0.145332 -10: 0.00886209 0.00901776 -12/13 Test #10: test_simulations ................. Passed 8.55 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%0.0395 0.0055 -13/13 Test #1: test_bowker ...................... Passed 11.31 sec +10: 0.811468 0.817753 +10: 0.686792 0.688569 +10: 0.844446 0.847752 +10: 0.726813 0.718924 +10: 0.385578 0.377988 +12/13 Test #10: test_simulations ................. Passed 11.12 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 0.0057 +13/13 Test #1: test_bowker ...................... Passed 11.54 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 11.32 sec +Total Test time (real) = 11.62 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2264,237 +2300,237 @@ -- 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: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.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/TreeExceptions.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.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/AbstractTreeDrawing.h --- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h +-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/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: 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/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 --- 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/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 --- 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/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: 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/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 +-- 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/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: 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/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' @@ -2553,12 +2589,14 @@ 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/2530739/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2530739/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/3634674 and its subdirectories -I: Current time: Sat Sep 27 00:12:39 -12 2025 -I: pbuilder-time-stamp: 1758975159 +I: removing directory /srv/workspace/pbuilder/2530739 and its subdirectories +I: Current time: Sat Oct 31 08:41:01 +14 2026 +I: pbuilder-time-stamp: 1793385661