Diff of the two buildlogs: -- --- b1/build.log 2025-03-08 12:15:23.615154714 +0000 +++ b2/build.log 2025-03-08 12:16:24.296403302 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 10 05:48:20 -12 2026 -I: pbuilder-time-stamp: 1775843300 +I: Current time: Sun Mar 9 02:15:26 +14 2025 +I: pbuilder-time-stamp: 1741436126 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -24,51 +24,83 @@ dpkg-source: info: applying unforce-cxxflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3706485/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3246696/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Mar 8 12:15 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3246696/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3246696/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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='113d3bbd75b047cf8f48997e1881b9b6' - 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='3706485' - PS1='# ' - PS2='> ' + INVOCATION_ID=74e42c8f40a84a21bb0bbc9b6d3df237 + 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=3246696 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.XeRciNcx/pbuilderrc_kbC2 --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.XeRciNcx/b1 --logfile b1/build.log libbpp-phyl-omics_2.4.1-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.XeRciNcx/pbuilderrc_1hde --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.XeRciNcx/b2 --logfile b2/build.log libbpp-phyl-omics_2.4.1-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3706485/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3246696/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -181,7 +213,7 @@ Get: 67 http://deb.debian.org/debian unstable/main amd64 libbpp-phyl-dev amd64 2.4.1-11+b2 [2997 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libbpp-seq-omics3t64 amd64 2.4.1-12 [230 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libbpp-seq-omics-dev amd64 2.4.1-12 [378 kB] -Fetched 48.9 MB in 1s (35.8 MB/s) +Fetched 48.9 MB in 0s (127 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) @@ -472,7 +504,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libbpp-phyl-omics-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-omics_2.4.1-7_source.changes +I: user script /srv/workspace/pbuilder/3246696/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3246696/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbpp-phyl-omics-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-omics_2.4.1-7_source.changes dpkg-buildpackage: info: source package libbpp-phyl-omics dpkg-buildpackage: info: source version 2.4.1-7 dpkg-buildpackage: info: source distribution unstable @@ -520,7 +556,7 @@ -- shared lib: /usr/lib/x86_64-linux-gnu/libbpp-phyl.so.12.0.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (3.2s) +-- Configuring done (0.3s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -545,58 +581,58 @@ make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-omics-2.4.1 /build/reproducible-path/libbpp-phyl-omics-2.4.1/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-phyl-omics-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/bpp-phyl-omics-static.dir/build.make src/CMakeFiles/bpp-phyl-omics-static.dir/build -make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/bpp-phyl-omics-static.dir/build.make src/CMakeFiles/bpp-phyl-omics-static.dir/build make -f src/CMakeFiles/bpp-phyl-omics-shared.dir/build.make src/CMakeFiles/bpp-phyl-omics-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' -[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp -[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp -[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp +make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o +[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp +cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g 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CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp +[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o +cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-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-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp [ 95%] Linking CXX static library libbpp-phyl-omics.a cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bpp-phyl-omics-static.dir/cmake_clean_target.cmake cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-omics-static.dir/link.txt --verbose=1 +[100%] Linking CXX shared library libbpp-phyl-omics.so +cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-omics-shared.dir/link.txt --verbose=1 /usr/bin/ar qc libbpp-phyl-omics.a "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o" /usr/bin/ranlib libbpp-phyl-omics.a make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' -[ 95%] Built target bpp-phyl-omics-static -[100%] Linking CXX shared library libbpp-phyl-omics.so -cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-omics-shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/bpp-phyl-omics-shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-phyl-omics.so.3 -o libbpp-phyl-omics.so.3.0.0 "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o" /usr/lib/x86_64-linux-gnu/libbpp-seq-omics.so.3.0.0 /usr/lib/x86_64-linux-gnu/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 cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl-omics.so.3.0.0 libbpp-phyl-omics.so.3 libbpp-phyl-omics.so +[100%] Built target bpp-phyl-omics-static make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' [100%] Built target bpp-phyl-omics-shared make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' @@ -626,17 +662,17 @@ -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h +-- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h --- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl-omics/bpp-phyl-omics-targets.cmake -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl-omics/bpp-phyl-omics-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-x86_64-linux-gnu' @@ -687,9 +723,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl-omics3t64-dbgsym' in '../libbpp-phyl-omics3t64-dbgsym_2.4.1-7_amd64.deb'. dpkg-deb: building package 'libbpp-phyl-omics3t64' in '../libbpp-phyl-omics3t64_2.4.1-7_amd64.deb'. dpkg-deb: building package 'libbpp-phyl-omics-dev' in '../libbpp-phyl-omics-dev_2.4.1-7_amd64.deb'. +dpkg-deb: building package 'libbpp-phyl-omics3t64-dbgsym' in '../libbpp-phyl-omics3t64-dbgsym_2.4.1-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl-omics_2.4.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl-omics_2.4.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -697,12 +733,14 @@ 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/3246696/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3246696/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/3706485 and its subdirectories -I: Current time: Fri Apr 10 06:38:21 -12 2026 -I: pbuilder-time-stamp: 1775846301 +I: removing directory /srv/workspace/pbuilder/3246696 and its subdirectories +I: Current time: Sun Mar 9 02:16:23 +14 2025 +I: pbuilder-time-stamp: 1741436183