Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 22:01:07.968501945 +0000 +++ b2/build.log 2024-01-07 22:03:20.354529010 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 8 16:20:39 -12 2025 -I: pbuilder-time-stamp: 1739074839 +I: Current time: Sun Feb 9 18:24:14 +14 2025 +I: pbuilder-time-stamp: 1739075054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -28,49 +28,81 @@ dpkg-source: info: applying connected_component_subgraphs.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2487637/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1381213/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 9 04:24 /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/1381213/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1381213/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='999c99ee70944775a18b2ec4cdf7f0b2' - 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='2487637' - PS1='# ' - PS2='> ' + INVOCATION_ID=1ab02e1aadbd404dadbe4ee59114d6c4 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1381213 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.sXqB7Uim/pbuilderrc_7yft --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sXqB7Uim/b1 --logfile b1/build.log ragout_2.3-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.sXqB7Uim/pbuilderrc_sS9G --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sXqB7Uim/b2 --logfile b2/build.log ragout_2.3-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink01-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -130,7 +162,7 @@ -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 9 04:24 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su @@ -156,7 +188,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2487637/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1381213/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +289,7 @@ Get: 55 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 python3-networkx all 2.8.8-1 [1425 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] -Fetched 34.8 MB in 0s (80.7 MB/s) +Fetched 34.8 MB in 0s (121 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18171 files and directories currently installed.) @@ -502,7 +534,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ragout-2.3/ && 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 > ../ragout_2.3-4_source.changes +I: user script /srv/workspace/pbuilder/1381213/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/1381213/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ragout-2.3/ && 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 > ../ragout_2.3-4_source.changes dpkg-buildpackage: info: source package ragout dpkg-buildpackage: info: source version 2.3-4 dpkg-buildpackage: info: source distribution unstable @@ -512,7 +548,7 @@ debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt binnengegaan dh_auto_clean || true I: pybuild base:240: python3.11 setup.py clean running clean @@ -522,7 +558,7 @@ rm -f bin/ragout-maf2synteny bin/ragout-overlap rm -rf .pybuild find . -name "*.o" -delete -make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -598,26 +634,26 @@ copying ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.11/build/ragout/tests/data copying ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.11/build/ragout/tests/data copying ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.11/build/ragout/tests/data -make[1]: Entering directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt binnengegaan make -C ragout/overlap/cpp_impl all -make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' wordt binnengegaan g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG build_graph.cpp -o build_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG fasta.cpp -o fasta.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG overlap.cpp -o overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG suffix_array.cpp -o suffix_array.o g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap -make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' wordt verlaten make -C ragout/maf2synteny/cpp_impl all -make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' wordt binnengegaan g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG breakpoint_graph.cpp -o breakpoint_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG compress_algorithms.cpp -o compress_algorithms.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG maf_tools.cpp -o maf_tools.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG permutation.cpp -o permutation.o g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny -make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' -make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' wordt verlaten +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt verlaten dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v @@ -635,16 +671,16 @@ warnings.warn( running build running build_py -make[1]: Entering directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt binnengegaan make -C ragout/overlap/cpp_impl all -make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' wordt binnengegaan g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap -make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' wordt verlaten make -C ragout/maf2synteny/cpp_impl all -make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' wordt binnengegaan g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny -make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' -make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' +make[2]: Map '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' wordt verlaten +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt verlaten running install_lib creating /build/reproducible-path/ragout-2.3/debian/tmp/usr creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib @@ -799,10 +835,10 @@ Installing ragout script to /build/reproducible-path/ragout-2.3/debian/tmp/usr/bin Installing C++ binaries debian/rules override_dh_install -make[1]: Entering directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt binnengegaan dh_install find debian -name LICENSE -delete -make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' +make[1]: Map '/build/reproducible-path/ragout-2.3' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild @@ -825,9 +861,9 @@ dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${python3:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'ragout' in '../ragout_2.3-4_arm64.deb'. -dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-4_arm64.deb'. -dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-4_all.deb'. +dpkg-deb: pakket 'ragout-dbgsym' wordt gebouwd in '../ragout-dbgsym_2.3-4_arm64.deb'. +dpkg-deb: pakket 'ragout' wordt gebouwd in '../ragout_2.3-4_arm64.deb'. +dpkg-deb: pakket 'ragout-examples' wordt gebouwd in '../ragout-examples_2.3-4_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-4_arm64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -835,12 +871,14 @@ 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/1381213/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1381213/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/2487637 and its subdirectories -I: Current time: Sat Feb 8 16:24:06 -12 2025 -I: pbuilder-time-stamp: 1739075046 +I: removing directory /srv/workspace/pbuilder/1381213 and its subdirectories +I: Current time: Sun Feb 9 18:26:18 +14 2025 +I: pbuilder-time-stamp: 1739075178