Diff of the two buildlogs: -- --- b1/build.log 2024-11-15 23:29:08.923683144 +0000 +++ b2/build.log 2024-11-15 23:30:36.847686222 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 18 17:50:57 -12 2025 -I: pbuilder-time-stamp: 1766123457 +I: Current time: Sat Nov 16 13:29:11 +14 2024 +I: pbuilder-time-stamp: 1731713351 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ dpkg-source: info: applying 32-bits.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/19358/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1397/tmp/hooks/D01_modify_environment starting +debug: Running on infom07-i386. +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 Nov 15 23:29 /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/1397/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1397/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='1c7d5e269c50459083ac38bf5f240828' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='19358' - PS1='# ' - PS2='> ' + INVOCATION_ID=ad159b1b46ea4ad992ee2570f641dea7 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=1397 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.eKwKJyoo/pbuilderrc_vgcR --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eKwKJyoo/b1 --logfile b1/build.log phylonium_1.7-3.dsc' - SUDO_GID='111' - 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.eKwKJyoo/pbuilderrc_7Fzv --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eKwKJyoo/b2 --logfile b2/build.log phylonium_1.7-3.dsc' + SUDO_GID=111 + 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 infom08-i386 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/19358/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1397/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -145,7 +177,7 @@ Get: 29 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libdivsufsort3 i386 2.0.1-6+b1 [50.0 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libdivsufsort-dev i386 2.0.1-6+b1 [19.1 kB] -Fetched 20.2 MB in 1s (13.5 MB/s) +Fetched 20.2 MB in 0s (97.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19957 files and directories currently installed.) @@ -284,7 +316,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/phylonium-1.7/ && 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 > ../phylonium_1.7-3_source.changes +I: user script /srv/workspace/pbuilder/1397/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1397/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/phylonium-1.7/ && 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 > ../phylonium_1.7-3_source.changes dpkg-buildpackage: info: source package phylonium dpkg-buildpackage: info: source version 1.7-3 dpkg-buildpackage: info: source distribution unstable @@ -404,7 +440,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_build - make -j6 + make -j5 make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' make all-recursive make[2]: Entering directory '/build/reproducible-path/phylonium-1.7' @@ -414,10 +450,10 @@ gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c ar cru libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c @@ -430,14 +466,14 @@ ar cru libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_sse2.a -rm -f librevseqcmp_avx2.a -ar cru librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o -ar: `u' modifier ignored since `D' is the default (see `U') rm -f libpfasta.a ar cru libpfasta.a libpfasta_a-pfasta.o -ar: ranlib librevseqcmp_avx2.a -`u' modifier ignored since `D' is the default (see `U') +ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpfasta.a +rm -f librevseqcmp_avx2.a +ar cru librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib librevseqcmp_avx2.a rm -f librevseqcmp.a ar cru librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ar: `u' modifier ignored since `D' is the default (see `U') @@ -475,7 +511,7 @@ make[2]: Leaving directory '/build/reproducible-path/phylonium-1.7' make[1]: Leaving directory '/build/reproducible-path/phylonium-1.7' dh_auto_test - make -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 + make -j5 check "TESTSUITEFLAGS=-j5 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' Making check in libs make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' @@ -494,7 +530,6 @@ g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx -g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx ../src/process.cxx:433: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 433 | #pragma omp parallel for num_threads(THREADS) ../src/process.cxx:445: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] @@ -511,6 +546,7 @@ 539 | #pragma omp atomic read ../src/process.cxx:545: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 545 | #pragma omp critical +g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx g++ -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++17 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx g++ -std=gnu++17 -ggdb -g -O2 -ffile-prefix-map=/build/reproducible-path/phylonium-1.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort64 -lm @@ -542,7 +578,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phylonium/ - make -j6 install DESTDIR=/build/reproducible-path/phylonium-1.7/debian/phylonium AM_UPDATE_INFO_DIR=no + make -j5 install DESTDIR=/build/reproducible-path/phylonium-1.7/debian/phylonium AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/phylonium-1.7' Making install in libs make[2]: Entering directory '/build/reproducible-path/phylonium-1.7/libs' @@ -604,12 +640,14 @@ 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/1397/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1397/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/19358 and its subdirectories -I: Current time: Thu Dec 18 17:52:07 -12 2025 -I: pbuilder-time-stamp: 1766123527 +I: removing directory /srv/workspace/pbuilder/1397 and its subdirectories +I: Current time: Sat Nov 16 13:30:35 +14 2024 +I: pbuilder-time-stamp: 1731713435