Diff of the two buildlogs: -- --- b1/build.log 2025-03-12 01:58:02.366483708 +0000 +++ b2/build.log 2025-03-12 02:00:15.472526782 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 13 20:19:47 -12 2026 -I: pbuilder-time-stamp: 1776154787 +I: Current time: Wed Mar 12 15:58:07 +14 2025 +I: pbuilder-time-stamp: 1741744687 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying malloc I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/694382/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/424061/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Mar 12 01:58 /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/424061/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/424061/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='d8130bfbc5984323bc08bc51834362d9' - 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='694382' - PS1='# ' - PS2='> ' + INVOCATION_ID=5867a8870a144de8a3d86f79c10bffe9 + 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=424061 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.EBRcym97/pbuilderrc_CxVJ --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EBRcym97/b1 --logfile b1/build.log libssw_1.2.5-1.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://192.168.101.4:3128' + 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.EBRcym97/pbuilderrc_3jvF --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EBRcym97/b2 --logfile b2/build.log libssw_1.2.5-1.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://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/694382/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/424061/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 129 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 163 MB in 1s (286 MB/s) +Fetched 163 MB in 2s (87.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpipeline1: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 ... 19897 files and directories currently installed.) @@ -692,8 +724,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 14 08:20:13 UTC 2026. -Universal Time is now: Tue Apr 14 08:20:13 UTC 2026. +Local time is now: Wed Mar 12 01:59:01 UTC 2025. +Universal Time is now: Wed Mar 12 01:59:01 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -999,7 +1031,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libssw-1.2.5/ && 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 > ../libssw_1.2.5-1_source.changes +I: user script /srv/workspace/pbuilder/424061/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/424061/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libssw-1.2.5/ && 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 > ../libssw_1.2.5-1_source.changes dpkg-buildpackage: info: source package libssw dpkg-buildpackage: info: source version 1.2.5-1 dpkg-buildpackage: info: source distribution experimental @@ -1018,7 +1054,7 @@ make[2]: Leaving directory '/build/reproducible-path/libssw-1.2.5/src' make[1]: Leaving directory '/build/reproducible-path/libssw-1.2.5' jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" dh_clean debian/rules binary dh binary --with javahelper --with jh_maven_repo_helper @@ -1038,11 +1074,11 @@ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libssw-1.2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O2 -I"/usr/lib/jvm/default-java/include" -I"/usr/lib/jvm/default-java/include/linux" -I/usr/lib/jvm/default-java/include/ -I/usr/lib/jvm/default-java/include/linux -fPIC -shared -rdynamic -o libsswjni.so sswjni.c ssw.c -Wl,-z,relro -Wl,-z,now cc -o example_c ssw.o example.c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libssw-1.2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O2 -Wl,-z,relro -Wl,-z,now -lm -lz jar cvf ssw.jar ssw/Aligner.class ssw/Alignment.class +ar rcs libssw.a ssw.o ssw_cpp.o +g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libssw-1.2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lz added manifest adding: ssw/Aligner.class(in = 2486) (out= 1527)(deflated 38%) adding: ssw/Alignment.class(in = 1029) (out= 602)(deflated 41%) -ar rcs libssw.a ssw.o ssw_cpp.o -g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libssw-1.2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lz cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libssw-1.2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O2 -o ssw-align main.c kseq.h -L. -lssw -lm -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/libssw-1.2.5/src' make[1]: Leaving directory '/build/reproducible-path/libssw-1.2.5' @@ -1439,7 +1475,7 @@ Query: 731 GAGATGCTGATGTATAT-ACT-T-ACA--TATT------TT-ACAGTGTATTCAAATAAA 778 Target: 9474 GAAAATAATTGCATATGATACAGT--GTTTGTGCCAAAATGTATTCATGGCTTTAAAAAC 9531 - ||**|| |||*||||*||*|*| | *|||||**|*||*| CPU time: 4.207154 seconds + ||**|| |||*||||*||*|*| | *|||||**|*||*| CPU time: 4.160633 seconds || ||*|*||||*|| Query: 779 GAGTAT-ATTACATAAGACATA-TCCTTTTGTAACCAACT---TT--TGTCATTAACAA- 830 @@ -1506,7 +1542,7 @@ dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below dpkg-gensymbols: warning: debian/libssw1/DEBIAN/symbols doesn't match completely debian/libssw1.symbols --- debian/libssw1.symbols (libssw1_1.2.5-1_arm64) -+++ dpkg-gensymbolscuporl 2026-04-13 20:20:54.659686486 -1200 ++++ dpkg-gensymbolsRzKZE1 2025-03-12 16:00:10.444204796 +1400 @@ -21,7 +21,8 @@ _ZNK20StripedSmithWaterman7Aligner13TranslateBaseEPKcRKiPa@Base 1.1 _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentEi@Base 1.2.4 @@ -1534,13 +1570,13 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libssw1' in '../libssw1_1.2.5-1_arm64.deb'. dpkg-deb: building package 'libssw1-dbgsym' in '../libssw1-dbgsym_1.2.5-1_arm64.deb'. -dpkg-deb: building package 'libssw-dev' in '../libssw-dev_1.2.5-1_arm64.deb'. +dpkg-deb: building package 'libssw1' in '../libssw1_1.2.5-1_arm64.deb'. dpkg-deb: building package 'libssw-java' in '../libssw-java_1.2.5-1_arm64.deb'. dpkg-deb: building package 'libssw-java-dbgsym' in '../libssw-java-dbgsym_1.2.5-1_arm64.deb'. -dpkg-deb: building package 'ssw-align' in '../ssw-align_1.2.5-1_arm64.deb'. dpkg-deb: building package 'ssw-align-dbgsym' in '../ssw-align-dbgsym_1.2.5-1_arm64.deb'. +dpkg-deb: building package 'libssw-dev' in '../libssw-dev_1.2.5-1_arm64.deb'. +dpkg-deb: building package 'ssw-align' in '../ssw-align_1.2.5-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libssw_1.2.5-1_arm64.buildinfo dpkg-genchanges --build=binary -O../libssw_1.2.5-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1548,12 +1584,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/424061/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/424061/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/694382 and its subdirectories -I: Current time: Mon Apr 13 20:20:57 -12 2026 -I: pbuilder-time-stamp: 1776154857 +I: removing directory /srv/workspace/pbuilder/424061 and its subdirectories +I: Current time: Wed Mar 12 16:00:14 +14 2025 +I: pbuilder-time-stamp: 1741744814