Diff of the two buildlogs: -- --- b1/build.log 2025-03-20 15:54:30.224257662 +0000 +++ b2/build.log 2025-03-20 15:55:39.865113332 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Mar 20 03:53:48 -12 2025 -I: pbuilder-time-stamp: 1742486028 +I: Current time: Thu Apr 23 12:17:31 +14 2026 +I: pbuilder-time-stamp: 1776896251 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying hurd I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2793843/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1092460/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 Apr 22 22:17 /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/1092460/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1092460/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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='66bcef1af7ef45c99ecd2898d72f1dd6' - 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='2793843' - PS1='# ' - PS2='> ' + INVOCATION_ID=3498ffbb6e294550af5ed61725ef1a81 + 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=1092460 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.NQn6MZJw/pbuilderrc_BAqW --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.NQn6MZJw/b1 --logfile b1/build.log bwa_0.7.18-1.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.NQn6MZJw/pbuilderrc_feUv --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.NQn6MZJw/b2 --logfile b2/build.log bwa_0.7.18-1.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 codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2793843/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1092460/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 21.0 MB in 0s (54.0 MB/s) +Fetched 21.0 MB in 0s (72.7 MB/s) Preconfiguring packages ... 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 ... 19899 files and directories currently installed.) @@ -280,7 +312,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bwa-0.7.18/ && 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 > ../bwa_0.7.18-1_source.changes +I: user script /srv/workspace/pbuilder/1092460/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1092460/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bwa-0.7.18/ && 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 > ../bwa_0.7.18-1_source.changes dpkg-buildpackage: info: source package bwa dpkg-buildpackage: info: source version 0.7.18-1 dpkg-buildpackage: info: source distribution unstable @@ -355,6 +391,7 @@ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtindex.c -o bwtindex.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwashm.c -o bwashm.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwase.c -o bwase.o +gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwaseqio.c -o bwaseqio.o bwashm.c: In function 'bwa_shm_stage': bwashm.c:33:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | ftruncate(shmid, BWA_CTL_SIZE); @@ -362,7 +399,6 @@ bwashm.c:70:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwaseqio.c -o bwaseqio.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtgap.c -o bwtgap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtaln.c -o bwtaln.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bamlite.c -o bamlite.o @@ -371,11 +407,13 @@ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 pemerge.c -o pemerge.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 maxk.c -o maxk.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_core.c -o bwtsw2_core.o +gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_main.c -o bwtsw2_main.o In file included from /usr/include/string.h:548, from kopen.c:6: In function 'strncpy', inlined from 'cmd2argv' at kopen.c:248:2, inlined from 'kopen' at kopen.c:306:13: +gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_aux.c -o bwtsw2_aux.o /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -391,8 +429,6 @@ /usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_main.c -o bwtsw2_main.o -gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwt_lite.c -o bwt_lite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -Wdate-time -D_FORTIFY_SOURCE=2 fastmap.c -o fastmap.o @@ -445,9 +481,9 @@ make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.18' dh_md5sums dh_builddeb +dpkg-deb: building package 'bwa' in '../bwa_0.7.18-1_arm64.deb'. dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.18-1_arm64.deb'. dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.18-1_arm64.deb'. -dpkg-deb: building package 'bwa' in '../bwa_0.7.18-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bwa_0.7.18-1_arm64.buildinfo dpkg-genchanges --build=binary -O../bwa_0.7.18-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -455,12 +491,14 @@ 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/1092460/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1092460/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/2793843 and its subdirectories -I: Current time: Thu Mar 20 03:54:29 -12 2025 -I: pbuilder-time-stamp: 1742486069 +I: removing directory /srv/workspace/pbuilder/1092460 and its subdirectories +I: Current time: Thu Apr 23 12:18:37 +14 2026 +I: pbuilder-time-stamp: 1776896317