Diff of the two buildlogs: -- --- b1/build.log 2024-12-01 08:58:23.290465462 +0000 +++ b2/build.log 2024-12-01 08:59:01.088771785 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 30 20:57:19 -12 2024 -I: pbuilder-time-stamp: 1733043439 +I: Current time: Sun Jan 4 05:21:25 +14 2026 +I: pbuilder-time-stamp: 1767453685 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying copy-samtools-test-properly.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3647001/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3629365/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Jan 3 15:21 /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/3629365/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3629365/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8ab2213a570f40cf8042c39d2d16f9da' - 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='3647001' - PS1='# ' - PS2='> ' + INVOCATION_ID=bec6e33f73f048a995f990db42ae4a7c + 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=3629365 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.Iu8XAWTi/pbuilderrc_MUbE --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.Iu8XAWTi/b1 --logfile b1/build.log dwgsim_0.1.14-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.Iu8XAWTi/pbuilderrc_LxcK --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.Iu8XAWTi/b2 --logfile b2/build.log dwgsim_0.1.14-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3647001/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3629365/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -169,7 +201,7 @@ Get: 51 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 24.3 MB in 0s (70.0 MB/s) +Fetched 24.3 MB in 3s (7504 kB/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 ... 19962 files and directories currently installed.) @@ -396,7 +428,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/dwgsim-0.1.14/ && 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 > ../dwgsim_0.1.14-3_source.changes +I: user script /srv/workspace/pbuilder/3629365/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3629365/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/dwgsim-0.1.14/ && 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 > ../dwgsim_0.1.14-3_source.changes dpkg-buildpackage: info: source package dwgsim dpkg-buildpackage: info: source version 0.1.14-3 dpkg-buildpackage: info: source distribution unstable @@ -406,7 +442,7 @@ debian/rules clean dh clean dh_auto_clean - make -j20 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip dwgsim *~ *.a *.so.* *.so *.dylib; make[1]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' @@ -421,10 +457,9 @@ sed -i 's/occour/occur/' src/dwgsim_opt.c sed -i 's/occour/occur/' debian/dwgsim.1 dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/dwgsim_opt.c -o src/dwgsim_opt.o -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut.c -o src/mut.o In file included from src/dwgsim_opt.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); @@ -432,10 +467,10 @@ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut.c -o src/mut.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/contigs.c -o src/contigs.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/regions_bed.c -o src/regions_bed.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_txt.c -o src/mut_txt.o -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_bed.c -o src/mut_bed.o In file included from src/mut_txt.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); @@ -443,7 +478,7 @@ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_vcf.c -o src/mut_vcf.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_bed.c -o src/mut_bed.o In file included from src/mut_bed.c:33: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); @@ -451,7 +486,7 @@ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_input.c -o src/mut_input.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_vcf.c -o src/mut_vcf.o In file included from src/mut_vcf.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); @@ -459,7 +494,7 @@ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/dwgsim.c -o src/dwgsim.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_input.c -o src/mut_input.o In file included from src/mut_input.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); @@ -467,6 +502,7 @@ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/dwgsim.c -o src/dwgsim.o src/dwgsim.c: In function 'dwgsim_core': src/dwgsim.c:864:35: warning: initialization of 'FILE *' from incompatible pointer type 'struct gzFile_s **' [-Wincompatible-pointer-types] 864 | FILE *fpo = (0 == j) ? opt->fp_bwa1: opt->fp_bwa2; @@ -780,7 +816,7 @@ make[1]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' ln -s /usr/share/doc/samtools/examples samtools dh_auto_test - make -j20 test + make -j42 test make[2]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' if [ -d tmp ]; then rm -r tmp; fi /bin/bash testdata/test.sh @@ -824,12 +860,14 @@ 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/3629365/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3629365/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/3647001 and its subdirectories -I: Current time: Sat Nov 30 20:58:22 -12 2024 -I: pbuilder-time-stamp: 1733043502 +I: removing directory /srv/workspace/pbuilder/3629365 and its subdirectories +I: Current time: Sun Jan 4 05:22:00 +14 2026 +I: pbuilder-time-stamp: 1767453720