Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 16:45:31.126337677 +0000 +++ b2/build.log 2024-05-09 16:46:39.395425411 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 11 11:07:07 -12 2025 -I: pbuilder-time-stamp: 1749683227 +I: Current time: Fri May 10 06:45:34 +14 2024 +I: pbuilder-time-stamp: 1715273134 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3785909/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3149202/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 May 9 16:45 /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/3149202/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3149202/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=42 ' - DISTRIBUTION='unstable' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d2ca307fdd304e8dba7373a3ce59dbe1' - 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='3785909' - PS1='# ' - PS2='> ' + INVOCATION_ID=8011ecd67c6c4dd7bd48620a6342bd21 + 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=3149202 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.gj2Rbs1O/pbuilderrc_AFbQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gj2Rbs1O/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.gj2Rbs1O/pbuilderrc_i6NI --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gj2Rbs1O/b2 --logfile b2/build.log muscle_5.1.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 10 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3785909/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 9 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3149202/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: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] -Fetched 19.0 MB in 0s (72.5 MB/s) +Fetched 19.0 MB in 0s (52.5 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 ... 19699 files and directories currently installed.) @@ -276,7 +308,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes +I: user script /srv/workspace/pbuilder/3149202/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3149202/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable @@ -286,7 +322,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j42 clean + cd src && make -j20 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' @@ -300,13 +336,14 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' - cd src && make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) + cd src && make -j20 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash mkdir -p Linux/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp +Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp @@ -344,7 +381,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp -Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp @@ -369,11 +405,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ @@ -392,6 +423,11 @@ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp @@ -466,8 +502,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. +dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -475,12 +511,14 @@ 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/3149202/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3149202/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/3785909 and its subdirectories -I: Current time: Wed Jun 11 11:08:29 -12 2025 -I: pbuilder-time-stamp: 1749683309 +I: removing directory /srv/workspace/pbuilder/3149202 and its subdirectories +I: Current time: Fri May 10 06:46:38 +14 2024 +I: pbuilder-time-stamp: 1715273198