Diff of the two buildlogs: -- --- b1/build.log 2024-10-29 07:34:17.738196566 +0000 +++ b2/build.log 2024-10-29 08:00:13.627064631 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 1 01:46:27 -12 2025 -I: pbuilder-time-stamp: 1764596787 +I: Current time: Tue Oct 29 21:34:21 +14 2024 +I: pbuilder-time-stamp: 1730187261 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/42979/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28213/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-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 Oct 29 07:34 /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/28213/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28213/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=22 ' - 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=10 ' + 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='21c8ccf631534ee3815f383216266084' - 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='42979' - PS1='# ' - PS2='> ' + INVOCATION_ID=c5321fe9d0ad443d8a6e2d3f50d51c00 + 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=28213 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.xlXNboZK/pbuilderrc_lFDy --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.xlXNboZK/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.xlXNboZK/pbuilderrc_a37a --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.xlXNboZK/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos6-i386 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) 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/42979/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/28213/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -148,7 +180,7 @@ Get: 30 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.8+dfsg-3 [106 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libgsl28 i386 2.8+dfsg-3 [978 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.8+dfsg-3 [1240 kB] -Fetched 22.4 MB in 0s (77.3 MB/s) +Fetched 22.4 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 ... 19934 files and directories currently installed.) @@ -291,7 +323,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/ && 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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/28213/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/28213/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/ && 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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -362,7 +398,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j22 + make -j10 make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' @@ -383,9 +419,9 @@ g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/readSeqFile.o art_SOLiD_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/read_SOLiD.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/samRead.o art_SOLiD_src/samRead.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_SOLiD art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art.o art_SOLiD_src/readSeqFile.o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_454 art_454_src/art_454.o art_454_src/art.o art_454_src/read_profile.o art_454_src/readSeqFile.o art_454_src/seqRead.o art_454_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_illumina art_illumina_src/art_illumina.o art_illumina_src/art_qual_scale.o art_illumina_src/empdist.o art_illumina_src/readSeqFile.o art_illumina_src/seqRead.o art_illumina_src/samRead.o -lgsl -lgslcblas -lm +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_SOLiD art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art.o art_SOLiD_src/readSeqFile.o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/samRead.o -lgsl -lgslcblas -lm make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_auto_test @@ -403,9 +439,9 @@ Single-end simulation -Total CPU time used: 0.058387 +Total CPU time used: 0.131435 -The random seed for the run: 1764596819 +The random seed for the run: 1730187329 Parameters Settings number of flow cycles: 100 @@ -436,9 +472,9 @@ Paired-end simulation -Total CPU time used: 0.046939 +Total CPU time used: 0.14252 -The random seed for the run: 1764596819 +The random seed for the run: 1730187330 Parameters Settings number of flow cycles: 100 @@ -474,9 +510,9 @@ Paired-end simulation -Total CPU time used: 0.049723 +Total CPU time used: 0.101787 -The random seed for the run: 1764596819 +The random seed for the run: 1730187330 Parameters Settings number of flow cycles: 200 @@ -512,9 +548,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 10.1749 +Total CPU time used: 22.1106 -The random seed for the run: 1764596820 +The random seed for the run: 1730187330 Parameters Settings number of flow cycles: 100 @@ -545,9 +581,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 8.42958 +Total CPU time used: 21.0325 -The random seed for the run: 1764596830 +The random seed for the run: 1730187353 Parameters Settings number of flow cycles: 100 @@ -580,7 +616,7 @@ Single-end simulation -Total CPU time used: 0.058371 +Total CPU time used: 0.153187 The random seed for the run: 777 @@ -613,7 +649,7 @@ Single-end simulation -Total CPU time used: 0.058879 +Total CPU time used: 0.111992 The random seed for the run: 777 @@ -647,9 +683,9 @@ Single-end simulation -Total CPU time used: 0.11788 +Total CPU time used: 0.306569 -The random seed for the run: 1764596839 +The random seed for the run: 1730187374 Parameters Settings fold of read coverage: 10X @@ -679,9 +715,9 @@ Single-end simulation -Total CPU time used: 0.151759 +Total CPU time used: 0.381654 -The random seed for the run: 1764596839 +The random seed for the run: 1730187375 Parameters Settings fold of read coverage: 20X @@ -709,9 +745,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.196787 +Total CPU time used: 0.48632 -The random seed for the run: 1764596839 +The random seed for the run: 1730187375 Parameters Settings fold of read coverage: 20X @@ -749,7 +785,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.092045 +Total CPU time used: 0.206833 The random seed for the run: 777 @@ -787,7 +823,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.099913 +Total CPU time used: 0.224031 The random seed for the run: 777 @@ -830,9 +866,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.314556 +Total CPU time used: 0.806488 -The random seed for the run: 1764596840 +The random seed for the run: 1730187376 Parameters Settings fold of read coverage: 50X @@ -866,9 +902,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 287.022 +Total CPU time used: 679.845 -The random seed for the run: 1764596840 +The random seed for the run: 1730187377 Parameters Settings # reads per amplion: 100 @@ -898,9 +934,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 176.334 +Total CPU time used: 409.049 -The random seed for the run: 1764597128 +The random seed for the run: 1730188070 Parameters Settings # read pairs per amplion: 80 @@ -931,9 +967,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 112.094 +Total CPU time used: 260.72 -The random seed for the run: 1764597305 +The random seed for the run: 1730188498 Parameters Settings # read pairs per amplion: 50 @@ -965,9 +1001,9 @@ Single-end Simulation -Total CPU time used: 0.061526 +Total CPU time used: 0.119276 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 35 @@ -999,9 +1035,9 @@ Single-end Simulation -Total CPU time used: 0.046871 +Total CPU time used: 0.108511 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 50 @@ -1033,9 +1069,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.030389 +Total CPU time used: 0.057552 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 150 @@ -1072,9 +1108,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.050638 +Total CPU time used: 0.105816 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 100 @@ -1111,9 +1147,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.03632 +Total CPU time used: 0.078117 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 100 @@ -1150,9 +1186,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.356236 +Total CPU time used: 0.844485 -The random seed for the run: 1764597418 +The random seed for the run: 1730188764 Parameters used during run Read Length: 100 @@ -1184,9 +1220,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 0.419752 +Total CPU time used: 0.75464 -The random seed for the run: 1764597419 +The random seed for the run: 1730188765 Parameters used during run Read Length: 100 @@ -1221,9 +1257,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 0.494401 +Total CPU time used: 0.900549 -The random seed for the run: 1764597419 +The random seed for the run: 1730188766 Parameters used during run Read Length: 100 @@ -1258,7 +1294,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.036409 +Total CPU time used: 0.066262 The random seed for the run: 777 @@ -1297,7 +1333,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.034207 +Total CPU time used: 0.092212 The random seed for the run: 777 @@ -1336,9 +1372,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.039225 +Total CPU time used: 0.078076 -The random seed for the run: 1764597420 +The random seed for the run: 1730188768 Parameters used during run Read Length: 100 @@ -1377,9 +1413,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.03612 +Total CPU time used: 0.074358 -The random seed for the run: 1764597420 +The random seed for the run: 1730188768 Parameters used during run Read Length: 75 @@ -1412,7 +1448,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j22 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j10 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Nothing to be done for 'install-data-am'. @@ -1467,8 +1503,8 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined +dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb @@ -1482,12 +1518,14 @@ 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/28213/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28213/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/42979 and its subdirectories -I: Current time: Mon Dec 1 01:57:14 -12 2025 -I: pbuilder-time-stamp: 1764597434 +I: removing directory /srv/workspace/pbuilder/28213 and its subdirectories +I: Current time: Tue Oct 29 22:00:12 +14 2024 +I: pbuilder-time-stamp: 1730188812