Diff of the two buildlogs: -- --- b1/build.log 2024-06-02 11:49:41.779059114 +0000 +++ b2/build.log 2024-06-02 11:51:02.039645192 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 1 23:46:25 -12 2024 -I: pbuilder-time-stamp: 1717328785 +I: Current time: Sun Jul 6 08:12:44 +14 2025 +I: pbuilder-time-stamp: 1751739164 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying tempfile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1023217/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2834135/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 Jul 5 18:12 /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/2834135/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2834135/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='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=42 ' + 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='e65df96fe6df463db31d26451ae45d89' - 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='1023217' - PS1='# ' - PS2='> ' + INVOCATION_ID=87a884fd392a48fabdf0670b23366a5c + 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=2834135 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.lgoarEEF/pbuilderrc_zA7q --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.lgoarEEF/b1 --logfile b1/build.log crac_2.5.2+dfsg-6.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.lgoarEEF/pbuilderrc_WrZY --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.lgoarEEF/b2 --logfile b2/build.log crac_2.5.2+dfsg-6.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 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 1 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1023217/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jul 4 14:06 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2834135/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -196,7 +228,7 @@ Get: 63 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 26.1 MB in 1s (43.8 MB/s) +Fetched 26.1 MB in 1s (32.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpopt0:amd64. (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 ... 19719 files and directories currently installed.) @@ -473,7 +505,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/crac-2.5.2+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 > ../crac_2.5.2+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/2834135/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2834135/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/crac-2.5.2+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 > ../crac_2.5.2+dfsg-6_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -685,7 +721,7 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' @@ -1037,7 +1073,7 @@ /usr/include/c++/13/new:126:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -lm -lpthread -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -lm -lpthread -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader @@ -1398,6 +1434,20 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +In file included from ./libReadsReader/readsReader.h:57, + from ./Read.h:55, + from ./ReadIndex.h:52, + from ./Classifier.h:56, + from Classifier.cpp:52: +./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1413,20 +1463,6 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -In file included from ./libReadsReader/readsReader.h:57, - from ./Read.h:55, - from ./ReadIndex.h:52, - from ./Classifier.h:56, - from Classifier.cpp:52: -./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ crac.cpp: In function 'int main(int, char**)': crac.cpp:1009:26: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 1009 | } catch (bad_alloc e) { @@ -1491,7 +1527,7 @@ Classifier.cpp:187:33: note: 'bioundetermined_type' was declared here 187 | BioUndeterminedInfo::Type bioundetermined_type; | ^~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' @@ -1631,7 +1667,7 @@ make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c crac-index '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' @@ -1656,7 +1692,7 @@ make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c crac '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' @@ -1756,12 +1792,14 @@ 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/2834135/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2834135/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/1023217 and its subdirectories -I: Current time: Sat Jun 1 23:49:41 -12 2024 -I: pbuilder-time-stamp: 1717328981 +I: removing directory /srv/workspace/pbuilder/2834135 and its subdirectories +I: Current time: Sun Jul 6 08:14:01 +14 2025 +I: pbuilder-time-stamp: 1751739241