Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 23:40:35.023690815 +0000 +++ b2/build.log 2024-05-13 23:43:04.905314664 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 15 18:01:36 -12 2025 -I: pbuilder-time-stamp: 1750053696 +I: Current time: Tue May 14 13:40:38 +14 2024 +I: pbuilder-time-stamp: 1715643638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4046159/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2379453/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 May 13 23:40 /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/2379453/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2379453/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=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='1dcaddb17b7c4d43a5ac262f1f7f1867' - 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='4046159' - PS1='# ' - PS2='> ' + INVOCATION_ID=806b63d9bd384b808a94a75bc73911c9 + 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=2379453 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.53HnRraD/pbuilderrc_aGW0 --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.53HnRraD/b1 --logfile b1/build.log flye_2.9.3+dfsg2-1.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.53HnRraD/pbuilderrc_CHYc --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.53HnRraD/b2 --logfile b2/build.log flye_2.9.3+dfsg2-1.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 codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 15 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4046159/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2379453/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -202,7 +234,7 @@ Get: 75 http://deb.debian.org/debian trixie/main arm64 libminimap2-dev arm64 2.27+dfsg-1 [114 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1+b1 [617 kB] -Fetched 30.7 MB in 0s (116 MB/s) +Fetched 30.7 MB in 0s (189 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19744 files and directories currently installed.) @@ -470,8 +502,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 16 06:01:55 UTC 2025. -Universal Time is now: Mon Jun 16 06:01:55 UTC 2025. +Local time is now: Mon May 13 23:41:03 UTC 2024. +Universal Time is now: Mon May 13 23:41:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -537,7 +569,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/flye-2.9.3+dfsg2/ && 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 > ../flye_2.9.3+dfsg2-1_source.changes +I: user script /srv/workspace/pbuilder/2379453/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2379453/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/flye-2.9.3+dfsg2/ && 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 > ../flye_2.9.3+dfsg2-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.3+dfsg2-1 dpkg-buildpackage: info: source distribution unstable @@ -655,7 +691,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence.cpp -o sequence/sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/sequence_container.cpp -o sequence/sequence_container.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG sequence/vertex_index.cpp -o sequence/vertex_index.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/graph_processing.cpp -o repeat_graph/graph_processing.o In file included from sequence/overlap.cpp:25: sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator+(difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: sequence/overlap.cpp:240:43: required from here @@ -671,16 +706,6 @@ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ -sequence/vertex_index.cpp: In member function ‘void KmerCounter::count(bool)’: -sequence/vertex_index.cpp:380:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::atomic’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] - 380 | std::memset(_flatCounter, 0, COUNTER_LEN); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo/cuckoohash_map.hh:8, - from sequence/vertex_index.h:15, - from sequence/vertex_index.cpp:12: -/usr/include/c++/13/atomic:753:12: note: ‘struct std::atomic’ declared here - 753 | struct atomic : __atomic_base - | ^~~~~~~~~~~~~~~~~~~~~ sequence/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(difference_type) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: /usr/include/c++/13/bits/stl_algo.h:1897:71: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ /usr/include/c++/13/bits/stl_algo.h:1931:38: required from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ @@ -699,6 +724,17 @@ sequence/../common/bfcontainer.h:141:21: note: because ‘BFContainer<{anonymous}::KmerMatch>::BFIterator’ has user-provided ‘BFContainer::BFIterator& BFContainer::BFIterator::operator=(const BFContainer::BFIterator&) [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576]’ 141 | BFIterator& operator=(const BFIterator &rhs) | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/graph_processing.cpp -o repeat_graph/graph_processing.o +sequence/vertex_index.cpp: In member function ‘void KmerCounter::count(bool)’: +sequence/vertex_index.cpp:380:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::atomic’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] + 380 | std::memset(_flatCounter, 0, COUNTER_LEN); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo/cuckoohash_map.hh:8, + from sequence/vertex_index.h:15, + from sequence/vertex_index.cpp:12: +/usr/include/c++/13/atomic:753:12: note: ‘struct std::atomic’ declared here + 753 | struct atomic : __atomic_base + | ^~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/haplotype_resolver.cpp -o repeat_graph/haplotype_resolver.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/main_repeat.cpp -o repeat_graph/main_repeat.o repeat_graph/main_repeat.cpp:152:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] @@ -938,12 +974,14 @@ 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/2379453/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2379453/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/4046159 and its subdirectories -I: Current time: Sun Jun 15 18:03:33 -12 2025 -I: pbuilder-time-stamp: 1750053813 +I: removing directory /srv/workspace/pbuilder/2379453 and its subdirectories +I: Current time: Tue May 14 13:43:03 +14 2024 +I: pbuilder-time-stamp: 1715643783