Diff of the two buildlogs: -- --- b1/build.log 2024-12-13 18:58:22.235910129 +0000 +++ b2/build.log 2024-12-13 19:00:31.130037712 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 15 13:19:26 -12 2026 -I: pbuilder-time-stamp: 1768526366 +I: Current time: Fri Jan 16 15:21:32 +14 2026 +I: pbuilder-time-stamp: 1768526492 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/693973/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1432108/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Jan 16 01:21 /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/1432108/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1432108/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(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='61f9ff9037374499978d9ffb862bc04a' - 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='693973' - PS1='# ' - PS2='> ' + INVOCATION_ID=c0c37d8230754a16943c9bb66115c938 + 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=1432108 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.eVL0r7yu/pbuilderrc_DAer --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.eVL0r7yu/b1 --logfile b1/build.log flye_2.9.5+dfsg-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.eVL0r7yu/pbuilderrc_ersr --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.eVL0r7yu/b2 --logfile b2/build.log flye_2.9.5+dfsg-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 codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/693973/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1432108/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -214,7 +246,7 @@ Get: 87 http://deb.debian.org/debian trixie/main arm64 libminimap2-dev arm64 2.27+dfsg-1+b3 [114 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] -Fetched 32.4 MB in 0s (131 MB/s) +Fetched 32.4 MB in 0s (100 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 20082 files and directories currently installed.) @@ -521,8 +553,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 16 01:19:47 UTC 2026. -Universal Time is now: Fri Jan 16 01:19:47 UTC 2026. +Local time is now: Fri Jan 16 01:21:53 UTC 2026. +Universal Time is now: Fri Jan 16 01:21:53 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -599,7 +631,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/flye-2.9.5+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 > ../flye_2.9.5+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1432108/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1432108/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/flye-2.9.5+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 > ../flye_2.9.5+dfsg-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -728,8 +764,7 @@ | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, - from assemble/extender.h:10, - from assemble/extender.cpp:14: + from assemble/main_assemble.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ @@ -743,7 +778,8 @@ | ^~~~~~~~~~~~~~ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from assemble/../sequence/overlap.h:12, - from assemble/main_assemble.cpp:14: + from assemble/extender.h:10, + from assemble/extender.cpp:14: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ @@ -824,6 +860,7 @@ 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-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/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/../common/bfcontainer.h: In instantiation of ‘BFContainer::BFIterator BFContainer::BFIterator::operator-(difference_type) const [with T = {anonymous}::KmerMatch; long unsigned int ChunkSize = 1048576; difference_type = long int]’: /usr/include/c++/14/bits/stl_algo.h:1855:71: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = BFContainer<{anonymous}::KmerMatch>::BFIterator; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, @@ -862,7 +899,6 @@ 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) | ^~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/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); @@ -933,8 +969,8 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/build/reproducible-path/flye-2.9.5+dfsg/lib/libcuckoo -I/build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree -I/build/reproducible-path/flye-2.9.5+dfsg/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG repeat_graph/read_aligner.cpp -o repeat_graph/read_aligner.o In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, - from repeat_graph/multiplicity_inferer.h:7, - from repeat_graph/multiplicity_inferer.cpp:5: + from repeat_graph/output_generator.h:13, + from repeat_graph/output_generator.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ @@ -949,8 +985,8 @@ /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:91:13: note: remove the ‘< >’ In file included from repeat_graph/../sequence/overlap.h:12, from repeat_graph/repeat_graph.h:11, - from repeat_graph/output_generator.h:13, - from repeat_graph/output_generator.cpp:5: + from repeat_graph/multiplicity_inferer.h:7, + from repeat_graph/multiplicity_inferer.cpp:5: /build/reproducible-path/flye-2.9.5+dfsg/lib/interval_tree/IntervalTree.h:59:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 59 | IntervalTree(void) | ^ @@ -1282,12 +1318,14 @@ 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/1432108/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1432108/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/693973 and its subdirectories -I: Current time: Thu Jan 15 13:21:20 -12 2026 -I: pbuilder-time-stamp: 1768526480 +I: removing directory /srv/workspace/pbuilder/1432108 and its subdirectories +I: Current time: Fri Jan 16 15:23:30 +14 2026 +I: pbuilder-time-stamp: 1768526610