Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 06:15:50.502181333 +0000 +++ b2/build.log 2024-01-07 06:17:18.530388297 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 18:14:13 -12 2024 -I: pbuilder-time-stamp: 1704608053 +I: Current time: Sun Feb 9 02:38:56 +14 2025 +I: pbuilder-time-stamp: 1739018336 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./centrifuge_1.0.3-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.EjVy6YmO/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.lxAAYaCN/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 9 17:01:32 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -36,49 +36,80 @@ dpkg-source: info: applying fix_arm_build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3215519/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1009986/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Feb 8 12:39 /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/1009986/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1009986/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,-fixfilepath parallel=15 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a7152a0196d14231acab301ee29c6f04' - 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='3215519' - PS1='# ' - PS2='> ' + INVOCATION_ID=a491a00a1fd34949bd2a5ab3d6725be0 + 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=1009986 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.c7etqucM/pbuilderrc_lryE --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.c7etqucM/b1 --logfile b1/build.log centrifuge_1.0.3-8.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://78.137.99.97:3128' + 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.c7etqucM/pbuilderrc_dI7W --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.c7etqucM/b2 --logfile b2/build.log centrifuge_1.0.3-8.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://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash @@ -138,7 +169,7 @@ -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 7 09:30 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 8 12:39 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su @@ -164,7 +195,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/3215519/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1009986/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -266,7 +297,7 @@ Get: 58 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libjellyfish-2.0-2 amd64 2.3.0-10 [65.1 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 jellyfish amd64 2.3.0-10 [790 kB] -Fetched 27.0 MB in 4s (6139 kB/s) +Fetched 27.0 MB in 0s (89.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) @@ -474,8 +505,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 7 06:14:37 UTC 2024. -Universal Time is now: Sun Jan 7 06:14:37 UTC 2024. +Local time is now: Sat Feb 8 12:39:13 UTC 2025. +Universal Time is now: Sat Feb 8 12:39:13 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjellyfish-2.0-2:amd64 (2.3.0-10) ... @@ -530,7 +561,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/centrifuge-1.0.3/ && 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 > ../centrifuge_1.0.3-8_source.changes +I: user script /srv/workspace/pbuilder/1009986/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1009986/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/centrifuge-1.0.3/ && 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 > ../centrifuge_1.0.3-8_source.changes dpkg-buildpackage: info: source package centrifuge dpkg-buildpackage: info: source version 1.0.3-8 dpkg-buildpackage: info: source distribution unstable @@ -540,7 +575,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' rm -f centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge-build-bin-debug centrifuge-class-debug centrifuge-inspect-bin-debug \ centrifuge-build-bin.exe centrifuge-class.exe centrifuge-inspect-bin.exe centrifuge-build-bin-debug.exe centrifuge-class-debug.exe centrifuge-inspect-bin-debug.exe \ @@ -557,7 +592,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' dh_auto_build -- BITS=64 BITS_FLAG= - make -j15 "INSTALL=install --strip-program=true" BITS=64 BITS_FLAG= + make -j16 "INSTALL=install --strip-program=true" BITS=64 BITS_FLAG= make[2]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' /usr/bin/g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -fdebug-prefix-map=/build/reproducible-path/centrifuge-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ @@ -580,6 +615,22 @@ -lpthread In file included from blockwise_sa.h:29, from bt2_idx.h:44, + from centrifuge_build.cpp:27: +diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': +diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; + | ^~ +diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; + | ^~~~~ +diff_sample.h:176:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; + | ^~ +diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; + | ^~~~~ +In file included from blockwise_sa.h:29, + from bt2_idx.h:44, from centrifuge.cpp:34: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] @@ -596,7 +647,8 @@ | ^~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:44, - from centrifuge_build.cpp:27: + from hier_idx.h:24, + from centrifuge_inspect.cpp:28: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; @@ -633,23 +685,6 @@ bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3641 | for(size_t k = 0; k < kmer_size; k++) { | ~~^~~~~~~~~~~ -In file included from blockwise_sa.h:29, - from bt2_idx.h:44, - from hier_idx.h:24, - from centrifuge_inspect.cpp:28: -diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': -diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; - | ^~ -diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; - | ^~~~~ -diff_sample.h:176:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; - | ^~ -diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; - | ^~~~~ In file included from centrifuge.cpp:47: classifier.h: In instantiation of 'int Classifier::go(const Scoring&, const Ebwt&, const Ebwt&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]': centrifuge.cpp:2660:94: required from here @@ -755,7 +790,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' dh_auto_install -- prefix=/usr/lib/centrifuge - make -j15 install DESTDIR=/build/reproducible-path/centrifuge-1.0.3/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge + make -j16 install DESTDIR=/build/reproducible-path/centrifuge-1.0.3/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge make[2]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' mkdir -p /build/reproducible-path/centrifuge-1.0.3/debian/centrifuge/usr/lib/centrifuge/bin mkdir -p /build/reproducible-path/centrifuge-1.0.3/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices @@ -816,12 +851,14 @@ 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/1009986/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1009986/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/3215519 and its subdirectories -I: Current time: Sat Jan 6 18:15:49 -12 2024 -I: pbuilder-time-stamp: 1704608149 +I: removing directory /srv/workspace/pbuilder/1009986 and its subdirectories +I: Current time: Sun Feb 9 02:40:21 +14 2025 +I: pbuilder-time-stamp: 1739018421