Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 12:34:33.079283990 +0000 +++ b2/build.log 2025-01-21 12:39:15.918538671 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 21 00:26:49 -12 2025 -I: pbuilder-time-stamp: 1737462409 +I: Current time: Tue Feb 24 08:57:36 +14 2026 +I: pbuilder-time-stamp: 1771873056 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1060897/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2118275/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Feb 23 18:57 /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/2118275/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2118275/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='4ab53224e0924d4285f78a5164866dee' - 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='1060897' - PS1='# ' - PS2='> ' + INVOCATION_ID=dd80d5790f294494a9188fd4660e4d82 + 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=2118275 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.D9mCi3Z6/pbuilderrc_Yzwb --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.D9mCi3Z6/b1 --logfile b1/build.log parsinsert_1.04-15.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.D9mCi3Z6/pbuilderrc_3bAF --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.D9mCi3Z6/b2 --logfile b2/build.log parsinsert_1.04-15.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 codethink02-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1060897/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2118275/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -137,7 +169,7 @@ Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] -Fetched 19.9 MB in 0s (49.2 MB/s) +Fetched 19.9 MB in 0s (86.5 MB/s) Preconfiguring packages ... 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 ... 19970 files and directories currently installed.) @@ -272,7 +304,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/parsinsert-1.04/ && 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 > ../parsinsert_1.04-15_source.changes +I: user script /srv/workspace/pbuilder/2118275/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2118275/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/parsinsert-1.04/ && 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 > ../parsinsert_1.04-15_source.changes dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-15 dpkg-buildpackage: info: source distribution unstable @@ -327,10 +363,6 @@ ParsInsert.cpp:417:25: note: in expansion of macro 'VERSION' 417 | DisplayT(USAGE, VERSION, APPNAME); | ^~~~~~~ -Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': -Taxonomy.cpp:96:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); - | ^~~~~~~~~~~~~ In file included from PNode.h:31, from SeqList.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': @@ -343,34 +375,14 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ -In file included from PNode.h:31, - from PNode.cpp:27: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ -In file included from ParsInsert.h:29, - from ParsInsert.cpp:34: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ +Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': +Taxonomy.cpp:96:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); + | ^~~~~~~~~~~~~ SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': SeqList.cpp:490:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 490 | DisplayT("Loading sequence %d [%s]\n", count, name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ SeqList.cpp:492:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 492 | DisplayT("Loading sequence %d\n", count); | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -394,6 +406,30 @@ SeqList.cpp:605:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 605 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from PNode.h:31, + from PNode.cpp:27: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ +In file included from ParsInsert.h:29, + from ParsInsert.cpp:34: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ PNode.cpp: In member function 'void CPTree::Parse(const char*)': PNode.cpp:299:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 299 | DisplayL("Could not process all the chars in NEWICK file\n"); @@ -896,7 +932,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 3 sec +Tree Sequence Read Completed: 10143 sequences, 0 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -983,15 +1019,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 9 sec +Internal Taxonomy Completed: 3 sec Setting internal parsimony sequences ... Calculating internal parsimony sequences ... Calculating Parsimony ... CalcParsimony 20000 nodes remaining CalcParsimony 19000 nodes remaining CalcParsimony 18000 nodes remaining CalcParsimony 17000 nodes remaining CalcParsimony 16000 nodes remaining CalcParsimony 15000 nodes remaining CalcParsimony 14000 nodes remaining CalcParsimony 13000 nodes remaining CalcParsimony 12000 nodes remaining CalcParsimony 11000 nodes remaining CalcParsimony 10000 nodes remaining CalcParsimony 9000 nodes remaining CalcParsimony 8000 nodes remaining CalcParsimony 7000 nodes remaining CalcParsimony 6000 nodes remaining CalcParsimony 5000 nodes remaining CalcParsimony 4000 nodes remaining CalcParsimony 3000 nodes remaining CalcParsimony 2000 nodes remaining CalcParsimony 1000 nodes remaining CalcParsimony 0 nodes remaining Applying parsimonious selections back down the tree. 10147 nodes were modified -Processed 20285 nodes in 8 seconds, 2536 nodes per sec -Parsimony Calculation Completed: 7 sec -[20 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 6 seconds, 3381 nodes per sec +Parsimony Calculation Completed: 5 sec +[9 sec elapsed] Searching for insertion points: **** Sequence is already in core tree: 100403 **** Sequence is already in core tree: 100628 Insert [ 100769](len=7683) [ 1235 sites] (147 - 6732) [Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Streptosporangineae;Nocardiopsaceae;Nocardiopsis] @@ -1990,29 +2026,29 @@ **** Sequence is already in core tree: 9947 Insert [ 99538](len=7683) [ 1184 sites] (137 - 6427) [Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Chryseobacterium] Insert [ 99764](len=7683) [ 1261 sites] (130 - 6790) [Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Brucellaceae;Brucella] -Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 2 sec} -[ 1000/20285] {32 sec} [I_1000] -[ 2000/20285] {56 sec} [7996] -[ 3000/20285] {84 sec} [39961] -[ 4000/20285] {107 sec} [81358] -[ 5000/20285] {131 sec} [I_5000] -[ 6000/20285] {153 sec} [4546] -[ 7000/20285] {173 sec} [67802] -[ 8000/20285] {195 sec} [135894] -[ 9000/20285] {210 sec} [I_9000] -[ 10000/20285] {225 sec} [137100] -[ 11000/20285] {242 sec} [I_11000] -[ 12000/20285] {254 sec} [63458] -[ 13000/20285] {272 sec} [47043] -[ 14000/20285] {286 sec} [I_14000] -[ 15000/20285] {298 sec} [44776] -[ 16000/20285] {309 sec} [16125] -[ 17000/20285] {319 sec} [I_17000] -[ 18000/20285] {326 sec} [99851] -[ 19000/20285] {332 sec} [104182] -[ 20000/20285] {337 sec} [63281] -Insertion of 957 sequences in [338 sec] -[357 sec elapsed] Insert Locations Completed: 337 sec +Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 1 sec} +[ 1000/20285] {15 sec} [I_1000] +[ 2000/20285] {28 sec} [7996] +[ 3000/20285] {42 sec} [39961] +[ 4000/20285] {55 sec} [81358] +[ 5000/20285] {69 sec} [I_5000] +[ 6000/20285] {82 sec} [4546] +[ 7000/20285] {95 sec} [67802] +[ 8000/20285] {106 sec} [135894] +[ 9000/20285] {115 sec} [I_9000] +[ 10000/20285] {123 sec} [137100] +[ 11000/20285] {129 sec} [I_11000] +[ 12000/20285] {137 sec} [63458] +[ 13000/20285] {143 sec} [47043] +[ 14000/20285] {153 sec} [I_14000] +[ 15000/20285] {160 sec} [44776] +[ 16000/20285] {168 sec} [16125] +[ 17000/20285] {173 sec} [I_17000] +[ 18000/20285] {176 sec} [99851] +[ 19000/20285] {184 sec} [104182] +[ 20000/20285] {189 sec} [63281] +Insertion of 957 sequences in [190 sec] +[198 sec elapsed] Insert Locations Completed: 189 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9218,8 +9254,8 @@ Family: 830 821 ( 98.92%) 821 876 ( 93.72%) Genus: 573 563 ( 98.25%) 563 706 ( 79.75%) Species: 49 49 (100.00%) 49 53 ( 92.45%) -Insert Time = 337, 10223 per hour -Process Completed: 357 sec +Insert Time = 189, 18228 per hour +Process Completed: 198 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9247,8 +9283,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_arm64.deb'. -dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_arm64.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-15_all.deb'. +dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-15_arm64.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-15_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9256,12 +9292,14 @@ 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/2118275/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2118275/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/1060897 and its subdirectories -I: Current time: Tue Jan 21 00:34:31 -12 2025 -I: pbuilder-time-stamp: 1737462871 +I: removing directory /srv/workspace/pbuilder/2118275 and its subdirectories +I: Current time: Tue Feb 24 09:02:14 +14 2026 +I: pbuilder-time-stamp: 1771873334