Diff of the two buildlogs: -- --- b1/build.log 2024-05-29 17:20:19.727206942 +0000 +++ b2/build.log 2024-05-29 17:22:28.325729162 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 29 05:18:06 -12 2024 -I: pbuilder-time-stamp: 1717003086 +I: Current time: Wed Jul 2 13:43:22 +14 2025 +I: pbuilder-time-stamp: 1751413402 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,51 +30,83 @@ 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/1368075/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2777506/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 1 23:43 /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/2777506/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2777506/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' + 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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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='15964e8c80804c53843e27928c6b61a3' - 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='1368075' - PS1='# ' - PS2='> ' + INVOCATION_ID=4cbcd9e9fa3a4d0b9da5be32f510bc6e + 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=2777506 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.9HJQdKej/pbuilderrc_GfqK --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.9HJQdKej/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' + 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.9HJQdKej/pbuilderrc_BGUN --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.9HJQdKej/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' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-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 May 28 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1368075/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2777506/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -139,7 +171,7 @@ Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] -Fetched 19.0 MB in 0s (97.8 MB/s) +Fetched 19.0 MB in 0s (53.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19716 files and directories currently installed.) @@ -270,7 +302,11 @@ 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/2777506/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2777506/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 @@ -307,10 +343,6 @@ g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -c -o SeqList.o SeqList.cpp g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -c -o Taxonomy.o Taxonomy.cpp g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -c -o ParsInsert.o ParsInsert.cpp -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); - | ^~~~~~~~~~~~~ ParsInsert.cpp:412:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 412 | DisplayL("%s\nCommand Line:[%s]\n", VERSION, cmd.c_str()); | ^~~~~~~ @@ -329,8 +361,12 @@ 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 PNode.cpp:27: + from SeqList.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); @@ -342,7 +378,7 @@ 432 | DisplayL("]\n"); | ^~~~~ In file included from PNode.h:31, - from SeqList.cpp:27: + 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); @@ -382,23 +418,23 @@ SeqList.cpp:531:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 531 | DisplayT("Loading sequence %d\n", seqCount); | ^~~~~~~~~~~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': SeqList.cpp:565:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 565 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -PNode.cpp:304:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqList.cpp:580:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 580 | DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +PNode.cpp:304:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: At global scope: ParsInsert.cpp:93:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 93 | char *statsName = "PI_Results.log"; @@ -894,7 +930,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 1 sec +Tree Sequence Read Completed: 10143 sequences, 0 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -981,15 +1017,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 2 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 3 seconds, 6762 nodes per sec -Parsimony Calculation Completed: 2 sec -[5 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 4 seconds, 5071 nodes per sec +Parsimony Calculation Completed: 3 sec +[7 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] @@ -1989,28 +2025,28 @@ 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: 1 sec} -[ 1000/20285] {7 sec} [I_1000] -[ 2000/20285] {13 sec} [7996] -[ 3000/20285] {18 sec} [39961] -[ 4000/20285] {23 sec} [81358] -[ 5000/20285] {28 sec} [I_5000] -[ 6000/20285] {32 sec} [4546] -[ 7000/20285] {36 sec} [67802] -[ 8000/20285] {41 sec} [135894] -[ 9000/20285] {44 sec} [I_9000] -[ 10000/20285] {47 sec} [137100] -[ 11000/20285] {49 sec} [I_11000] -[ 12000/20285] {53 sec} [63458] -[ 13000/20285] {56 sec} [47043] -[ 14000/20285] {59 sec} [I_14000] -[ 15000/20285] {61 sec} [44776] -[ 16000/20285] {64 sec} [16125] -[ 17000/20285] {66 sec} [I_17000] -[ 18000/20285] {68 sec} [99851] -[ 19000/20285] {70 sec} [104182] -[ 20000/20285] {71 sec} [63281] -Insertion of 957 sequences in [71 sec] -[75 sec elapsed] Insert Locations Completed: 70 sec +[ 1000/20285] {6 sec} [I_1000] +[ 2000/20285] {11 sec} [7996] +[ 3000/20285] {16 sec} [39961] +[ 4000/20285] {20 sec} [81358] +[ 5000/20285] {25 sec} [I_5000] +[ 6000/20285] {29 sec} [4546] +[ 7000/20285] {33 sec} [67802] +[ 8000/20285] {37 sec} [135894] +[ 9000/20285] {40 sec} [I_9000] +[ 10000/20285] {43 sec} [137100] +[ 11000/20285] {46 sec} [I_11000] +[ 12000/20285] {50 sec} [63458] +[ 13000/20285] {52 sec} [47043] +[ 14000/20285] {56 sec} [I_14000] +[ 15000/20285] {58 sec} [44776] +[ 16000/20285] {60 sec} [16125] +[ 17000/20285] {62 sec} [I_17000] +[ 18000/20285] {63 sec} [99851] +[ 19000/20285] {65 sec} [104182] +[ 20000/20285] {66 sec} [63281] +Insertion of 957 sequences in [66 sec] +[72 sec elapsed] Insert Locations Completed: 65 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9216,8 +9252,8 @@ 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 = 70, 49217 per hour -Process Completed: 76 sec +Insert Time = 65, 53003 per hour +Process Completed: 72 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9244,8 +9280,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_amd64.deb'. dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_amd64.deb'. +dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_amd64.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-15_all.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-15_amd64.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-15_amd64.changes @@ -9254,12 +9290,14 @@ 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/2777506/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2777506/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/1368075 and its subdirectories -I: Current time: Wed May 29 05:20:18 -12 2024 -I: pbuilder-time-stamp: 1717003218 +I: removing directory /srv/workspace/pbuilder/2777506 and its subdirectories +I: Current time: Wed Jul 2 13:45:27 +14 2025 +I: pbuilder-time-stamp: 1751413527