Diff of the two buildlogs: -- --- b1/build.log 2025-03-06 21:40:19.361317813 +0000 +++ b2/build.log 2025-03-06 21:42:40.618978092 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 8 16:01:04 -12 2026 -I: pbuilder-time-stamp: 1775707264 +I: Current time: Fri Mar 7 11:40:23 +14 2025 +I: pbuilder-time-stamp: 1741297223 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ 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/3351412/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1363368/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Mar 6 21:40 /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/1363368/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1363368/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-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=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='c1c027a534b54b0d96c1042983a3a54b' - 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='3351412' - PS1='# ' - PS2='> ' + INVOCATION_ID=10bcd648e3de4efeb4f494c131298712 + 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=1363368 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.ifZqX66r/pbuilderrc_N3r6 --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.ifZqX66r/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.ifZqX66r/pbuilderrc_09XQ --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.ifZqX66r/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 infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3351412/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1363368/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -136,7 +168,7 @@ Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 2s (12.1 MB/s) +Fetched 20.6 MB in 2s (9129 kB/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 ... 19783 files and directories currently installed.) @@ -271,7 +303,11 @@ 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/1363368/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1363368/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 @@ -331,7 +367,7 @@ 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); | ^~~~~~~~~~~~~ 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); @@ -343,7 +379,7 @@ 432 | DisplayL("]\n"); | ^~~~~ 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); @@ -393,13 +429,6 @@ 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"; @@ -413,6 +442,13 @@ ParsInsert.cpp:96:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | char *seqFilename = "PI_Tree.fasta"; | ^~~~~~~~~~~~~~~ +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: In function 'int main(int, char**)': ParsInsert.cpp:248:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 248 | DisplayL("%s\n", COPYRIGHT); @@ -895,7 +931,7 @@ 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] @@ -990,7 +1026,7 @@ Processed 20285 nodes in 3 seconds, 6762 nodes per sec Parsimony Calculation Completed: 2 sec -[5 sec elapsed] Searching for insertion points: +[4 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] @@ -1990,28 +2026,28 @@ 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] {33 sec} [4546] -[ 7000/20285] {37 sec} [67802] -[ 8000/20285] {42 sec} [135894] -[ 9000/20285] {45 sec} [I_9000] -[ 10000/20285] {48 sec} [137100] -[ 11000/20285] {51 sec} [I_11000] -[ 12000/20285] {54 sec} [63458] -[ 13000/20285] {57 sec} [47043] -[ 14000/20285] {60 sec} [I_14000] -[ 15000/20285] {63 sec} [44776] -[ 16000/20285] {65 sec} [16125] -[ 17000/20285] {68 sec} [I_17000] -[ 18000/20285] {69 sec} [99851] -[ 19000/20285] {71 sec} [104182] -[ 20000/20285] {72 sec} [63281] -Insertion of 957 sequences in [72 sec] -[76 sec elapsed] Insert Locations Completed: 71 sec +[ 1000/20285] {6 sec} [I_1000] +[ 2000/20285] {11 sec} [7996] +[ 3000/20285] {16 sec} [39961] +[ 4000/20285] {21 sec} [81358] +[ 5000/20285] {26 sec} [I_5000] +[ 6000/20285] {31 sec} [4546] +[ 7000/20285] {36 sec} [67802] +[ 8000/20285] {40 sec} [135894] +[ 9000/20285] {43 sec} [I_9000] +[ 10000/20285] {46 sec} [137100] +[ 11000/20285] {49 sec} [I_11000] +[ 12000/20285] {51 sec} [63458] +[ 13000/20285] {54 sec} [47043] +[ 14000/20285] {57 sec} [I_14000] +[ 15000/20285] {60 sec} [44776] +[ 16000/20285] {62 sec} [16125] +[ 17000/20285] {64 sec} [I_17000] +[ 18000/20285] {65 sec} [99851] +[ 19000/20285] {67 sec} [104182] +[ 20000/20285] {68 sec} [63281] +Insertion of 957 sequences in [68 sec] +[71 sec elapsed] Insert Locations Completed: 67 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9217,8 +9253,8 @@ 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 = 71, 48523 per hour -Process Completed: 76 sec +Insert Time = 67, 51420 per hour +Process Completed: 71 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9245,8 +9281,8 @@ 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 @@ -9255,12 +9291,14 @@ 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/1363368/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1363368/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/3351412 and its subdirectories -I: Current time: Wed Apr 8 16:03:15 -12 2026 -I: pbuilder-time-stamp: 1775707395 +I: removing directory /srv/workspace/pbuilder/1363368 and its subdirectories +I: Current time: Fri Mar 7 11:42:39 +14 2025 +I: pbuilder-time-stamp: 1741297359