Diff of the two buildlogs: -- --- b1/build.log 2024-04-26 18:11:43.008506041 +0000 +++ b2/build.log 2024-04-26 18:17:57.992480999 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 29 12:26:10 -12 2025 -I: pbuilder-time-stamp: 1748564770 +I: Current time: Sat Apr 27 08:11:48 +14 2024 +I: pbuilder-time-stamp: 1714155108 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ 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/27385/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7486/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 Apr 26 18:12 /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/7486/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7486/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='415bfbed5578481191a1fcc87ecf6971' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='27385' - PS1='# ' - PS2='> ' + INVOCATION_ID=f312129b426c40b8a9081463d8bf7574 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=7486 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.h9pd0DeJ/pbuilderrc_qHph --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.h9pd0DeJ/b1 --logfile b1/build.log parsinsert_1.04-15.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.h9pd0DeJ/pbuilderrc_cLt1 --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.h9pd0DeJ/b2 --logfile b2/build.log parsinsert_1.04-15.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27385/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:12 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/7486/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] -Fetched 19.3 MB in 2s (10.6 MB/s) +Fetched 19.3 MB in 0s (49.9 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 ... 19882 files and directories currently installed.) @@ -279,7 +311,11 @@ 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/7486/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/7486/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 @@ -293,7 +329,7 @@ mv parsinsert ParsInsert || true mv: cannot stat 'parsinsert': No such file or directory dh_auto_clean - make -j22 clean + make -j10 clean make[2]: Entering directory '/build/reproducible-path/parsinsert-1.04' rm -f ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o *.fasta *.log *.results *.tree make[2]: Leaving directory '/build/reproducible-path/parsinsert-1.04' @@ -308,7 +344,7 @@ make[1]: Entering directory '/build/reproducible-path/parsinsert-1.04' blhc: ignore-line-regexp: ^g\+\+ .* -fPIE.*$ dh_auto_build - make -j22 "INSTALL=install --strip-program=true" + make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/parsinsert-1.04' 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 AttrList.o AttrList.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 Knox_Stddef.o Knox_Stddef.cpp @@ -334,10 +370,6 @@ 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*)': @@ -350,18 +382,6 @@ 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"); - | ^~~~~ 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); @@ -389,6 +409,22 @@ 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"); + | ^~~~~ +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 ParsInsert.h:29, from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': @@ -900,7 +936,7 @@ Reading Newick Tree: [core_rdp.ntree] opening source file: [core_rdp.ntree] Opening file: core_rdp.ntree ...Parsing Newick file: core_rdp.ntree ...Processed 246406 chars of 246447 -Newick Tree Read Completed: 10143 taxa, 0 sec +Newick Tree Read Completed: 10143 taxa, 1 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] Tree Sequence Read Completed: 10143 sequences, 1 sec @@ -908,7 +944,7 @@ Duplicate sequence found [175015] Duplicate sequence found [290252] Loading sequence 998 [174865] -Insert Sequecne Read Completed: 998 sequences, 0 sec +Insert Sequecne Read Completed: 998 sequences, 1 sec Checking Taxa Taxonomy 318 of 20285 nodes are missing taxonomy 40556 131780 113792 97603 21481 98089 130706 112397 @@ -996,9 +1032,9 @@ 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 13 seconds, 1560 nodes per sec -Parsimony Calculation Completed: 12 sec -[19 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 7 seconds, 2898 nodes per sec +Parsimony Calculation Completed: 6 sec +[16 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] @@ -1997,29 +2033,29 @@ **** 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: 3 sec} -[ 1000/20285] {13 sec} [I_1000] -[ 2000/20285] {22 sec} [7996] -[ 3000/20285] {30 sec} [39961] -[ 4000/20285] {40 sec} [81358] -[ 5000/20285] {49 sec} [I_5000] -[ 6000/20285] {58 sec} [4546] -[ 7000/20285] {70 sec} [67802] -[ 8000/20285] {81 sec} [135894] -[ 9000/20285] {98 sec} [I_9000] -[ 10000/20285] {105 sec} [137100] -[ 11000/20285] {114 sec} [I_11000] -[ 12000/20285] {123 sec} [63458] -[ 13000/20285] {133 sec} [47043] -[ 14000/20285] {142 sec} [I_14000] -[ 15000/20285] {161 sec} [44776] -[ 16000/20285] {180 sec} [16125] -[ 17000/20285] {199 sec} [I_17000] -[ 18000/20285] {222 sec} [99851] -[ 19000/20285] {231 sec} [104182] -[ 20000/20285] {239 sec} [63281] -Insertion of 957 sequences in [242 sec] -[260 sec elapsed] Insert Locations Completed: 241 sec +Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 1 sec} +[ 1000/20285] {19 sec} [I_1000] +[ 2000/20285] {34 sec} [7996] +[ 3000/20285] {48 sec} [39961] +[ 4000/20285] {62 sec} [81358] +[ 5000/20285] {80 sec} [I_5000] +[ 6000/20285] {96 sec} [4546] +[ 7000/20285] {114 sec} [67802] +[ 8000/20285] {134 sec} [135894] +[ 9000/20285] {149 sec} [I_9000] +[ 10000/20285] {162 sec} [137100] +[ 11000/20285] {177 sec} [I_11000] +[ 12000/20285] {194 sec} [63458] +[ 13000/20285] {216 sec} [47043] +[ 14000/20285] {228 sec} [I_14000] +[ 15000/20285] {239 sec} [44776] +[ 16000/20285] {248 sec} [16125] +[ 17000/20285] {254 sec} [I_17000] +[ 18000/20285] {259 sec} [99851] +[ 19000/20285] {264 sec} [104182] +[ 20000/20285] {267 sec} [63281] +Insertion of 957 sequences in [268 sec] +[283 sec elapsed] Insert Locations Completed: 267 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9225,8 +9261,8 @@ 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 = 241, 14295 per hour -Process Completed: 279 sec +Insert Time = 267, 12903 per hour +Process Completed: 283 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9254,8 +9290,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_i386.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_i386.deb'. +dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-15_all.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-15_i386.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-15_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9263,12 +9299,14 @@ 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/7486/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7486/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/27385 and its subdirectories -I: Current time: Thu May 29 12:34:33 -12 2025 -I: pbuilder-time-stamp: 1748565274 +I: removing directory /srv/workspace/pbuilder/7486 and its subdirectories +I: Current time: Sat Apr 27 08:17:57 +14 2024 +I: pbuilder-time-stamp: 1714155477