Diff of the two buildlogs: -- --- b1/build.log 2023-04-11 18:48:27.577036554 +0000 +++ b2/build.log 2023-04-11 18:54:55.248042684 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 13 13:05:09 -12 2024 -I: pbuilder-time-stamp: 1715648709 +I: Current time: Wed Apr 12 08:48:32 +14 2023 +I: pbuilder-time-stamp: 1681238912 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./parsinsert_1.04.orig.tar.gz] I: copying [./parsinsert_1.04-12.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Aug 3 18:06:12 2022 -12 +gpgv: Signature made Thu Aug 4 20:06:12 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,11 +30,20 @@ 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/6474/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10594/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/10594/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10594/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -44,38 +53,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='6474' + PPID='10594' PS1='# ' PS2='> ' 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.hNnGXJrs/pbuilderrc_R1Jc --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hNnGXJrs/b1 --logfile b1/build.log parsinsert_1.04-12.dsc' + 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.hNnGXJrs/pbuilderrc_Vh46 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hNnGXJrs/b2 --logfile b2/build.log --extrapackages usrmerge parsinsert_1.04-12.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink11-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 04:50 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6474/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 11 00:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/10594/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +150,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 0s (42.0 MB/s) +Fetched 18.3 MB in 0s (42.2 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 ... 19616 files and directories currently installed.) @@ -275,8 +284,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_1.04-12_source.changes +I: user script /srv/workspace/pbuilder/10594/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/10594/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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_1.04-12_source.changes dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-12 dpkg-buildpackage: info: source distribution unstable @@ -338,8 +356,12 @@ | | long unsigned int | unsigned int | %08lX +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); @@ -350,12 +372,8 @@ 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 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); @@ -425,6 +443,14 @@ ParsInsert.cpp:96:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | char *seqFilename = "PI_Tree.fasta"; | ^~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': +SeqList.cpp:202:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 202 | fgets(buffer, sizeof(buffer)-1, f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': +SeqList.cpp:229:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 229 | fgets(buffer, sizeof(buffer)-1, f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -602,14 +628,6 @@ ParsInsert.cpp:958:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 958 | DisplayL("\n"); | ^~~~ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': -SeqList.cpp:202:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 202 | fgets(buffer, sizeof(buffer)-1, f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': -SeqList.cpp:229:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 229 | fgets(buffer, sizeof(buffer)-1, f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int SetInternalTaxonomy(CPTree*)': ParsInsert.cpp:1092:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1092 | DisplayT("\rSetting Internal Taxonomy %d nodes remaining ", nSeqRemaining); @@ -912,10 +930,10 @@ 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 +Tree Sequence Read Completed: 10143 sequences, 0 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -1010,7 +1028,7 @@ Processed 20285 nodes in 7 seconds, 2898 nodes per sec Parsimony Calculation Completed: 6 sec -[15 sec elapsed] Searching for insertion points: +[14 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] @@ -2011,27 +2029,27 @@ 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] {22 sec} [I_1000] -[ 2000/20285] {42 sec} [7996] +[ 2000/20285] {43 sec} [7996] [ 3000/20285] {62 sec} [39961] [ 4000/20285] {81 sec} [81358] -[ 5000/20285] {100 sec} [I_5000] +[ 5000/20285] {99 sec} [I_5000] [ 6000/20285] {118 sec} [4546] -[ 7000/20285] {134 sec} [67802] -[ 8000/20285] {150 sec} [135894] -[ 9000/20285] {162 sec} [I_9000] +[ 7000/20285] {135 sec} [67802] +[ 8000/20285] {151 sec} [135894] +[ 9000/20285] {163 sec} [I_9000] [ 10000/20285] {175 sec} [137100] [ 11000/20285] {187 sec} [I_11000] -[ 12000/20285] {199 sec} [63458] -[ 13000/20285] {212 sec} [47043] -[ 14000/20285] {224 sec} [I_14000] -[ 15000/20285] {236 sec} [44776] -[ 16000/20285] {245 sec} [16125] -[ 17000/20285] {253 sec} [I_17000] -[ 18000/20285] {259 sec} [99851] -[ 19000/20285] {265 sec} [104182] -[ 20000/20285] {269 sec} [63281] -Insertion of 957 sequences in [270 sec] -[284 sec elapsed] Insert Locations Completed: 269 sec +[ 12000/20285] {198 sec} [63458] +[ 13000/20285] {210 sec} [47043] +[ 14000/20285] {222 sec} [I_14000] +[ 15000/20285] {233 sec} [44776] +[ 16000/20285] {241 sec} [16125] +[ 17000/20285] {248 sec} [I_17000] +[ 18000/20285] {254 sec} [99851] +[ 19000/20285] {259 sec} [104182] +[ 20000/20285] {263 sec} [63281] +Insertion of 957 sequences in [264 sec] +[277 sec elapsed] Insert Locations Completed: 263 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9237,8 +9255,8 @@ 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 = 269, 12807 per hour -Process Completed: 285 sec +Insert Time = 263, 13099 per hour +Process Completed: 278 sec make[1]: Leaving directory '/build/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9264,9 +9282,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-12_arm64.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-12_all.deb'. dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-12_arm64.deb'. -dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-12_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-12_arm64.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9274,12 +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/10594/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10594/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/6474 and its subdirectories -I: Current time: Mon May 13 13:11:25 -12 2024 -I: pbuilder-time-stamp: 1715649085 +I: removing directory /srv/workspace/pbuilder/10594 and its subdirectories +I: Current time: Wed Apr 12 08:54:54 +14 2023 +I: pbuilder-time-stamp: 1681239294