Diff of the two buildlogs: -- --- b1/build.log 2024-11-05 14:45:40.215886674 +0000 +++ b2/build.log 2024-11-05 14:51:40.999007518 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 8 09:02:25 -12 2025 -I: pbuilder-time-stamp: 1765227745 +I: Current time: Wed Nov 6 04:45:44 +14 2024 +I: pbuilder-time-stamp: 1730817944 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying test_scope_for_junit.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1578991/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3920172/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Nov 5 14:45 /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/3920172/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3920172/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='20f64c0b54e84df5a4dba93a6b2630cc' - 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='1578991' - PS1='# ' - PS2='> ' + INVOCATION_ID=76027b82da374933b6d41989c56d558e + 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=3920172 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.KTyGTzik/pbuilderrc_UZfF --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.KTyGTzik/b1 --logfile b1/build.log snpsift_5.2.e+dfsg-1.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.KTyGTzik/pbuilderrc_O2w9 --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.KTyGTzik/b2 --logfile b2/build.log snpsift_5.2.e+dfsg-1.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 codethink01-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1578991/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3920172/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -461,7 +493,7 @@ Get: 318 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.5 [108 kB] -Fetched 305 MB in 1s (220 MB/s) +Fetched 305 MB in 2s (186 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:arm64. (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 ... 20087 files and directories currently installed.) @@ -1509,8 +1541,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 8 21:03:11 UTC 2025. -Universal Time is now: Mon Dec 8 21:03:11 UTC 2025. +Local time is now: Tue Nov 5 14:46:33 UTC 2024. +Universal Time is now: Tue Nov 5 14:46:33 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1961,7 +1993,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpsift-5.2.e+dfsg/ && 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 > ../snpsift_5.2.e+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3920172/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3920172/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpsift-5.2.e+dfsg/ && 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 > ../snpsift_5.2.e+dfsg-1_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.2.e+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1974,7 +2010,7 @@ bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibsnpsift-java jh_clean -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/snpsift-5.2.e+dfsg' # Removing all the sidx files created during the tests. Then one of them must @@ -2384,8 +2420,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 27.140 s -[INFO] Finished at: 2025-12-08T09:04:07-12:00 +[INFO] Total time: 15.622 s +[INFO] Finished at: 2024-11-06T04:47:22+14:00 [INFO] ------------------------------------------------------------------------ debian/rules execute_before_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpsift-5.2.e+dfsg' @@ -2465,7 +2501,7 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 25.805 s - in org.snpsift.tests.unit.TestCasesAnnotateTabix +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.062 s - in org.snpsift.tests.unit.TestCasesAnnotateTabix [INFO] Running org.snpsift.tests.unit.TestCasesEnumArray EnumArray: length: 17 / 17, number of enums: 6 0: 'one' (1) @@ -2479,13 +2515,13 @@ 8: 'three' (3) 9: 'four' (4) -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.726 s - in org.snpsift.tests.unit.TestCasesEnumArray +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.698 s - in org.snpsift.tests.unit.TestCasesEnumArray [INFO] Running org.snpsift.tests.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesIntervals +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesIntervals [INFO] Running org.snpsift.tests.unit.TestCasesFilterChrPos -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.snpsift.tests.unit.TestCasesFilterChrPos +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.snpsift.tests.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.tests.unit.TestCasesAnnotateUseIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -2529,7 +2565,7 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.784 s - in org.snpsift.tests.unit.TestCasesAnnotateUseIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.766 s - in org.snpsift.tests.unit.TestCasesAnnotateUseIndex [INFO] Running org.snpsift.tests.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -2573,11 +2609,11 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.775 s - in org.snpsift.tests.unit.TestCasesAnnotateMem +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.897 s - in org.snpsift.tests.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.tests.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test TestCasesFilterGt.test_02(62): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.snpsift.tests.unit.TestCasesFilterGt +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.snpsift.tests.unit.TestCasesFilterGt [INFO] Running org.snpsift.tests.unit.TestCasesConcordance TestCasesConcordance.test_01(68): Test TestCasesConcordance.test_02(74): Test @@ -2591,9 +2627,9 @@ TestCasesConcordance.test_10(153): Test TestCasesConcordance.test_11(164): Test TestCasesConcordance.test_12(181): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.snpsift.tests.unit.TestCasesConcordance +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.snpsift.tests.unit.TestCasesConcordance [INFO] Running org.snpsift.tests.unit.TestCasesVariantTypeCounter -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpsift.tests.unit.TestCasesVariantTypeCounter +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.tests.unit.TestCasesVariantTypeCounter [INFO] Running org.snpsift.tests.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -2637,9 +2673,9 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.096 s - in org.snpsift.tests.unit.TestCasesAnnotateCreateIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.241 s - in org.snpsift.tests.unit.TestCasesAnnotateCreateIndex [INFO] Running org.snpsift.tests.unit.TestCasesStringArray -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.136 s - in org.snpsift.tests.unit.TestCasesStringArray +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.944 s - in org.snpsift.tests.unit.TestCasesStringArray [INFO] Running org.snpsift.tests.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test @@ -2658,13 +2694,13 @@ TestCasesCaseControl.test_02_Str(71): Test TestCasesCaseControl.test_03_Str(89): Test TestCasesCaseControl.test_04_Str(113): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.301 s - in org.snpsift.tests.unit.TestCasesCaseControl +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.snpsift.tests.unit.TestCasesCaseControl [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnBool -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.893 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnBool +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.832 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnBool [INFO] Running org.snpsift.tests.unit.TestCasesIndex TestCasesIndex.test_01(32): Test TestCasesIndex.test_02(84): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.721 s - in org.snpsift.tests.unit.TestCasesIndex +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.663 s - in org.snpsift.tests.unit.TestCasesIndex [INFO] Running org.snpsift.tests.unit.TestCasesPrivate TestCasesPrivate.test_01(48): Test TestCasesPrivate.test_02(59): Test @@ -2674,19 +2710,19 @@ TestCasesPrivate.test_06(95): Test TestCasesPrivate.test_07(101): Test TestCasesPrivate.test_08(107): Test -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.snpsift.tests.unit.TestCasesPrivate +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpsift.tests.unit.TestCasesPrivate [INFO] Running org.snpsift.tests.unit.TestCasesSplit TestCasesSplit.test_01(28): Test TestCasesSplit.test_02(58): Test TestCasesSplit.test_03(84): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.snpsift.tests.unit.TestCasesSplit +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesSplit [INFO] Running org.snpsift.tests.unit.TestCasesVarType TestCasesVarType.test_05_multiple(82): Test TestCasesVarType.test_01_SNP(58): Test TestCasesVarType.test_02_MNP(64): Test TestCasesVarType.test_03_INS(70): Test TestCasesVarType.test_04_DEL(76): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.snpsift.tests.unit.TestCasesVarType +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.snpsift.tests.unit.TestCasesVarType [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameSnp DataFrame: SNP_A, size: 100, current index: 100, memory: 63.4 KB Field types: @@ -3132,9 +3168,9 @@ 98 47093 | C | T | E | null | 653352657 | true | WUADUERWVVTEILAAAWWEQGIIUKQTGFVSEPVTJSEWOEWXDUVMQMTIHNQPTSFSEQDBHZBNESFTNMMBHTCZRTQJGILVEE | null | 0.08956523678408113 | QTH | 99 47588 | C | T | Z | null | 1873761820 | false | YNJMWKISSQSPVODXUFKNLGZUIAZNNDFNUFAVMYECUHCAZJBYCLWWKTSGVR | null | 0.9680541190017328 | UCFAOCDFSUNIOOVESGTIPFVKUARMUBGZXYUKKFAFXYZOHHJFVMANHSBRDCSOPTTCSZJSNBGPIFIBAHZYTPM | -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.snpsift.tests.unit.TestCasesDataFrameSnp +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.snpsift.tests.unit.TestCasesDataFrameSnp [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnChar -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.961 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnChar +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnChar [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameMixed DataFrame: MIXED, size: 100, current index: 100, memory: 63.4 KB Field types: @@ -3247,7 +3283,7 @@ 98 50305 | GGA | AAGG | G | null | -1078219233 | null | LOOZKHCWJZYEZKSPMSDXYJXODFUCNQJPJJQLSMLNNQFYIWKZIBFJARVKVELGNMJBSLVSOJJPATNF | null | 0.7680804977882877 | null | 99 50789 | CTCC | TGATA | N | null | -1627198920 | false | JAJASVDEOFQ | null | 0.5578843763975981 | GYRGQQXTQSITYGVHCIJQYUMGDLDKITYVVNHWOBSZWJLXTOEH | -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpsift.tests.unit.TestCasesDataFrameMixed +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.tests.unit.TestCasesDataFrameMixed [INFO] Running org.snpsift.tests.unit.TestCasesExtractFields TestCasesExtractFields.test_31_ann(291): Test TestCasesExtractFields.test_00(71): Test @@ -3284,21 +3320,21 @@ TestCasesExtractFields.test_33(312): Test TestCasesExtractFields.test_34(323): Test TestCasesExtractFields.test_35(340): Test -[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.snpsift.tests.unit.TestCasesExtractFields +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.snpsift.tests.unit.TestCasesExtractFields [INFO] Running org.snpsift.tests.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.snpsift.tests.unit.TestCasesGeneSets +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.snpsift.tests.unit.TestCasesGeneSets [INFO] Running org.snpsift.tests.unit.TestCasesGt TestCasesGt.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.snpsift.tests.unit.TestCasesGt +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.snpsift.tests.unit.TestCasesGt [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnFloat -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.68 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnFloat +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.534 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnFloat [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnInt -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.382 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnInt +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.169 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnInt [INFO] Running org.snpsift.tests.unit.TestCasesHwe -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.snpsift.tests.unit.TestCasesHwe +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpsift.tests.unit.TestCasesHwe [INFO] Running org.snpsift.tests.unit.TestCasesPosIndex -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesPosIndex +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesPosIndex [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameDel DataFrame: DEL, size: 100, current index: 100, memory: 63.4 KB Field types: @@ -3411,7 +3447,7 @@ 98 49907 | CAC | | P | null | 966658647 | true | KGDJSHWQNTLSEYGZ | null | 0.6885368220839251 | GTPFQOWDDNZNFTEUCOAEOMVYXBUMZTNLV | 99 50128 | CA | | E | null | 128095220 | false | NUJYTDVTSDBWKWGYBDKAHAQERJYIGNHYAUFUMIMLNOFPVQJAFDXGIRWIXOBXA | null | 0.4811475357641687 | ZGKNAOXKXJTBFDIJHRUHLXSCTNALYGQVYKSHPRPBNLLZYRIMNEOBUKWLLZRFRXCBJ | -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesDataFrameDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesDataFrameDel [INFO] Running org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test @@ -3419,7 +3455,7 @@ TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.081 s - in org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.15 s - in org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache [INFO] Running org.snpsift.tests.unit.TestCasesSort TestCasesSort.test_01(30): Test [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesSort @@ -3427,10 +3463,10 @@ 1 1000 . A T . . ZZZ_FIELD_FLOAT=3.14;ZZZ_FIELD_STRING=Value1;ZZZ_FIELD_FLAG=false;ZZZ_FIELD_INT=123 [ZZZ_FIELD_FLOAT, ZZZ_FIELD_FLAG, ZZZ_FIELD_INT, ZZZ_FIELD_STRING] [FIELD_FLOAT, FIELD_STRING, FIELD_FLAG, FIELD_INT] -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.snpsift.tests.unit.TestCasesVariantDatabase +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.snpsift.tests.unit.TestCasesVariantDatabase [INFO] Running org.snpsift.tests.unit.TestCasesVcfCheck TestCasesVcfCheck.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesVcfCheck +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.tests.unit.TestCasesVcfCheck [INFO] Running org.snpsift.tests.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test @@ -3500,10 +3536,10 @@ TestCasesFilter.test_27_ann2(812): Test TestCasesFilter.test_26_ann(721): Test TestCasesFilter.test_27_ann(778): Test -[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.074 s - in org.snpsift.tests.unit.TestCasesFilter +[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.994 s - in org.snpsift.tests.unit.TestCasesFilter [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnString DataFrameColumnString.resize(76): Converting column 'Test' to EnumArray. Found 6 enums found. Size before: 44 B, after: 5 B -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.31 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnString +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.141 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnString [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameMnp DataFrame: MNP, size: 100, current index: 100, memory: 63.4 KB Field types: @@ -3731,7 +3767,7 @@ [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesDataFrameIns [INFO] Running org.snpsift.tests.unit.TestCasesFilterALL -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.snpsift.tests.unit.TestCasesFilterALL +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.snpsift.tests.unit.TestCasesFilterALL [INFO] Running org.snpsift.tests.unit.TestCasesAnnotate TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -3775,7 +3811,7 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.754 s - in org.snpsift.tests.unit.TestCasesAnnotate +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.557 s - in org.snpsift.tests.unit.TestCasesAnnotate [INFO] Running org.snpsift.tests.unit.TestCasesDbNsfp TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test @@ -3783,7 +3819,7 @@ TestCasesDbNsfp.test_04(179): Test TestCasesDbNsfp.test_05(200): Test TestCasesDbNsfp.test_06(223): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.773 s - in org.snpsift.tests.unit.TestCasesDbNsfp +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.772 s - in org.snpsift.tests.unit.TestCasesDbNsfp [INFO] Running org.snpsift.tests.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists @@ -3814,11 +3850,11 @@ WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. TestCasesGwasCatalog.test_02(50): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.114 s - in org.snpsift.tests.unit.TestCasesGwasCatalog +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.943 s - in org.snpsift.tests.unit.TestCasesGwasCatalog [INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnLong -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.513 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnLong +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.288 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnLong [INFO] Running org.snpsift.tests.unit.TestCasesBoolArray -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.531 s - in org.snpsift.tests.unit.TestCasesBoolArray +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 s - in org.snpsift.tests.unit.TestCasesBoolArray [INFO] Running org.snpsift.tests.unit.TestCasesLd [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesLd [INFO] @@ -3829,8 +3865,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 03:44 min -[INFO] Finished at: 2025-12-08T09:07:55-12:00 +[INFO] Total time: 03:33 min +[INFO] Finished at: 2024-11-06T04:50:58+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -3854,8 +3890,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.141 s -[INFO] Finished at: 2025-12-08T09:07:59-12:00 +[INFO] Total time: 0.478 s +[INFO] Finished at: 2024-11-06T04:51:00+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/reproducible-path/snpsift-5.2.e\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom @@ -3955,15 +3991,15 @@ dh_missing dh_installdeb dh_gencontrol +dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined -dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined -dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'snpsift' in '../snpsift_5.2.e+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.2.e+dfsg-1_all.deb'. +dpkg-deb: building package 'snpsift' in '../snpsift_5.2.e+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.2.e+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.2.e+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.2.e+dfsg-1_arm64.changes @@ -3972,12 +4008,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3920172/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3920172/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/1578991 and its subdirectories -I: Current time: Mon Dec 8 09:08:37 -12 2025 -I: pbuilder-time-stamp: 1765228117 +I: removing directory /srv/workspace/pbuilder/3920172 and its subdirectories +I: Current time: Wed Nov 6 04:51:36 +14 2024 +I: pbuilder-time-stamp: 1730818296