Diff of the two buildlogs: -- --- b1/build.log 2024-04-29 14:59:09.273992830 +0000 +++ b2/build.log 2024-04-29 15:03:02.084072948 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 29 02:53:54 -12 2024 -I: pbuilder-time-stamp: 1714402434 +I: Current time: Mon Jun 2 11:22:13 +14 2025 +I: pbuilder-time-stamp: 1748812933 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/577231/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1302049/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Jun 1 21:22 /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/1302049/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1302049/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='16c3b879e9114a278f849cb76842efe1' - 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='577231' - PS1='# ' - PS2='> ' + INVOCATION_ID=748119d33c4c45bda3a4620cb92a5124 + 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=1302049 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.6TBwqYbG/pbuilderrc_tV16 --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.6TBwqYbG/b1 --logfile b1/build.log snpsift_5.1+dfsg2-2.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.6TBwqYbG/pbuilderrc_C1pd --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.6TBwqYbG/b2 --logfile b2/build.log snpsift_5.1+dfsg2-2.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 codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 23 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/577231/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1302049/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -696,7 +728,7 @@ Get: 345 http://deb.debian.org/debian trixie/main arm64 maven all 3.8.7-2 [19.3 kB] Get: 346 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 347 http://deb.debian.org/debian trixie/main arm64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 339 MB in 6s (58.3 MB/s) +Fetched 339 MB in 1s (244 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. @@ -1843,8 +1875,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 29 14:55:51 UTC 2024. -Universal Time is now: Mon Apr 29 14:55:51 UTC 2024. +Local time is now: Sun Jun 1 21:23:05 UTC 2025. +Universal Time is now: Sun Jun 1 21:23:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2318,7 +2350,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpsift-5.1+dfsg2/ && 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_5.1+dfsg2-2_source.changes +I: user script /srv/workspace/pbuilder/1302049/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1302049/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpsift-5.1+dfsg2/ && 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_5.1+dfsg2-2_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-2 dpkg-buildpackage: info: source distribution unstable @@ -3974,8 +4010,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 21.456 s -[INFO] Finished at: 2024-04-29T02:56:56-12:00 +[INFO] Total time: 18.134 s +[INFO] Finished at: 2025-06-02T11:23:59+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpsift-5.1+dfsg2' @@ -4024,11 +4060,11 @@ 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: 0.33 s - in org.snpsift.testCases.unit.TestCasesConcordance +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.323 s - in org.snpsift.testCases.unit.TestCasesConcordance [INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt TestCasesFilterGt.test_01(28): Test TestCasesFilterGt.test_02(62): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.snpsift.testCases.unit.TestCasesFilterGt +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.snpsift.testCases.unit.TestCasesFilterGt [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4072,13 +4108,13 @@ 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: 13.666 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.089 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [INFO] Running org.snpsift.testCases.unit.TestCasesIndex TestCasesIndex.test_01(32): Test TestCasesIndex.test_02(84): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.577 s - in org.snpsift.testCases.unit.TestCasesIndex +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.74 s - in org.snpsift.testCases.unit.TestCasesIndex [INFO] Running org.snpsift.testCases.unit.TestCasesHwe -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.snpsift.testCases.unit.TestCasesHwe +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.snpsift.testCases.unit.TestCasesHwe [INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test @@ -4097,12 +4133,12 @@ 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: 0.349 s - in org.snpsift.testCases.unit.TestCasesCaseControl +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.341 s - in org.snpsift.testCases.unit.TestCasesCaseControl [INFO] Running org.snpsift.testCases.unit.TestCasesFilterChrPos Annotate: ./test/filterChrPos_01.txt ./test/filterChrPos_01.vcf Annotate: ./test/filterChrPos_02.txt ./test/filterChrPos_02.vcf Annotate: ./test/filterChrPos_03.txt ./test/filterChrPos_03.vcf -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos [INFO] Running org.snpsift.testCases.unit.TestCasesLd [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesLd [INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields @@ -4141,7 +4177,7 @@ 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: 0.117 s - in org.snpsift.testCases.unit.TestCasesExtractFields +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.snpsift.testCases.unit.TestCasesExtractFields [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4185,7 +4221,7 @@ 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: 12.325 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.348 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem [INFO] Running org.snpsift.testCases.unit.TestCasesSplit TestCasesSplit.test_01(28): Test TestCasesSplit.test_02(58): Test @@ -4194,9 +4230,9 @@ [INFO] Running org.snpsift.testCases.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpsift.testCases.unit.TestCasesIntervals +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesIntervals [INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.snpsift.testCases.unit.TestCasesFilterALL +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.snpsift.testCases.unit.TestCasesFilterALL [INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists @@ -4227,7 +4263,7 @@ 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: 0.767 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.693 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog [INFO] Running org.snpsift.testCases.unit.TestCasesPrivate TestCasesPrivate.test_01(48): Test TestCasesPrivate.test_02(59): Test @@ -4237,20 +4273,20 @@ 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: 0.025 s - in org.snpsift.testCases.unit.TestCasesPrivate +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets TestCasesGeneSets.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.snpsift.testCases.unit.TestCasesGeneSets +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.snpsift.testCases.unit.TestCasesGeneSets [INFO] Running org.snpsift.testCases.unit.TestCasesSort TestCasesSort.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesSort +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.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: 0.009 s - in org.snpsift.testCases.unit.TestCasesVarType +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.snpsift.testCases.unit.TestCasesVarType [INFO] Running org.snpsift.testCases.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test @@ -4320,7 +4356,7 @@ 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: 1.055 s - in org.snpsift.testCases.unit.TestCasesFilter +[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.978 s - in org.snpsift.testCases.unit.TestCasesFilter [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test @@ -4328,7 +4364,7 @@ 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: 3.361 s - in org.snpsift.testCases.unit.TestCasesDbNsfp +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.351 s - in org.snpsift.testCases.unit.TestCasesDbNsfp [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test @@ -4336,7 +4372,7 @@ 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: 8.893 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.728 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4380,10 +4416,10 @@ 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: 12.526 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.036 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex [INFO] Running org.snpsift.testCases.unit.TestCasesGt TestCasesGt.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.snpsift.testCases.unit.TestCasesGt +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4427,7 +4463,7 @@ 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: 12.274 s - in org.snpsift.testCases.unit.TestCasesAnnotate +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.06 s - in org.snpsift.testCases.unit.TestCasesAnnotate [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4471,10 +4507,10 @@ 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: 12.191 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.007 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix [INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck TestCasesVcfCheck.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesVcfCheck +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesVcfCheck [INFO] [INFO] Results: [INFO] @@ -4483,8 +4519,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:33 min -[INFO] Finished at: 2024-04-29T02:58:33-12:00 +[INFO] Total time: 01:23 min +[INFO] Finished at: 2025-06-02T11:25:25+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/snpsift-5.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -4508,8 +4544,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.561 s -[INFO] Finished at: 2024-04-29T02:58:35-12:00 +[INFO] Total time: 0.622 s +[INFO] Finished at: 2025-06-02T11:25:27+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/reproducible-path/snpsift-5.1\+dfsg2 --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom @@ -4609,16 +4645,16 @@ 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 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. -dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-2_all.deb'. dpkg-deb: building package 'snpsift' in '../snpsift_5.1+dfsg2-2_all.deb'. +dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-2_all.deb'. +dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.1+dfsg2-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4626,12 +4662,14 @@ 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/1302049/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1302049/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/577231 and its subdirectories -I: Current time: Mon Apr 29 02:59:08 -12 2024 -I: pbuilder-time-stamp: 1714402748 +I: removing directory /srv/workspace/pbuilder/1302049 and its subdirectories +I: Current time: Mon Jun 2 11:26:00 +14 2025 +I: pbuilder-time-stamp: 1748813160