Diff of the two buildlogs: -- --- b1/build.log 2023-04-15 10:34:06.410955511 +0000 +++ b2/build.log 2023-04-15 10:59:39.590847194 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 14 22:12:41 -12 2023 -I: pbuilder-time-stamp: 1681553561 +I: Current time: Sat May 18 06:57:14 +14 2024 +I: pbuilder-time-stamp: 1715965034 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 [./snpeff_5.1+d+dfsg.orig.tar.xz] I: copying [./snpeff_5.1+d+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Jan 20 08:36:39 2023 -12 +gpgv: Signature made Sat Jan 21 10:36:39 2023 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snpeff_5.1+d+dfsg-3.dsc: no acceptable signature found @@ -32,52 +32,84 @@ dpkg-source: info: applying lowering_heap_allocation.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18070/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5498/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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 May 18 06:57 /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/5498/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5498/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' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='18070' - PS1='# ' - PS2='> ' + 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=5498 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.nl0OK18Y/pbuilderrc_qkk5 --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.nl0OK18Y/b1 --logfile b1/build.log snpeff_5.1+d+dfsg-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.nl0OK18Y/pbuilderrc_S0th --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.nl0OK18Y/b2 --logfile b2/build.log --extrapackages usrmerge snpeff_5.1+d+dfsg-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink12-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 Apr 11 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18070/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 17 09:10 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/5498/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -556,7 +588,7 @@ Get: 399 http://deb.debian.org/debian bookworm/main arm64 maven all 3.8.7-1 [18.9 kB] Get: 400 http://deb.debian.org/debian bookworm/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 401 http://deb.debian.org/debian bookworm/main arm64 maven-debian-helper all 2.6.2 [108 kB] -Fetched 497 MB in 49s (10.1 MB/s) +Fetched 497 MB in 30s (16.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19616 files and directories currently installed.) @@ -2362,8 +2394,17 @@ 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/snpeff-5.1+d+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 > ../snpeff_5.1+d+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/5498/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/5498/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/snpeff-5.1+d+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 > ../snpeff_5.1+d+dfsg-3_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.1+d+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -2373,7 +2414,7 @@ debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt binnengegaan dh_auto_clean 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 -plibsnpeff-java @@ -2385,7 +2426,7 @@ if [ -e SnpEff.java.old ]; then \ mv SnpEff.java.old src/main/java/org/snpeff/SnpEff.java; \ fi -make[1]: Leaving directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt verlaten jh_clean dh_clean debian/rules binary @@ -2393,7 +2434,7 @@ dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt binnengegaan # We replace the compiling timestamp by the one in d/changelog to enhance # build reproducibility. cp src/main/java/org/snpeff/SnpEff.java SnpEff.java.old @@ -2432,7 +2473,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) -make[1]: Leaving directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt verlaten jh_linkjars dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/snpeff-5.1\+d\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/snpeff-5.1\+d\+dfsg/debian -Dmaven.repo.local=/build/snpeff-5.1\+d\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US @@ -5829,11 +5870,11 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:37 min -[INFO] Finished at: 2023-04-14T22:18:52-12:00 +[INFO] Total time: 03:38 min +[INFO] Finished at: 2024-05-18T07:04:28+14:00 [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test -make[1]: Entering directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt binnengegaan # Moving the unit tests into a subdir of src/test so that Maven sees them. mkdir -p src/test/java/org/snpeff/snpEffect/testCases cp -a src/main/java/org/snpeff/snpEffect/testCases/integration src/test/java/org/snpeff/snpEffect/testCases @@ -5879,14 +5920,14 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 30.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 41.284 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable TestCasesCodonTable.test_01(28): Test TestCasesCodonTable.test_02(59): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.753 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.145 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic TestCasesIntergenic.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.617 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.959 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test @@ -5905,7 +5946,7 @@ TestCasesIntervals.test_07_05(362): Test TestCasesIntervals.test_08_02(413): Test TestCasesIntervals.test_08_03(438): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 26.547 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 34.523 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest @@ -5914,7 +5955,7 @@ TestCasesFisherExactTest.test_03_fisher(103): Test TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test TestCasesFisherExactTest.test_04_fisher(208): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel TestCasesApplyDel.test_apply_variant_01(21): Test TestCasesApplyDel.test_apply_variant_02(31): Test @@ -5929,13 +5970,13 @@ TestCasesApplyDel.test_apply_variant_11(176): Test TestCasesApplyDel.test_apply_variant_12(199): Test TestCasesApplyDel.test_apply_variant_13(223): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.182 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.079 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse TestCasesAnnParse.test_EffectType(29): Test TestCasesAnnParse.test_old_SO(45): Test TestCasesAnnParse.test_old_SO_vcf(53): Test TestCasesAnnParse.testCase_tfbs_ablation(71): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.802 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.903 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup TestCasesHgvsDnaDup.test_01(31): Test TestCasesHgvsDnaDup.test_02(54): Test @@ -5948,7 +5989,7 @@ TestCasesHgvsDnaDup.test_09(247): Test TestCasesHgvsDnaDup.test_10(277): Test TestCasesHgvsDnaDup.test_11(308): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.293 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.672 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence TestCasesDnaNSequence.test_02_long_replaceBase(243): Test TestCasesDnaNSequence.test_13_reverseWc(253): Test @@ -5959,7 +6000,7 @@ TestCasesDnaNSequence.test_02_long_getBase(223): Test TestCasesDnaNSequence.test_01_short_getBase(184): Test TestCasesDnaNSequence.test_01_short_replaceBase(204): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.376 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.83 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test TestCasesApplyMixed.test_apply_variant_06_longer(169): Test @@ -5979,10 +6020,10 @@ TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test TestCasesApplyMixed.test_apply_variant_01_longer(22): Test -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.281 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.442 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 TestCasesEffectCollapse2.test_01(40): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.337 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.773 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations TestCasesStructuralTranslocations.test02_2_nonFs(532): Test TestCasesStructuralTranslocations.test01_0_nonFs(286): Test @@ -6011,7 +6052,7 @@ TestCasesStructuralTranslocations.test04_0_nonFs(778): Test TestCasesStructuralTranslocations.test02_1_nonFs(477): Test TestCasesStructuralTranslocations.test06_no_gene(981): Test -[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 49.54 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 51.208 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer TestCasesSequenceIndexer.test_01(69): Test TestCasesSequenceIndexer.test_02(100): Test @@ -6023,12 +6064,12 @@ TestCasesSequenceIndexer.test_08(247): Test TestCasesSequenceIndexer.test_09(267): Test TestCasesSequenceIndexer.test_10(287): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.56 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.03 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric TestCasesHypergeometric.test_0(77): Test TestCasesHypergeometric.test_01_hyper(83): Test TestCasesHypergeometric.test_02_hyper(202): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -6042,7 +6083,7 @@ TestCasesDnaSequence.test_01_short_getBase(218): Test TestCasesDnaSequence.test_04_Pe(287): Test TestCasesDnaSequence.test_01_short_replaceBase(238): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.856 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.772 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns TestCasesIns.test_01(38): Test .................................................................................................... @@ -6056,13 +6097,13 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.193 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.085 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats TestCasesIntStats.test_01(31): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.537 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.383 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte TestCasesDnaSequenceByte.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp TestCasesApplySnp.test_apply_variant_01(21): Test TestCasesApplySnp.test_apply_variant_02(31): Test @@ -6071,11 +6112,11 @@ TestCasesApplySnp.test_apply_variant_06(77): Test TestCasesApplySnp.test_apply_variant_08(95): Test TestCasesApplySnp.test_apply_variant_09(106): Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.345 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.47 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesJaspar TestCasesJaspar.test_01(22): Test TestCasesJaspar.test_02(56): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.106 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.496 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp TestCasesApplyMnp.test_apply_variant_01(22): Test TestCasesApplyMnp.test_apply_variant_02(33): Test @@ -6090,10 +6131,10 @@ TestCasesApplyMnp.test_apply_variant_11(176): Test TestCasesApplyMnp.test_apply_variant_12(197): Test TestCasesApplyMnp.test_apply_variant_13(219): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.365 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.541 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta TestCasesFasta.test_01(23): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.36 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.764 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps TestCasesSnps.test_01(43): Test .................................................................................................... @@ -6107,12 +6148,12 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.166 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.668 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs TestCasesHgvs.test_01(56): Test TestCasesHgvs.test_02(69): Test TestCasesHgvs.test_03(83): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.465 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.474 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv TestCasesStructuralInv.test01_invGene(214): Test TestCasesStructuralInv.test02(249): Test @@ -6125,16 +6166,16 @@ TestCasesStructuralInv.test09(370): Test TestCasesStructuralInv.test10(387): Test TestCasesStructuralInv.test01_invTr(231): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.851 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.07 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader TestCasesSeekableReader.test_00(60): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf TestCasesSeekableReader.test_01(74): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.064 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.819 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare TestCasesChiSquare.test_1(26): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup TestCasesStructuralDup.test01_dupGene(157): Test TestCasesStructuralDup.test02(194): Test @@ -6147,14 +6188,14 @@ TestCasesStructuralDup.test09(324): Test TestCasesStructuralDup.test10(345): Test TestCasesStructuralDup.test01_dupTr(175): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.615 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.759 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers TestCasesNmers.test_03_Nmers(33): Test -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.025 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign TestCasesAlign.test_01(22): Test TestCasesAlign.test_02(45): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite TestCasesSpliceSite.test_01(34): Test .................................................................................................... @@ -6168,19 +6209,19 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.831 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.532 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector TestCasesGenotypeVector.test_01(23): Test TestCasesGenotypeVector.test_02(48): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup TestCasesHgvsProtDup.test_01(31): Test TestCasesHgvsProtDup.test_02(70): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.839 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.623 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction TestCasesProteinInteraction.test_02_split_codon_base(58): Test TestCasesProteinInteraction.test_01_split_codon_base(26): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.874 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.157 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron TestCasesHgvsIntron.test_01_intron(23): Test ............................................................... @@ -6197,13 +6238,13 @@ 1300 ........................................................................................................... 1500 ....................................................... 1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.364 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.204 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative TestCasesHgvsDnaDupNegative.test_01(34): Test TestCasesHgvsDnaDupNegative.test_02(61): Test TestCasesHgvsDnaDupNegative.test_03(91): Test TestCasesHgvsDnaDupNegative.test_04(122): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.751 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.736 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test @@ -6266,7 +6307,7 @@ Max words: 8 ......... Max words: 9 ......... Done. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 34.586 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 38.416 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -6316,7 +6357,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 61.288 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 68.737 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel TestCasesStructuralDel.test02(249): Test TestCasesStructuralDel.test03(266): Test @@ -6329,24 +6370,24 @@ TestCasesStructuralDel.test10(398): Test TestCasesStructuralDel.test01_delTr(230): Test TestCasesStructuralDel.test01_delGene(212): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.654 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.292 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage TestCasesCochranArmitage.test_01(18): Test TestCasesCochranArmitage.test_02(28): Test TestCasesCochranArmitage.test_03(37): Test TestCasesCochranArmitage.test_04(46): Test TestCasesCochranArmitage.test_05(57): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString TestCasesIubString.test_01(29): Test TestCasesIubString.test_02(39): Test TestCasesIubString.test_03(49): Test TestCasesIubString.test_04(68): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test @@ -6361,7 +6402,7 @@ TestCasesApplyIns.test_apply_variant_11(159): Test TestCasesApplyIns.test_apply_variant_12(178): Test TestCasesApplyIns.test_apply_variant_13(192): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.955 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.616 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList TestCasesGenePvalueList.test_01(28): Test TestCasesGenePvalueList.test_02(46): Test @@ -6372,7 +6413,7 @@ TestCasesGenePvalueList.test_07(155): Test TestCasesGenePvalueList.test_08(187): Test TestCasesGenePvalueList.test_09(209): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.011 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.966 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf TestCasesVcf.test_22_huge_headers(363): Test TestCasesVcf.test_12_readHeader_NL(257): Test @@ -6402,19 +6443,19 @@ TestCasesVcf.test_13_chrOri(268): Test TestCasesVcf.test_04_del(72): Test TestCasesVcf.test_14_VcfInfoValue(296): Test -[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 45.815 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 65.042 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.729 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.553 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils TestCasesMarkerUtils.test_collapseZeroGap(107): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.401 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial TestCasesBinomial.test_01(86): Test TestCasesBinomial.test_02(191): Test TestCasesBinomial.test_03(299): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... @@ -6428,7 +6469,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.059 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.602 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds TestCasesCds.test_CdsPos(35): Test .................................................................................................... @@ -6445,7 +6486,7 @@ TestCasesCds.test_cdsStartEnd_1(73): Test TestCasesCds.test_cdsStartEnd_2(96): Test WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.361 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.111 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test @@ -6457,20 +6498,20 @@ TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test TestCasesVariantRealignment.test_05_savant_opposite(174): Test TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.206 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.425 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse TestCasesEffectCollapse.test_01(68): Test TestCasesEffectCollapse.test_02(74): Test TestCasesEffectCollapse.test_03(80): Test TestCasesEffectCollapse.test_04(86): Test TestCasesEffectCollapse.test_05(92): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.143 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.177 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular TestCasesCircular.test_circular_01(26): Test TestCasesCircular.test_circular_02(54): Test TestCasesCircular.test_circular_03(83): Test TestCasesCircular.test_circular_04(103): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -6491,14 +6532,14 @@ TestCasesNextProt.test_05_nextprotFactory(98): Test TestCasesNextProt.test_02_nextprotFactory(42): Test TestCasesNextProt.test_13_nextprotFactory(277): Test -[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBuild TestCasesBuild.test_01_chromoNamesDoNotMatch_Gff(18): Test TestCasesBuild.test_02_chromoNamesDoNotMatch_GffFasta(54): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.641 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.723 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion TestCasesSpliceRegion.test_01(33): Test -..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.423 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.738 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray TestCasesIntervalTree.test_01(141): Test . @@ -6524,7 +6565,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.376 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.93 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome TestCasesReactome.test_01(32): Test TestCasesReactome.test_01(48): Out: 0.9051482536448667 @@ -6540,7 +6581,7 @@ TestCasesReactome.test_05(149): Test TestCasesReactome.test_05(165): Out: -0.9154962776570641 TestCasesReactome.test_05(170): Out: 0.34014843250566407 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels TestCasesDels.test_01(138): Test .................................................................................................... @@ -6554,7 +6595,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.308 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.454 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant TestCasesIntervalVariant.test_01(36): Test .................................................................................................... @@ -6567,7 +6608,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.989 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.144 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap TestCasesOverlap.test_binSeq_01(26): Test TestCasesOverlap.test_binSeq_02(32): Test @@ -6582,7 +6623,7 @@ TestCasesOverlap.test_binSeq_11(87): Test TestCasesOverlap.test_binSeq_12(94): Test TestCasesOverlap.test_binSeq_13(100): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree TestCasesIntervalTree.test_01(141): Test . @@ -6608,7 +6649,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.105 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.408 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . @@ -6634,7 +6675,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.175 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.762 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri [INFO] [INFO] Results: [INFO] @@ -6643,10 +6684,10 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 11:18 min -[INFO] Finished at: 2023-04-14T22:30:14-12:00 +[INFO] Total time: 14:03 min +[INFO] Finished at: 2024-05-18T07:18:39+14:00 [INFO] ------------------------------------------------------------------------ -make[1]: Leaving directory '/build/snpeff-5.1+d+dfsg' +make[1]: Map '/build/snpeff-5.1+d+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -6668,8 +6709,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.279 s -[INFO] Finished at: 2023-04-14T22:30:19-12:00 +[INFO] Total time: 2.870 s +[INFO] Finished at: 2024-05-18T07:18:48+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/snpeff-5.1\+d\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom @@ -6744,7 +6785,7 @@ [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. -Apr 14, 2023 10:30:32 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 18, 2024 7:19:07 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/snpeff-5.1+d+dfsg/pom.xml: Dependency not found org.biojava:biojava-structure:jar:6.x ERROR: pom.xml: dependency is not packaged in the Maven repository for Debian: org.biojava:biojava-structure:6.x @@ -6878,17 +6919,17 @@ dh_missing dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${java:Depends} unused, but is defined -dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:CompileDepends} unused, but is defined -dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:DocDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${java:Depends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.1+d+dfsg-3_all.deb'. -dpkg-deb: building package 'snpeff' in '../snpeff_5.1+d+dfsg-3_all.deb'. -dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.1+d+dfsg-3_all.deb'. +dpkg-deb: pakket 'libsnpeff-java' wordt gebouwd in '../libsnpeff-java_5.1+d+dfsg-3_all.deb'. +dpkg-deb: pakket 'snpeff' wordt gebouwd in '../snpeff_5.1+d+dfsg-3_all.deb'. +dpkg-deb: pakket 'libsnpeff-java-doc' wordt gebouwd in '../libsnpeff-java-doc_5.1+d+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.1+d+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.1+d+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6896,12 +6937,14 @@ 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/5498/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5498/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/18070 and its subdirectories -I: Current time: Fri Apr 14 22:34:05 -12 2023 -I: pbuilder-time-stamp: 1681554845 +I: removing directory /srv/workspace/pbuilder/5498 and its subdirectories +I: Current time: Sat May 18 07:22:38 +14 2024 +I: pbuilder-time-stamp: 1715966558