Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 07:51:08.357586376 +0000 +++ b2/build.log 2024-05-07 08:00:35.357452889 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 19:39:14 -12 2024 -I: pbuilder-time-stamp: 1715067554 +I: Current time: Tue Jun 10 04:14:14 +14 2025 +I: pbuilder-time-stamp: 1749478454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,51 +33,83 @@ 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/1544530/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/561241/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 9 14:14 /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/561241/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/561241/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='amd64' - 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='477d440a8afc4515a2d3f5b0e1dfda3b' - 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='1544530' - PS1='# ' - PS2='> ' + INVOCATION_ID=45b67a4edcc349c9bd106d2c9125e2b6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=561241 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.GVSlJHet/pbuilderrc_2kNs --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.GVSlJHet/b1 --logfile b1/build.log snpeff_5.2.b+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' + 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.GVSlJHet/pbuilderrc_zCt2 --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.GVSlJHet/b2 --logfile b2/build.log snpeff_5.2.b+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' I: uname -a - Linux infom01-amd64 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1544530/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/561241/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -1915,8 +1947,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue May 7 07:43:31 UTC 2024. -Universal Time is now: Tue May 7 07:43:31 UTC 2024. +Local time is now: Mon Jun 9 14:16:31 UTC 2025. +Universal Time is now: Mon Jun 9 14:16:31 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2453,7 +2485,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpeff-5.2.b+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_5.2.b+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/561241/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/561241/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpeff-5.2.b+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_5.2.b+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.b+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2560,55 +2596,55 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.snpeff.sam... -[WARNING] Loading source files for package org.snpeff... -[WARNING] Loading source files for package org.snpeff.serializer... -[WARNING] Loading source files for package org.snpeff.filter... -[WARNING] Loading source files for package org.snpeff.nextProt... [WARNING] Loading source files for package org.snpeff.reactome... [WARNING] Loading source files for package org.snpeff.reactome.events... -[WARNING] Loading source files for package org.snpeff.collections... -[WARNING] Loading source files for package org.snpeff.gsa... -[WARNING] Loading source files for package org.snpeff.genotypes... -[WARNING] Loading source files for package org.snpeff.interval.tree... -[WARNING] Loading source files for package org.snpeff.interval... -[WARNING] Loading source files for package org.snpeff.interval.codonChange... -[WARNING] Loading source files for package org.snpeff.stats... -[WARNING] Loading source files for package org.snpeff.stats.plot... -[WARNING] Loading source files for package org.snpeff.nmer... -[WARNING] Loading source files for package org.snpeff.util... -[WARNING] Loading source files for package org.snpeff.codons... -[WARNING] Loading source files for package org.snpeff.fastq... -[WARNING] Loading source files for package org.snpeff.vcf... -[WARNING] Loading source files for package org.snpeff.snpEffect... -[WARNING] Loading source files for package org.snpeff.snpEffect.factory... -[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... -[WARNING] Loading source files for package org.snpeff.pdb... -[WARNING] Loading source files for package org.snpeff.ped... [WARNING] Loading source files for package org.snpeff.coverage... -[WARNING] Loading source files for package org.snpeff.spliceSites... -[WARNING] Loading source files for package org.snpeff.geneOntology... -[WARNING] Loading source files for package org.snpeff.outputFormatter... -[WARNING] Loading source files for package org.snpeff.motif... -[WARNING] Loading source files for package org.snpeff.gtex... +[WARNING] Loading source files for package org.snpeff.nextProt... +[WARNING] Loading source files for package org.snpeff.stats.plot... +[WARNING] Loading source files for package org.snpeff.stats... [WARNING] Loading source files for package org.snpeff.svg... -[WARNING] Loading source files for package org.snpeff.logStatsServer... -[WARNING] Loading source files for package org.snpeff.genBank... [WARNING] Loading source files for package org.snpeff.overlap... -[WARNING] Loading source files for package org.snpeff.osCmd... -[WARNING] Loading source files for package org.snpeff.binseq.comparator... -[WARNING] Loading source files for package org.snpeff.binseq... -[WARNING] Loading source files for package org.snpeff.binseq.coder... -[WARNING] Loading source files for package org.snpeff.binseq.indexer... -[WARNING] Loading source files for package org.snpeff.complexity... +[WARNING] Loading source files for package org.snpeff.ped... +[WARNING] Loading source files for package org.snpeff.motif... +[WARNING] Loading source files for package org.snpeff.filter... +[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... +[WARNING] Loading source files for package org.snpeff.snpEffect... +[WARNING] Loading source files for package org.snpeff.snpEffect.factory... +[WARNING] Loading source files for package org.snpeff.fastq... +[WARNING] Loading source files for package org.snpeff.interval... +[WARNING] Loading source files for package org.snpeff.interval.tree... +[WARNING] Loading source files for package org.snpeff.interval.codonChange... [WARNING] Loading source files for package org.snpeff.fileIterator... [WARNING] Loading source files for package org.snpeff.fileIterator.microCosm... [WARNING] Loading source files for package org.snpeff.fileIterator.parser... +[WARNING] Loading source files for package org.snpeff.serializer... +[WARNING] Loading source files for package org.snpeff.collections... +[WARNING] Loading source files for package org.snpeff.genBank... +[WARNING] Loading source files for package org.snpeff... +[WARNING] Loading source files for package org.snpeff.gsa... +[WARNING] Loading source files for package org.snpeff.complexity... +[WARNING] Loading source files for package org.snpeff.spliceSites... +[WARNING] Loading source files for package org.snpeff.genotypes... [WARNING] Loading source files for package org.snpeff.align... -[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... +[WARNING] Loading source files for package org.snpeff.outputFormatter... +[WARNING] Loading source files for package org.snpeff.util... +[WARNING] Loading source files for package org.snpeff.osCmd... +[WARNING] Loading source files for package org.snpeff.gtex... +[WARNING] Loading source files for package org.snpeff.nmer... +[WARNING] Loading source files for package org.snpeff.geneOntology... [WARNING] Loading source files for package org.snpeff.probablility... +[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... +[WARNING] Loading source files for package org.snpeff.binseq... +[WARNING] Loading source files for package org.snpeff.binseq.comparator... +[WARNING] Loading source files for package org.snpeff.binseq.indexer... +[WARNING] Loading source files for package org.snpeff.binseq.coder... +[WARNING] Loading source files for package org.snpeff.sam... +[WARNING] Loading source files for package org.snpeff.codons... +[WARNING] Loading source files for package org.snpeff.vcf... +[WARNING] Loading source files for package org.snpeff.pdb... [WARNING] Loading source files for package org.snpeff.geneSets... [WARNING] Loading source files for package org.snpeff.geneSets.algorithm... +[WARNING] Loading source files for package org.snpeff.logStatsServer... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 @@ -3449,442 +3485,442 @@ [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/package-tree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeaderRecordSq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeaderRecord.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Fastq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Pcingola.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileSplitBytType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.InputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.GeneDatabaseFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileConsensus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Qseq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationConsensusMultipleBed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Zzz.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/PromoterSequences.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/MarkerSerializer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/TxtSerializable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/Filter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/VariantEffectFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtSequenceConservation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/CvTerm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlAnnotation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlNode.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoformInteraction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtMarkerFactory.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/Location.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtDb.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtHandler.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Monitor.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/GeneIds.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Entity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Entity.TransferFunction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Monitor.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Reactome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Depolymerisation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Polymerisation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/CatalystActivity.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Pathway.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Reaction.html... 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/build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfGenotype.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfInfoType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfNmd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/IdMapperEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/ProteinInteractions.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/PdbFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/DistanceResult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/PdbUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/IdMapper.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneStats.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSetsRanked.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSets.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/Result.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSetsRanked.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueGreedyAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/NoneAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueGreedyAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedyVariableSize.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.EnrichmentAlgorithmType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueGreedyAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/NoneAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedy.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/VersionCheck.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.RequestResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/package-use.html... @@ -5356,8 +5392,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 24.731 s -[INFO] Finished at: 2024-05-06T19:44:55-12:00 +[INFO] Total time: 23.078 s +[INFO] Finished at: 2025-06-10T04:17:40+14:00 [INFO] ------------------------------------------------------------------------ dh_auto_test /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/reproducible-path/snpeff-5.2.b\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian/maven-repo --batch-mode test @@ -5386,38 +5422,32 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns -TestCasesApplyIns.test_apply_variant_01(21): Test -TestCasesApplyIns.test_apply_variant_02(32): Test -TestCasesApplyIns.test_apply_variant_03(43): Test -TestCasesApplyIns.test_apply_variant_04(54): Test -TestCasesApplyIns.test_apply_variant_05(72): Test -TestCasesApplyIns.test_apply_variant_06(90): Test -TestCasesApplyIns.test_apply_variant_07(108): Test -TestCasesApplyIns.test_apply_variant_08(126): Test -TestCasesApplyIns.test_apply_variant_09(137): Test -TestCasesApplyIns.test_apply_variant_10(148): Test -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: 4.906 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns -[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: 0.484 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels -TestCasesDels.test_01(138): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.337 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[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: 1.666 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test +TestCasesApplyMixed.test_apply_variant_06_longer(169): Test +TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test +TestCasesApplyMixed.test_apply_variant_04_longer(98): Test +TestCasesApplyMixed.test_apply_variant_09_longer(259): Test +TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test +TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test +TestCasesApplyMixed.test_apply_variant_02_longer(42): Test +TestCasesApplyMixed.test_apply_variant_07_longer(203): Test +TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test +TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test +TestCasesApplyMixed.test_apply_variant_05_longer(134): Test +TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test +TestCasesApplyMixed.test_apply_variant_03_longer(64): Test +TestCasesApplyMixed.test_apply_variant_08_longer(237): Test +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: 5.398 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test @@ -5429,143 +5459,7 @@ 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: 2.5 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment -[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: 0.869 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -TestCasesStructuralDel.test02(249): Test -TestCasesStructuralDel.test03(266): Test -TestCasesStructuralDel.test04(283): Test -TestCasesStructuralDel.test05(302): Test -TestCasesStructuralDel.test06(321): Test -TestCasesStructuralDel.test07(342): Test -TestCasesStructuralDel.test08(360): Test -TestCasesStructuralDel.test09(379): Test -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: 2.432 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -TestCasesHgvsIntron.test_01_intron(23): Test -............................................................... -100 ............................................................ -200 ................................................................ -300 ......................................................... -400 ......................................................................................................................... -600 ......................................................................................................... -800 ....................................................... -900 .................................................................. -1000 ............................................................. -1100 .................................................................. -1200 ......................................................... -1300 ........................................................................................................... -1500 ....................................................... -1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.257 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -TestCasesStructuralTranslocations.test02_2_nonFs(532): Test -TestCasesStructuralTranslocations.test01_0_nonFs(286): Test -TestCasesStructuralTranslocations.test01_0(260): Test -TestCasesStructuralTranslocations.test01_1(314): Test -TestCasesStructuralTranslocations.test01_2(341): Test -TestCasesStructuralTranslocations.test01_3(368): Test -TestCasesStructuralTranslocations.test02_0(423): Test -TestCasesStructuralTranslocations.test02_1(450): Test -TestCasesStructuralTranslocations.test02_2(505): Test -TestCasesStructuralTranslocations.test02_3(560): Test -TestCasesStructuralTranslocations.test03_0(587): Test -TestCasesStructuralTranslocations.test03_1(614): Test -TestCasesStructuralTranslocations.test03_2(669): Test -TestCasesStructuralTranslocations.test03_3(724): Test -TestCasesStructuralTranslocations.test04_0(751): Test -TestCasesStructuralTranslocations.test04_1(806): Test -TestCasesStructuralTranslocations.test04_2(833): Test -TestCasesStructuralTranslocations.test04_3(860): Test -TestCasesStructuralTranslocations.test05_2_one_gene(951): Test -TestCasesStructuralTranslocations.test04_3_nonFs(887): Test -TestCasesStructuralTranslocations.test03_1_nonFs(641): Test -TestCasesStructuralTranslocations.test05_1_one_gene(919): Test -TestCasesStructuralTranslocations.test03_2_nonFs(696): Test -TestCasesStructuralTranslocations.test01_3_noFs(395): Test -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: 6.884 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -TestCasesApplyMnp.test_apply_variant_01(22): Test -TestCasesApplyMnp.test_apply_variant_02(33): Test -TestCasesApplyMnp.test_apply_variant_03(44): Test -TestCasesApplyMnp.test_apply_variant_04(61): Test -TestCasesApplyMnp.test_apply_variant_05(79): Test -TestCasesApplyMnp.test_apply_variant_06(97): Test -TestCasesApplyMnp.test_apply_variant_07(115): Test -TestCasesApplyMnp.test_apply_variant_08(133): Test -TestCasesApplyMnp.test_apply_variant_09(144): Test -TestCasesApplyMnp.test_apply_variant_10(155): Test -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: 3.438 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -[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: 0.143 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.572 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -TestCasesStructuralDup.test01_dupGene(157): Test -TestCasesStructuralDup.test02(194): Test -TestCasesStructuralDup.test03(212): Test -TestCasesStructuralDup.test04(229): Test -TestCasesStructuralDup.test05(247): Test -TestCasesStructuralDup.test06(265): Test -TestCasesStructuralDup.test07(286): Test -TestCasesStructuralDup.test08(303): Test -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: 5.442 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -[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: 0.193 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -TestCasesCodonTable.test_01(28): Test -TestCasesCodonTable.test_02(59): Test -00:00:36 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.698 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . @@ -5591,116 +5485,40 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.307 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns -TestCasesIns.test_01(38): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.553 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns -[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: 0.5 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf -TestCasesVcf.test_22_huge_headers(363): Test -TestCasesVcf.test_12_readHeader_NL(257): Test -TestCasesVcf.test_36_cleanupUnderscores(703): Test -TestCasesVcf.test_23_VcfUnsorted(379): Test -TestCasesVcf.test_00(40): Test -TestCasesVcf.test_01(54): Test -TestCasesVcf.test_29(568): Test -TestCasesVcf.test_16_indels(321): Test -TestCasesVcf.test_09_empty_ALT(195): Test -TestCasesVcf.test_27_vcfInfoHeaderReplace(489): Test -TestCasesVcf.test_18_vcf_tabix(348): Test -TestCasesVcf.test_26_vcfInfoHeaderAdd(456): Test -TestCasesVcf.test_14_VcfInfoKey(283): Test -TestCasesVcf.test_10_empty_QUAL(210): Test -TestCasesVcf.test_06_mixed_change(121): Test -TestCasesVcf.test_12_readHeader(237): Test -TestCasesVcf.test_15_Eff_format_version_guess(309): Test -TestCasesVcf.test_28_vcfInfoReplace(533): Test -TestCasesVcf.test_30_gVCF_NON_REF(590): Test -TestCasesVcf.test_05_choking_on_dot_slash_dot(89): Test -TestCasesVcf.test_08_alt_del(169): Test -TestCasesVcf.test_07_long_lines(143): Test -TestCasesVcf.test_11_empty(225): Test -TestCasesVcf.test_33_translocations(652): Test -TestCasesVcf.test_35_translocations_parsing(680): Test -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: 11.19 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[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: 0.558 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar -[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: 0.462 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -TestCasesApplySnp.test_apply_variant_01(21): Test -TestCasesApplySnp.test_apply_variant_02(31): Test -TestCasesApplySnp.test_apply_variant_04(41): Test -TestCasesApplySnp.test_apply_variant_05(59): Test -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: 2.072 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest -TestCasesFisherExactTest.test_05_fisher(313): Test -TestCasesFisherExactTest.test_0(97): Test -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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -TestCasesIntervalVariant.test_01(36): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.273 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -[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: 1.83 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -TestCasesStructuralInv.test01_invGene(214): Test -TestCasesStructuralInv.test02(249): Test -TestCasesStructuralInv.test03(266): Test -TestCasesStructuralInv.test04(283): Test -TestCasesStructuralInv.test05(300): Test -TestCasesStructuralInv.test06(317): Test -TestCasesStructuralInv.test07(334): Test -TestCasesStructuralInv.test08(352): Test -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: 3.401 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.562 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +TestCasesDnaNSequence.test_02_long_replaceBase(243): Test +TestCasesDnaNSequence.test_13_reverseWc(253): Test +TestCasesDnaNSequence.test_02_long_getBases(233): Test +TestCasesDnaNSequence.test_01_short_getBases(194): Test +TestCasesDnaNSequence.test_01_short(175): Test +TestCasesDnaNSequence.test_02_long(214): Test +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: 2.207 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[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.TestCasesGenePvalueList +TestCasesGenePvalueList.test_01(28): Test +TestCasesGenePvalueList.test_02(46): Test +TestCasesGenePvalueList.test_03(64): Test +TestCasesGenePvalueList.test_04(82): Test +TestCasesGenePvalueList.test_05(111): Test +TestCasesGenePvalueList.test_06(129): Test +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: 2.072 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[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] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps TestCasesMnps.test_01(187): Test .................................................................................................... @@ -5714,23 +5532,9 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.591 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -TestCasesSpliceSite.test_01(34): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds -TestCasesCds.test_CdsPos(35): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.689 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5742,19 +5546,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -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: 1.022 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds -[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular -[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: 0.089 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.201 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test @@ -5817,74 +5609,22 @@ Max words: 8 ......... Max words: 9 ......... Done. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.25 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup -TestCasesHgvsDnaDup.test_01(31): Test -TestCasesHgvsDnaDup.test_02(54): Test -TestCasesHgvsDnaDup.test_03(81): Test -TestCasesHgvsDnaDup.test_04(111): Test -TestCasesHgvsDnaDup.test_05(141): Test -TestCasesHgvsDnaDup.test_06(167): Test -TestCasesHgvsDnaDup.test_07(195): Test -TestCasesHgvsDnaDup.test_08(221): Test -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: 3.429 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.212 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[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: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[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: 0.234 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [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: 1.229 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild -[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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString -[INFO] Running 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.TestCasesDnaNSequence -TestCasesDnaNSequence.test_02_long_replaceBase(243): Test -TestCasesDnaNSequence.test_13_reverseWc(253): Test -TestCasesDnaNSequence.test_02_long_getBases(233): Test -TestCasesDnaNSequence.test_01_short_getBases(194): Test -TestCasesDnaNSequence.test_01_short(175): Test -TestCasesDnaNSequence.test_02_long(214): Test -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: 2.087 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.661 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -[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: 0.282 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -TestCasesHgvsExon.test_01_coding(27): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.057 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5894,9 +5634,89 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.162 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +900 ................................................................................................... +TestCasesFileIndexChrPos.test_01(88): Test +TestCasesFileIndexChrPos.test_02(109): Test +TestCasesFileIndexChrPos.test_03(131): Test +TestCasesFileIndexChrPos.test_04(158): Test +TestCasesFileIndexChrPos.test_05(186): Test +TestCasesFileIndexChrPos.test_06(214): Test +TestCasesFileIndexChrPos.test_07(242): Test +TestCasesFileIndexChrPos.test_10(267): Test +TestCasesFileIndexChrPos.test_11(300): Test +TestCasesFileIndexChrPos.test_20(347): Test +TestCasesFileIndexChrPos.test_21(369): Test +TestCasesFileIndexChrPos.test_22(391): Test +TestCasesFileIndexChrPos.test_23(413): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 ................................................................................................... +TestCasesFileIndexChrPos.test_24(477): Test +.................................................................................................... +100 +TestCasesFileIndexChrPos.test_00_long_file(70): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 ................................................................................................... +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.153 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +TestCasesApplyMnp.test_apply_variant_01(22): Test +TestCasesApplyMnp.test_apply_variant_02(33): Test +TestCasesApplyMnp.test_apply_variant_03(44): Test +TestCasesApplyMnp.test_apply_variant_04(61): Test +TestCasesApplyMnp.test_apply_variant_05(79): Test +TestCasesApplyMnp.test_apply_variant_06(97): Test +TestCasesApplyMnp.test_apply_variant_07(115): Test +TestCasesApplyMnp.test_apply_variant_08(133): Test +TestCasesApplyMnp.test_apply_variant_09(144): Test +TestCasesApplyMnp.test_apply_variant_10(155): Test +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: 3.228 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +TestCasesStructuralTranslocations.test02_2_nonFs(532): Test +TestCasesStructuralTranslocations.test01_0_nonFs(286): Test +TestCasesStructuralTranslocations.test01_0(260): Test +TestCasesStructuralTranslocations.test01_1(314): Test +TestCasesStructuralTranslocations.test01_2(341): Test +TestCasesStructuralTranslocations.test01_3(368): Test +TestCasesStructuralTranslocations.test02_0(423): Test +TestCasesStructuralTranslocations.test02_1(450): Test +TestCasesStructuralTranslocations.test02_2(505): Test +TestCasesStructuralTranslocations.test02_3(560): Test +TestCasesStructuralTranslocations.test03_0(587): Test +TestCasesStructuralTranslocations.test03_1(614): Test +TestCasesStructuralTranslocations.test03_2(669): Test +TestCasesStructuralTranslocations.test03_3(724): Test +TestCasesStructuralTranslocations.test04_0(751): Test +TestCasesStructuralTranslocations.test04_1(806): Test +TestCasesStructuralTranslocations.test04_2(833): Test +TestCasesStructuralTranslocations.test04_3(860): Test +TestCasesStructuralTranslocations.test05_2_one_gene(951): Test +TestCasesStructuralTranslocations.test04_3_nonFs(887): Test +TestCasesStructuralTranslocations.test03_1_nonFs(641): Test +TestCasesStructuralTranslocations.test05_1_one_gene(919): Test +TestCasesStructuralTranslocations.test03_2_nonFs(696): Test +TestCasesStructuralTranslocations.test01_3_noFs(395): Test +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: 6.413 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test @@ -5915,15 +5735,9 @@ 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: 4.131 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -[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: 0.873 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos -TestCasesFileIndexChrPos.test_00_short_file(79): Test +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.919 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps +TestCasesSnps.test_01(43): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5933,20 +5747,30 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 ................................................................................................... -TestCasesFileIndexChrPos.test_01(88): Test -TestCasesFileIndexChrPos.test_02(109): Test -TestCasesFileIndexChrPos.test_03(131): Test -TestCasesFileIndexChrPos.test_04(158): Test -TestCasesFileIndexChrPos.test_05(186): Test -TestCasesFileIndexChrPos.test_06(214): Test -TestCasesFileIndexChrPos.test_07(242): Test -TestCasesFileIndexChrPos.test_10(267): Test -TestCasesFileIndexChrPos.test_11(300): Test -TestCasesFileIndexChrPos.test_20(347): Test -TestCasesFileIndexChrPos.test_21(369): Test -TestCasesFileIndexChrPos.test_22(391): Test -TestCasesFileIndexChrPos.test_23(413): Test +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.815 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +TestCasesApplyDel.test_apply_variant_01(21): Test +TestCasesApplyDel.test_apply_variant_02(31): Test +TestCasesApplyDel.test_apply_variant_03(42): Test +TestCasesApplyDel.test_apply_variant_04(59): Test +TestCasesApplyDel.test_apply_variant_05(77): Test +TestCasesApplyDel.test_apply_variant_06(95): Test +TestCasesApplyDel.test_apply_variant_07(113): Test +TestCasesApplyDel.test_apply_variant_08(131): Test +TestCasesApplyDel.test_apply_variant_09(142): Test +TestCasesApplyDel.test_apply_variant_10(153): Test +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: 3.581 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[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: 0.483 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +TestCasesIntervalVariant.test_01(36): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5956,11 +5780,93 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 ................................................................................................... -TestCasesFileIndexChrPos.test_24(477): Test +900 .................................................................................................... +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.785 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +TestCasesFisherExactTest.test_05_fisher(313): Test +TestCasesFisherExactTest.test_0(97): Test +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: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf +TestCasesVcf.test_22_huge_headers(363): Test +TestCasesVcf.test_12_readHeader_NL(257): Test +TestCasesVcf.test_36_cleanupUnderscores(703): Test +TestCasesVcf.test_23_VcfUnsorted(379): Test +TestCasesVcf.test_00(40): Test +TestCasesVcf.test_01(54): Test +TestCasesVcf.test_29(568): Test +TestCasesVcf.test_16_indels(321): Test +TestCasesVcf.test_09_empty_ALT(195): Test +TestCasesVcf.test_27_vcfInfoHeaderReplace(489): Test +TestCasesVcf.test_18_vcf_tabix(348): Test +TestCasesVcf.test_26_vcfInfoHeaderAdd(456): Test +TestCasesVcf.test_14_VcfInfoKey(283): Test +TestCasesVcf.test_10_empty_QUAL(210): Test +TestCasesVcf.test_06_mixed_change(121): Test +TestCasesVcf.test_12_readHeader(237): Test +TestCasesVcf.test_15_Eff_format_version_guess(309): Test +TestCasesVcf.test_28_vcfInfoReplace(533): Test +TestCasesVcf.test_30_gVCF_NON_REF(590): Test +TestCasesVcf.test_05_choking_on_dot_slash_dot(89): Test +TestCasesVcf.test_08_alt_del(169): Test +TestCasesVcf.test_07_long_lines(143): Test +TestCasesVcf.test_11_empty(225): Test +TestCasesVcf.test_33_translocations(652): Test +TestCasesVcf.test_35_translocations_parsing(680): Test +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: 9.211 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[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: 0.942 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +TestCasesCodonTable.test_01(28): Test +TestCasesCodonTable.test_02(59): Test +00:01:32 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.28 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +TestCasesApplyIns.test_apply_variant_01(21): Test +TestCasesApplyIns.test_apply_variant_02(32): Test +TestCasesApplyIns.test_apply_variant_03(43): Test +TestCasesApplyIns.test_apply_variant_04(54): Test +TestCasesApplyIns.test_apply_variant_05(72): Test +TestCasesApplyIns.test_apply_variant_06(90): Test +TestCasesApplyIns.test_apply_variant_07(108): Test +TestCasesApplyIns.test_apply_variant_08(126): Test +TestCasesApplyIns.test_apply_variant_09(137): Test +TestCasesApplyIns.test_apply_variant_10(148): Test +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: 3.655 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[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: 0.265 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels +TestCasesDels.test_01(138): Test .................................................................................................... -100 -TestCasesFileIndexChrPos.test_00_long_file(70): Test +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.1 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[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: 0.089 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +TestCasesSpliceSite.test_01(34): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5970,20 +5876,16 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.416 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos -[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: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.8 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel -[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: 1.188 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[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: 1.09 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign TestCasesAlign.test_01(23): Test TestCasesAlign.test_02(113): Test @@ -5992,7 +5894,63 @@ diff : | | | Name2 : XcgtactgatagtcagtcatgctagtcagX -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[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: 0.502 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +TestCasesSequenceIndexer.test_01(69): Test +TestCasesSequenceIndexer.test_02(100): Test +TestCasesSequenceIndexer.test_03(125): Test +TestCasesSequenceIndexer.test_04(152): Test +TestCasesSequenceIndexer.test_05(182): Test +TestCasesSequenceIndexer.test_06(207): Test +TestCasesSequenceIndexer.test_07(225): Test +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: 2.883 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.635 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[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: 0.63 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -6013,38 +5971,36 @@ 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: 0.016 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -TestCasesSequenceIndexer.test_01(69): Test -TestCasesSequenceIndexer.test_02(100): Test -TestCasesSequenceIndexer.test_03(125): Test -TestCasesSequenceIndexer.test_04(152): Test -TestCasesSequenceIndexer.test_05(182): Test -TestCasesSequenceIndexer.test_06(207): Test -TestCasesSequenceIndexer.test_07(225): Test -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: 3.79 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome -TestCasesReactome.test_01(32): Test -TestCasesReactome.test_01(48): Out: 0.9051482536448667 -TestCasesReactome.test_02(57): Test -TestCasesReactome.test_02(75): Out: -0.8192933610763514 -TestCasesReactome.test_02(80): Out: 2.1152011710898737 -TestCasesReactome.test_03(89): Test -TestCasesReactome.test_03(105): Out: 0.86631007995171 -TestCasesReactome.test_03(110): Out: 2.1219547901144384 -TestCasesReactome.test_04(119): Test -TestCasesReactome.test_04(135): Out: 0.6973026352658382 -TestCasesReactome.test_04(140): Out: -0.5583420748968899 -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: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome -[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: 0.343 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[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: 0.645 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[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: 0.302 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds +TestCasesCds.test_CdsPos(35): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +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: 1.056 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -6058,92 +6014,129 @@ 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: 5.338 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence -[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: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test -TestCasesApplyMixed.test_apply_variant_06_longer(169): Test -TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test -TestCasesApplyMixed.test_apply_variant_04_longer(98): Test -TestCasesApplyMixed.test_apply_variant_09_longer(259): Test -TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test -TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test -TestCasesApplyMixed.test_apply_variant_02_longer(42): Test -TestCasesApplyMixed.test_apply_variant_07_longer(203): Test -TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test -TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test -TestCasesApplyMixed.test_apply_variant_05_longer(134): Test -TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test -TestCasesApplyMixed.test_apply_variant_03_longer(64): Test -TestCasesApplyMixed.test_apply_variant_08_longer(237): Test -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: 5.744 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -TestCasesOverlap.test_binSeq_01(26): Test -TestCasesOverlap.test_binSeq_02(32): Test -TestCasesOverlap.test_binSeq_03(38): Test -TestCasesOverlap.test_binSeq_04(44): Test -TestCasesOverlap.test_binSeq_05(50): Test -TestCasesOverlap.test_binSeq_06(56): Test -TestCasesOverlap.test_binSeq_07(62): Test -TestCasesOverlap.test_binSeq_08(68): Test -TestCasesOverlap.test_binSeq_09(74): Test -TestCasesOverlap.test_binSeq_10(80): Test -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: 0.013 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -[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: 0.782 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -[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: 0.318 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -TestCasesApplyDel.test_apply_variant_01(21): Test -TestCasesApplyDel.test_apply_variant_02(31): Test -TestCasesApplyDel.test_apply_variant_03(42): Test -TestCasesApplyDel.test_apply_variant_04(59): Test -TestCasesApplyDel.test_apply_variant_05(77): Test -TestCasesApplyDel.test_apply_variant_06(95): Test -TestCasesApplyDel.test_apply_variant_07(113): Test -TestCasesApplyDel.test_apply_variant_08(131): Test -TestCasesApplyDel.test_apply_variant_09(142): Test -TestCasesApplyDel.test_apply_variant_10(153): Test -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: 3.32 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.153 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[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: 0.52 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[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: 0.047 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [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: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList -TestCasesGenePvalueList.test_01(28): Test -TestCasesGenePvalueList.test_02(46): Test -TestCasesGenePvalueList.test_03(64): Test -TestCasesGenePvalueList.test_04(82): Test -TestCasesGenePvalueList.test_05(111): Test -TestCasesGenePvalueList.test_06(129): Test -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: 2.196 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +TestCasesHgvsIntron.test_01_intron(23): Test +............................................................... +100 ............................................................ +200 ................................................................ +300 ......................................................... +400 ......................................................................................................................... +600 ......................................................................................................... +800 ....................................................... +900 .................................................................. +1000 ............................................................. +1100 .................................................................. +1200 ......................................................... +1300 ........................................................................................................... +1500 ....................................................... +1600 ............................................................... +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.26 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +TestCasesStructuralDel.test02(249): Test +TestCasesStructuralDel.test03(266): Test +TestCasesStructuralDel.test04(283): Test +TestCasesStructuralDel.test05(302): Test +TestCasesStructuralDel.test06(321): Test +TestCasesStructuralDel.test07(342): Test +TestCasesStructuralDel.test08(360): Test +TestCasesStructuralDel.test09(379): Test +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: 2.677 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +TestCasesStructuralInv.test01_invGene(214): Test +TestCasesStructuralInv.test02(249): Test +TestCasesStructuralInv.test03(266): Test +TestCasesStructuralInv.test04(283): Test +TestCasesStructuralInv.test05(300): Test +TestCasesStructuralInv.test06(317): Test +TestCasesStructuralInv.test07(334): Test +TestCasesStructuralInv.test08(352): Test +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: 3.189 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +TestCasesHgvsDnaDup.test_01(31): Test +TestCasesHgvsDnaDup.test_02(54): Test +TestCasesHgvsDnaDup.test_03(81): Test +TestCasesHgvsDnaDup.test_04(111): Test +TestCasesHgvsDnaDup.test_05(141): Test +TestCasesHgvsDnaDup.test_06(167): Test +TestCasesHgvsDnaDup.test_07(195): Test +TestCasesHgvsDnaDup.test_08(221): Test +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: 2.471 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.223 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[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 [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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps -TestCasesSnps.test_01(43): Test +[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: 0.171 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome +TestCasesReactome.test_01(32): Test +TestCasesReactome.test_01(48): Out: 0.9051482536448667 +TestCasesReactome.test_02(57): Test +TestCasesReactome.test_02(75): Out: -0.8192933610763514 +TestCasesReactome.test_02(80): Out: 2.1152011710898737 +TestCasesReactome.test_03(89): Test +TestCasesReactome.test_03(105): Out: 0.86631007995171 +TestCasesReactome.test_03(110): Out: 2.1219547901144384 +TestCasesReactome.test_04(119): Test +TestCasesReactome.test_04(135): Out: 0.6973026352658382 +TestCasesReactome.test_04(140): Out: -0.5583420748968899 +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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns +TestCasesIns.test_01(38): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -6155,12 +6148,55 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.978 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.906 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +TestCasesOverlap.test_binSeq_01(26): Test +TestCasesOverlap.test_binSeq_02(32): Test +TestCasesOverlap.test_binSeq_03(38): Test +TestCasesOverlap.test_binSeq_04(44): Test +TestCasesOverlap.test_binSeq_05(50): Test +TestCasesOverlap.test_binSeq_06(56): Test +TestCasesOverlap.test_binSeq_07(62): Test +TestCasesOverlap.test_binSeq_08(68): Test +TestCasesOverlap.test_binSeq_09(74): Test +TestCasesOverlap.test_binSeq_10(80): Test +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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +TestCasesApplySnp.test_apply_variant_01(21): Test +TestCasesApplySnp.test_apply_variant_02(31): Test +TestCasesApplySnp.test_apply_variant_04(41): Test +TestCasesApplySnp.test_apply_variant_05(59): Test +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: 1.829 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +TestCasesStructuralDup.test01_dupGene(157): Test +TestCasesStructuralDup.test02(194): Test +TestCasesStructuralDup.test03(212): Test +TestCasesStructuralDup.test04(229): Test +TestCasesStructuralDup.test05(247): Test +TestCasesStructuralDup.test06(265): Test +TestCasesStructuralDup.test07(286): Test +TestCasesStructuralDup.test08(303): Test +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: 3.116 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.573 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString +[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: 0.204 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] [INFO] Results: [INFO] @@ -6169,8 +6205,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:41 min -[INFO] Finished at: 2024-05-06T19:47:38-12:00 +[INFO] Total time: 02:20 min +[INFO] Finished at: 2025-06-10T04:20:02+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -6193,8 +6229,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.488 s -[INFO] Finished at: 2024-05-06T19:47:40-12:00 +[INFO] Total time: 0.466 s +[INFO] Finished at: 2025-06-10T04:20:04+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.b\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom @@ -6269,7 +6305,7 @@ [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. -May 06, 2024 7:47:51 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Jun 10, 2025 4:20:15 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.b+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 @@ -6412,8 +6448,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.b+dfsg-1_all.deb'. -dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.b+dfsg-1_all.deb'. +dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.b+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.b+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6421,12 +6457,14 @@ 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/561241/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/561241/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/1544530 and its subdirectories -I: Current time: Mon May 6 19:51:07 -12 2024 -I: pbuilder-time-stamp: 1715068267 +I: removing directory /srv/workspace/pbuilder/561241 and its subdirectories +I: Current time: Tue Jun 10 04:23:34 +14 2025 +I: pbuilder-time-stamp: 1749479014