Diff of the two buildlogs: -- --- b1/build.log 2024-04-13 15:12:39.888493927 +0000 +++ b2/build.log 2024-04-13 15:17:22.708423451 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 13 03:06:10 -12 2024 -I: pbuilder-time-stamp: 1713020770 +I: Current time: Sat May 17 11:35:43 +14 2025 +I: pbuilder-time-stamp: 1747431343 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,54 +28,86 @@ dpkg-source: info: applying omit_tests_with_problematic_data.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21687/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/32085/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 16 21:35 /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/32085/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/32085/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='0b42430105a146a3a4a0f645272a5e2c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='21687' - PS1='# ' - PS2='> ' + INVOCATION_ID=7075d70f85ac491eac2e952671743f66 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=32085 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.55hnq6KP/pbuilderrc_lWsA --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.55hnq6KP/b1 --logfile b1/build.log biojava-live_1.9.7+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.55hnq6KP/pbuilderrc_Fvfi --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.55hnq6KP/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21687/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 15 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/32085/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -402,7 +434,7 @@ Get: 271 http://deb.debian.org/debian trixie/main i386 maven all 3.8.7-2 [19.3 kB] Get: 272 http://deb.debian.org/debian trixie/main i386 maven-repo-helper all 1.11 [142 kB] Get: 273 http://deb.debian.org/debian trixie/main i386 maven-debian-helper all 2.6.4 [108 kB] -Fetched 266 MB in 4s (60.1 MB/s) +Fetched 266 MB in 4s (60.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sgml-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19874 files and directories currently installed.) @@ -1703,7 +1735,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava-live-1.9.7+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 > ../biojava-live_1.9.7+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/32085/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/32085/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava-live-1.9.7+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 > ../biojava-live_1.9.7+dfsg-1_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1806,8 +1842,8 @@ [INFO] Compiling 44 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Recompile with -Xlint:removal for details. -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Some input files use unchecked or unsafe operations. -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Recompile with -Xlint:unchecked for details. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources @@ -2552,8 +2588,8 @@ [INFO] Compiling 44 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Recompile with -Xlint:removal for details. -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Some input files use unchecked or unsafe operations. -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Recompile with -Xlint:unchecked for details. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking core 1.9.7 @@ -2974,20 +3010,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 45.053 s] -[INFO] bytecode ........................................... SUCCESS [ 6.866 s] -[INFO] core ............................................... SUCCESS [ 45.779 s] -[INFO] alignment .......................................... SUCCESS [ 4.240 s] -[INFO] biosql ............................................. SUCCESS [ 5.757 s] -[INFO] blast .............................................. SUCCESS [ 4.921 s] -[INFO] sequencing ......................................... SUCCESS [ 4.852 s] -[INFO] gui ................................................ SUCCESS [ 7.410 s] -[INFO] phylo .............................................. SUCCESS [ 4.276 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 22.284 s] +[INFO] bytecode ........................................... SUCCESS [ 3.388 s] +[INFO] core ............................................... SUCCESS [ 22.008 s] +[INFO] alignment .......................................... SUCCESS [ 2.137 s] +[INFO] biosql ............................................. SUCCESS [ 2.693 s] +[INFO] blast .............................................. SUCCESS [ 2.448 s] +[INFO] sequencing ......................................... SUCCESS [ 2.614 s] +[INFO] gui ................................................ SUCCESS [ 3.857 s] +[INFO] phylo .............................................. SUCCESS [ 2.289 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:10 min -[INFO] Finished at: 2024-04-13T15:09:30Z +[INFO] Total time: 01:04 min +[INFO] Finished at: 2025-05-16T21:37:37Z [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/biojava-live-1.9.7\+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/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode test @@ -3050,342 +3086,20 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 s - in org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Running org.biojava.bio.seq.CircularSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.CircularSequenceTest -[INFO] Running org.biojava.bio.seq.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.bio.seq.SeqSerializationTest -[INFO] Running org.biojava.bio.seq.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.seq.RNAToolsTest -[INFO] Running org.biojava.bio.seq.FilterUtilsTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FilterUtilsTest -[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.FeatureFilterTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureFilterTest -[INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest -[INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest -template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.impl.ViewSequenceTest -[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.DNAToolsTest -[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest -idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.864 s - in org.biojava.bio.seq.io.SeqIOToolsTest -[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.929 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Running org.biojava.bio.seq.ProteinToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.ProteinToolsTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.MaxMismatchPatternTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Running org.biojava.bio.search.SeqContentPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SeqContentPatternTest -[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -java.lang.NullPointerException: name is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -org.biojava.bio.seq.db.IllegalIDException: No table found with name test. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -java.lang.NullPointerException: table is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest -org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN - at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) - at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) - at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) - at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.proteomics.aaindex.AAindexTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Running org.biojava.bio.proteomics.MassCalcTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.proteomics.MassCalcTest -[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Running org.biojava.bio.dist.DistSerTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.dist.DistSerTest -[INFO] Running org.biojava.bio.dist.DistributionToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.bio.dist.DistributionToolsTest -[INFO] Running org.biojava.bio.dist.DistributionTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.DistributionTest -[INFO] Running org.biojava.bio.dp.EmissionStateEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dp.EmissionStateEventTest -[INFO] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.dp.MarkovModelEventTest -[INFO] Running org.biojava.bio.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.dp.DPSerializationTest -[INFO] Running org.biojava.bio.MergeAnnotationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest -[INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Running org.biojava.bio.symbol.NameTokenizationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.NameTokenizationTest -[INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.BetweenLocationTest -[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.761 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Running org.biojava.bio.symbol.CircularLocationTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.CircularLocationTest -[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolEventTest -[INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CrossProductTokenizationTest -[INFO] Running org.biojava.bio.symbol.TranslationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TranslationTest -[INFO] Running org.biojava.bio.symbol.PointLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest -[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Running org.biojava.bio.symbol.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.098 s - in org.biojava.bio.symbol.SymbolListTest -[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest -Adding symbol list taccaccagga$ -Adding symbol list taccaccagga$ -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest -[INFO] Running org.biojava.bio.symbol.RangeLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.RangeLocationTest -[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest -[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest -symbolForIndex -getAlphabet -indexForSymbol -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest -[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Running org.biojava.bio.symbol.MergeLocationTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest -[INFO] Running org.biojava.bio.symbol.MotifToolsTest -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MotifToolsTest -[INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.symbol.CompoundLocationTest -[INFO] Running org.biojava.bio.program.phred.PhredToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest -[INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Running org.biojava.bio.AnnotationTypeTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.AnnotationTypeTest -[INFO] Running org.biojava.directory.OBDARegistryParserTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.OBDARegistryParserTest -[INFO] Running org.biojava.directory.RegistryConfigurationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.RegistryConfigurationTest -[INFO] Running org.biojava.directory.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.directory.SystemRegistryTest -[INFO] Running org.biojava.ontology.TermImplTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest -[INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.ontology.OntologyTest -[INFO] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 s - in org.biojava.ontology.ParseOBOFileTest -[INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest -[INFO] Running org.biojava.utils.ListToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest -[INFO] Running org.biojava.utils.automata.NfaTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.automata.NfaTest -[INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.utils.walker.WalkerFactoryTest -[INFO] Running org.biojava.utils.walker.WalkerTest -Increasing counter: Overlaps([20,50]) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) -Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -Feature: ByClass(org.biojava.bio.seq.ComponentFeature) -Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.utils.walker.WalkerTest -[INFO] Running org.biojava.utils.regex.RegexTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.RegexTest -[INFO] Running org.biojava.utils.regex.PatternCheckerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest -[INFO] Running org.biojava.utils.process.AllTests -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.utils.process.AllTests -[INFO] Running org.biojava.utils.process.ExternalProcessTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.utils.process.ExternalProcessTest -[INFO] Running org.biojava.utils.SmallMapTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest -[INFO] Running org.biojava.utils.RepeatedCharSequenceTest -JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.RepeatedCharSequenceTest -[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.naming.ObdaUriParserTest + +urn:obda.org:format:embl/ac +:trail +oneName +lead: +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes -Binding: urn -> org.biojava.naming.ObdaContext@14e5a39 +Binding: urn -> org.biojava.naming.ObdaContext@1660f4e Reached urn Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@1de7f3d +Binding: open-bio.org -> org.biojava.naming.ObdaContext@8806ef Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed @@ -3393,7 +3107,7 @@ module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } -Binding: type -> org.biojava.naming.ObdaContext@166ae3a +Binding: type -> org.biojava.naming.ObdaContext@1205a84 Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types @@ -3402,7 +3116,7 @@ type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } -Binding: type -> org.biojava.naming.ObdaContext@f4b83d +Binding: type -> org.biojava.naming.ObdaContext@10587f1 Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this @@ -3411,7 +3125,7 @@ ontology. This is not important. The important thing is that we have unique identifiers for common types that all projects use and interact with. } -Binding: format -> org.biojava.naming.ObdaContext@131289 +Binding: format -> org.biojava.naming.ObdaContext@176b067 Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this @@ -3422,7 +3136,7 @@ type of URN is purely there to identify the format of the stream, not the manner in which it should be processed. } -Binding: alphabet -> org.biojava.naming.ObdaContext@5e69a5 +Binding: alphabet -> org.biojava.naming.ObdaContext@17b7b6 Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as @@ -3434,14 +3148,14 @@ Alphabets do not define a mapping to or from strings, but should be used wherever the type of the content of a sequence needs to be stated. } -Binding: format -> org.biojava.naming.ObdaContext@a1116a +Binding: format -> org.biojava.naming.ObdaContext@1063c0a Reached urn:open-bio.org:format Attributes: {description=description: A namespace for OBDA URNs that define formats. All URNs within this namespace must be of the type urn:open-bio.org:type:format. Any URN in this namespace that is not of that type is not a valid OBDA URN. } -Binding: enzyme -> org.biojava.naming.ObdaContext@1e17893 +Binding: enzyme -> org.biojava.naming.ObdaContext@6d1014 Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from @@ -3457,29 +3171,29 @@ ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } -Binding: genbank -> org.biojava.naming.ObdaContext@1eea77c +Binding: genbank -> org.biojava.naming.ObdaContext@707e36 Reached urn:open-bio.org:format:genbank Attributes: {description=description: The GENBANK file format associated with the GENBANK sequence database. } -Binding: swissprot -> org.biojava.naming.ObdaContext@82e6a5 +Binding: swissprot -> org.biojava.naming.ObdaContext@14ddd49 Reached urn:open-bio.org:format:swissprot Attributes: {description=description: The SWISSPROT file format as used in the SWISSPROT sequence database. } -Binding: embl -> org.biojava.naming.ObdaContext@c4915e +Binding: embl -> org.biojava.naming.ObdaContext@1554b06 Reached urn:open-bio.org:format:embl Attributes: {description=description: The EMBL file format associated with entries in the EMBL sequence database. } -Binding: alphabet -> org.biojava.naming.ObdaContext@fb4575 +Binding: alphabet -> org.biojava.naming.ObdaContext@14e1548 Reached urn:open-bio.org:alphabet Attributes: {description=description: A namespace within which to store alphabet identifiers. Alphabets should represent URNs that represent objects of the type identified by urn:open-bio.org:type:alphabet, and any useage outside of this is not supported. } -Binding: rna -> org.biojava.naming.ObdaContext@c2c551 +Binding: rna -> org.biojava.naming.ObdaContext@3a4799 Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry @@ -3487,7 +3201,7 @@ are reprsented by the four letters a, g, c and u. However, this is not a formal requirement for a resource to declare this alphabet as its type. } -Binding: protein -> org.biojava.naming.ObdaContext@184b3a2 +Binding: protein -> org.biojava.naming.ObdaContext@11276c2 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, @@ -3495,7 +3209,7 @@ to be represented by characters, but this is not a formal requirement for a resource to publish an alphabet equal to this identifier. } -Binding: dna -> org.biojava.naming.ObdaContext@1648d2d +Binding: dna -> org.biojava.naming.ObdaContext@aa12dd Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry @@ -3503,22 +3217,344 @@ are reprsented by the four letters a, g, c and t. However, this is not a formal requirement for a resource to declare this alphabet as its type. } -lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@1ccb12d} +lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@16eabae} My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1ca495} +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@729b1e} My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@19d4443, format=org.biojava.naming.ObdaContext@13eca84, alphabet=org.biojava.naming.ObdaContext@147dfed} +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@bbd20a, format=org.biojava.naming.ObdaContext@503868, alphabet=org.biojava.naming.ObdaContext@95a785} My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@38e4dc, genbank=org.biojava.naming.ObdaContext@1fc0084, swissprot=org.biojava.naming.ObdaContext@1788d5, embl=org.biojava.naming.ObdaContext@1ec9f8d} +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@4f6be2, genbank=org.biojava.naming.ObdaContext@aac163, swissprot=org.biojava.naming.ObdaContext@17030a6, embl=org.biojava.naming.ObdaContext@1c0542} My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.naming.ObdaInitialContextFactoryTest -[INFO] Running org.biojava.naming.ObdaUriParserTest - -urn:obda.org:format:embl/ac -:trail -oneName -lead: -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.naming.ObdaUriParserTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.naming.ObdaInitialContextFactoryTest +[INFO] Running org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.directory.SystemRegistryTest +[INFO] Running org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.directory.RegistryConfigurationTest +[INFO] Running org.biojava.directory.OBDARegistryParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.OBDARegistryParserTest +[INFO] Running org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.utils.process.AllTests +[INFO] Running org.biojava.utils.process.ExternalProcessTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Running org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Running org.biojava.utils.regex.RegexTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.regex.RegexTest +[INFO] Running org.biojava.utils.RepeatedCharSequenceTest +JAM +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Running org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.utils.automata.NfaTest +[INFO] Running org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Running org.biojava.utils.walker.WalkerTest +Increasing counter: Overlaps([20,50]) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) +Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +Feature: ByClass(org.biojava.bio.seq.ComponentFeature) +Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.utils.walker.WalkerTest +[INFO] Running org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest +[INFO] Running org.biojava.utils.SmallMapTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest +[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.ontology.OntologyTest +[INFO] Running org.biojava.ontology.TripleImplTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest +[INFO] Running org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Running org.biojava.ontology.TermImplTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TermImplTest +[INFO] Running org.biojava.bio.MergeAnnotationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest +[INFO] Running org.biojava.bio.AnnotationTypeTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.AnnotationTypeTest +[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Running org.biojava.bio.proteomics.MassCalcTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.proteomics.MassCalcTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest +org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN + at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) + at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) + at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) + at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.proteomics.aaindex.AAindexTest +[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +java.lang.NullPointerException: name is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +org.biojava.bio.seq.db.IllegalIDException: No table found with name test. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +java.lang.NullPointerException: table is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +[INFO] Running org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.CircularSequenceTest +[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.bio.seq.SeqSerializationTest +[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.6 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest +idb length: 79 +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.459 s - in org.biojava.bio.seq.io.SeqIOToolsTest +[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Running org.biojava.bio.seq.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.RNAToolsTest +[INFO] Running org.biojava.bio.seq.ProteinToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.ProteinToolsTest +[INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Running org.biojava.bio.seq.FeatureFilterTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureFilterTest +[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.FilterUtilsTest +[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest +template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.impl.ViewSequenceTest +[INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Running org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Running org.biojava.bio.program.phred.PhredToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.phred.PhredToolsTest +[INFO] Running org.biojava.bio.symbol.BetweenLocationTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.103 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest +symbolForIndex +getAlphabet +indexForSymbol +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.MergeLocationTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MergeLocationTest +[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Running org.biojava.bio.symbol.TranslationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.TranslationTest +[INFO] Running org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Running org.biojava.bio.symbol.PointLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest +[INFO] Running org.biojava.bio.symbol.MotifToolsTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MotifToolsTest +[INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest +Adding symbol list taccaccagga$ +Adding symbol list taccaccagga$ +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest +[INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CrossProductTokenizationTest +[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.CircularLocationTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.CircularLocationTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Running org.biojava.bio.symbol.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Running org.biojava.bio.symbol.RangeLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.RangeLocationTest +[INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest +[INFO] Running org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.719 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest +[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.DoubleAlphabetTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Running org.biojava.bio.search.SeqContentPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SeqContentPatternTest +[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Running org.biojava.bio.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.dist.DistSerTest +[INFO] Running org.biojava.bio.dist.DistributionToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Running org.biojava.bio.dist.DistributionTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dist.DistributionTest +[INFO] Running org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Running org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dp.MarkovModelEventTest +[INFO] Running org.biojava.bio.dp.EmissionStateEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dp.EmissionStateEventTest [INFO] Running org.biojavax.SimpleNoteTest testGetValue testToString @@ -3530,16 +3566,7 @@ testSetRank testSetTerm testSetValue -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNoteTest -[INFO] Running org.biojavax.SimpleDocRefAuthorTest -testIsConsortium -testToString -testCompareTo -testGetName -testHashCode -testEquals -testGetExtendedName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefAuthorTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote @@ -3558,125 +3585,6 @@ testRemoveProperty2 testContainsProperty [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleRichAnnotationTest -[INFO] Running org.biojavax.ga.impl.SimplePopulationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimplePopulationTest -[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest -[INFO] Running org.biojavax.ga.util.WeightedSetTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest -[INFO] Running org.biojavax.ga.util.GAToolsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest -[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest -[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest -[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest -[INFO] Running org.biojavax.SimpleCommentTest -testSetComment -testToString -testCompareTo -testGetRank -testHashCode -testGetComment -testEquals -testSetRank -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCommentTest -[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest -testEquals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest -[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest -testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest -[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest -testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichLocationTest -[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest -Location 467: 467 -Location 340..565: 340..565 -Location <345..500: <345..500 -Location <1..888: <1..888 -Location (102.110): (102.110) -Location (23.45)..600: (23.45)..600 -Location (122.133)..(204.221): (122.133)..(204.221) -Location 123^124: 123^124 -Location 145^177: 145^177 -Location join(12..78,134..202): join(12..78,134..202) -Location complement(1..23): complement(1..23) -Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) -Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) -Location complement(34..(122.126)): complement(34..(122.126)) -Location complement((122.126)..34): complement((122.126)..34) -Location J00194:100..202: J00194:100..202 -Location (8298.8300)..10206: (8298.8300)..10206 -Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest -[INFO] Running org.biojavax.bio.seq.io.Bug2255Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.io.Bug2255Test -[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest -[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -testGetNameClass -testToString -testCompareTo -testSetNameClass -testGetName -testHashCode -testEquals -testSetName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -[INFO] Running org.biojavax.bio.SimpleBioEntryTest -testGetNamespace -testGetNoteSet -testGetRankedDocRefs -testGetRelationships -testGetTaxon -testSetDescription -testGetAccession -testGetRankedCrossRefs -testToString -testCompareTo -testGetName -testRemoveComment -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testSetNoteSet -testRemoveRankedCrossRef -testRemoveRankedDocRef -testRemoveRelationship -testGetVersion -testGetDescription -testSetIdentifier -testGetComments -testHashCode -testEquals -testAddRankedCrossRef -testAddRankedDocRef -testAddRelationship -testSetDivision -testGetDivision -testSetTaxon -testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.SimpleRankedCrossRefTest testToString testGetCrossRef @@ -3686,8 +3594,6 @@ testEquals testSetRank [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedCrossRefTest -[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Running org.biojavax.SimpleCrossRefTest testGetNoteSet testGetAccession @@ -3699,7 +3605,7 @@ testHashCode testGetDbname testEquals -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleCrossRefTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCrossRefTest [INFO] Running org.biojavax.SimpleRankedDocRefTest testGetStart testSetLocation @@ -3711,46 +3617,54 @@ testEquals testGetEnd testSetRank -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Running org.biojavax.EmptyRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testGetNote +testSetNoteSet +testContains +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testEquals +testContainsProperty +[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.EmptyRichAnnotationTest [INFO] Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteBioEntry testGetRemoteSymbolList [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.DummyCrossReferenceResolverTest -[INFO] Running org.biojavax.SimpleNamespaceTest -testGetAuthority -testSetDescription -testToString -testGetAcronym -testCompareTo -testGetName -testSetAuthority -testGetDescription -testHashCode -testSetAcronym -testEquals -testGetURI -testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleNamespaceTest -[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest -testGetSubject -testSetDescriptors +[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Running org.biojavax.ga.util.GAToolsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest +[INFO] Running org.biojavax.ga.util.WeightedSetTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest +[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Running org.biojavax.ga.impl.SimplePopulationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest +[INFO] Running org.biojavax.SimpleDocRefAuthorTest +testIsConsortium testToString -testGetSynonyms -testRemoveDescriptor testCompareTo -testAddSynonym testGetName -testGetOntology -testGetPredicate -testGetAnnotation -testGetDescription -testGetDescriptors testHashCode -testAddDescriptor testEquals -testGetObject -testRemoveSynonym -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableTripleTest +testGetExtendedName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest testSetTripleSet testCreateTriple @@ -3776,7 +3690,7 @@ testEquals testGetOps testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableOntologyTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.ontology.SimpleComparableTermTest testSetDescription testGetRankedCrossRefs @@ -3798,23 +3712,128 @@ testRemoveSynonym testSetObsolete testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableTermTest -[INFO] Running org.biojavax.EmptyRichAnnotationTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ontology.SimpleComparableTermTest +[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest +testGetSubject +testSetDescriptors +testToString +testGetSynonyms +testRemoveDescriptor +testCompareTo +testAddSynonym +testGetName +testGetOntology +testGetPredicate +testGetAnnotation +testGetDescription +testGetDescriptors +testHashCode +testAddDescriptor +testEquals +testGetObject +testRemoveSynonym +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ontology.SimpleComparableTripleTest +[INFO] Running org.biojavax.bio.SimpleBioEntryTest +testGetNamespace testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testGetNote +testGetRankedDocRefs +testGetRelationships +testGetTaxon +testSetDescription +testGetAccession +testGetRankedCrossRefs +testToString +testCompareTo +testGetName +testRemoveComment +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation testSetNoteSet -testContains -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty +testRemoveRankedCrossRef +testRemoveRankedDocRef +testRemoveRelationship +testGetVersion +testGetDescription +testSetIdentifier +testGetComments +testHashCode testEquals -testContainsProperty -[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.EmptyRichAnnotationTest +testAddRankedCrossRef +testAddRankedDocRef +testAddRelationship +testSetDivision +testGetDivision +testSetTaxon +testAddComment +[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.bio.SimpleBioEntryTest +[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Running org.biojavax.bio.seq.io.Bug2255Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.io.Bug2255Test +[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest +Location 467: 467 +Location 340..565: 340..565 +Location <345..500: <345..500 +Location <1..888: <1..888 +Location (102.110): (102.110) +Location (23.45)..600: (23.45)..600 +Location (122.133)..(204.221): (122.133)..(204.221) +Location 123^124: 123^124 +Location 145^177: 145^177 +Location join(12..78,134..202): join(12..78,134..202) +Location complement(1..23): complement(1..23) +Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) +Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) +Location complement(34..(122.126)): complement(34..(122.126)) +Location complement((122.126)..34): complement((122.126)..34) +Location J00194:100..202: J00194:100..202 +Location (8298.8300)..10206: (8298.8300)..10206 +Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest +[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest +testEquals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +testEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest +testEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest +[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +testGetNameClass +testToString +testCompareTo +testSetNameClass +testGetName +testHashCode +testEquals +testSetName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +[INFO] Running org.biojavax.SimpleCommentTest +testSetComment +testToString +testCompareTo +testGetRank +testHashCode +testGetComment +testEquals +testSetRank +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleCommentTest [INFO] Running org.biojavax.SimpleDocRefTest testGetTitle testToString @@ -3829,7 +3848,24 @@ testEquals testGetCRC testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleDocRefTest +[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Running org.biojavax.SimpleNamespaceTest +testGetAuthority +testSetDescription +testToString +testGetAcronym +testCompareTo +testGetName +testSetAuthority +testGetDescription +testHashCode +testSetAcronym +testEquals +testGetURI +testSetURI +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleNamespaceTest [INFO] [INFO] Results: [INFO] @@ -3858,11 +3894,11 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.571 s - in org.biojava.bio.alignment.SubstitutionMatrixTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] [INFO] Results: [INFO] @@ -3892,7 +3928,7 @@ [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. -[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3920,42 +3956,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- +[INFO] Running org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.253 s - in org.biojava.bio.program.sax.BlastTest +[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.091 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.396 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.297 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.256 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.584 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.286 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.676 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.768 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.048 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.437 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.396 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.468 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.151 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.831 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.bio.program.sax.BlastTest -[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] [INFO] Results: [INFO] @@ -3984,31 +4020,31 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.scf.SCFTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.475 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.226 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Running org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Running org.biojava.bio.program.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.program.fastq.FastqTest -[INFO] Running org.biojava.bio.program.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest +[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Running org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.FastqTest +[INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.FastqToolsTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] [INFO] Results: [INFO] @@ -4056,7 +4092,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -4066,19 +4102,19 @@ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] [INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] -[INFO] bytecode ........................................... SUCCESS [ 0.657 s] -[INFO] core ............................................... SUCCESS [ 10.499 s] -[INFO] alignment .......................................... SUCCESS [ 10.162 s] -[INFO] biosql ............................................. SUCCESS [ 10.126 s] -[INFO] blast .............................................. SUCCESS [ 10.137 s] -[INFO] sequencing ......................................... SUCCESS [ 10.148 s] -[INFO] gui ................................................ SUCCESS [ 0.075 s] -[INFO] phylo .............................................. SUCCESS [ 10.131 s] +[INFO] bytecode ........................................... SUCCESS [ 0.390 s] +[INFO] core ............................................... SUCCESS [ 10.256 s] +[INFO] alignment .......................................... SUCCESS [ 10.071 s] +[INFO] biosql ............................................. SUCCESS [ 10.139 s] +[INFO] blast .............................................. SUCCESS [ 10.065 s] +[INFO] sequencing ......................................... SUCCESS [ 10.068 s] +[INFO] gui ................................................ SUCCESS [ 0.037 s] +[INFO] phylo .............................................. SUCCESS [ 10.063 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:02 min -[INFO] Finished at: 2024-04-13T15:10:33Z +[INFO] Total time: 01:01 min +[INFO] Finished at: 2025-05-16T21:38:39Z [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -4209,20 +4245,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.494 s] -[INFO] bytecode ........................................... SUCCESS [ 0.058 s] -[INFO] core ............................................... SUCCESS [ 0.046 s] -[INFO] alignment .......................................... SUCCESS [ 0.035 s] -[INFO] biosql ............................................. SUCCESS [ 0.035 s] -[INFO] blast .............................................. SUCCESS [ 0.033 s] -[INFO] sequencing ......................................... SUCCESS [ 0.035 s] -[INFO] gui ................................................ SUCCESS [ 0.049 s] -[INFO] phylo .............................................. SUCCESS [ 0.033 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.254 s] +[INFO] bytecode ........................................... SUCCESS [ 0.030 s] +[INFO] core ............................................... SUCCESS [ 0.023 s] +[INFO] alignment .......................................... SUCCESS [ 0.019 s] +[INFO] biosql ............................................. SUCCESS [ 0.017 s] +[INFO] blast .............................................. SUCCESS [ 0.019 s] +[INFO] sequencing ......................................... SUCCESS [ 0.016 s] +[INFO] gui ................................................ SUCCESS [ 0.018 s] +[INFO] phylo .............................................. SUCCESS [ 0.025 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.081 s -[INFO] Finished at: 2024-04-13T15:10:36Z +[INFO] Total time: 0.561 s +[INFO] Finished at: 2025-05-16T21:38:41Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/reproducible-path/biojava-live-1.9.7\+dfsg --non-explore Analysing pom.xml... @@ -4307,8 +4343,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-1_all.deb'. -dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.7+dfsg-1_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-1_all.deb'. +dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.7+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4316,12 +4352,14 @@ 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/32085/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/32085/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/21687 and its subdirectories -I: Current time: Sat Apr 13 03:12:39 -12 2024 -I: pbuilder-time-stamp: 1713021159 +I: removing directory /srv/workspace/pbuilder/32085 and its subdirectories +I: Current time: Sat May 17 11:40:21 +14 2025 +I: pbuilder-time-stamp: 1747431621