Diff of the two buildlogs: -- --- b1/build.log 2024-05-17 12:01:56.523707642 +0000 +++ b2/build.log 2024-05-17 12:19:11.059723067 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 19 06:18:35 -12 2025 -I: pbuilder-time-stamp: 1750357115 +I: Current time: Sat May 18 02:01:59 +14 2024 +I: pbuilder-time-stamp: 1715947319 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ 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/3683673/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 17 12:02 /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/519350/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e6252dd3547d4453bb0cf0586014de50' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3683673' - PS1='# ' - PS2='> ' + INVOCATION_ID=02cdc4b695fe4873ae8d6ca192816aee + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=519350 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.5Um3qsL4/pbuilderrc_WIuA --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5Um3qsL4/b1 --logfile b1/build.log biojava-live_1.9.7+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.5Um3qsL4/pbuilderrc_UU2o --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5Um3qsL4/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 18 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3683673/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 17 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -405,7 +437,7 @@ Get: 277 http://deb.debian.org/debian unstable/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 257 MB in 29s (8876 kB/s) +Fetched 257 MB in 9s (29.0 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 ... 19719 files and directories currently installed.) @@ -1730,7 +1762,11 @@ 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/519350/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/519350/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 @@ -3001,20 +3037,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 17.639 s] -[INFO] bytecode ........................................... SUCCESS [ 5.083 s] -[INFO] core ............................................... SUCCESS [ 25.851 s] -[INFO] alignment .......................................... SUCCESS [ 3.994 s] -[INFO] biosql ............................................. SUCCESS [ 2.616 s] -[INFO] blast .............................................. SUCCESS [ 7.548 s] -[INFO] sequencing ......................................... SUCCESS [ 6.517 s] -[INFO] gui ................................................ SUCCESS [ 4.406 s] -[INFO] phylo .............................................. SUCCESS [ 2.261 s] +[INFO] biojava-legacy ..................................... SUCCESS [01:51 min] +[INFO] bytecode ........................................... SUCCESS [ 13.830 s] +[INFO] core ............................................... SUCCESS [01:40 min] +[INFO] alignment .......................................... SUCCESS [ 34.971 s] +[INFO] biosql ............................................. SUCCESS [ 34.377 s] +[INFO] blast .............................................. SUCCESS [ 17.994 s] +[INFO] sequencing ......................................... SUCCESS [ 27.872 s] +[INFO] gui ................................................ SUCCESS [ 42.808 s] +[INFO] phylo .............................................. SUCCESS [ 21.692 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:17 min -[INFO] Finished at: 2025-06-19T18:21:58Z +[INFO] Total time: 06:47 min +[INFO] Finished at: 2024-05-17T12:11:29Z [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 @@ -3077,30 +3113,79 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojavax.SimpleDocRefAuthorTest -testIsConsortium +[INFO] Running org.biojavax.SimpleDocRefTest +testGetTitle testToString +testGetLocation +testSetCrossref +testGetCrossref testCompareTo -testGetName +testGetAuthors +testGetAuthorList testHashCode +testSetRemark testEquals -testGetExtendedName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojavax.SimpleDocRefAuthorTest -[INFO] Running org.biojavax.SimpleNamespaceTest -testGetAuthority -testSetDescription +testGetCRC +testGetRemark +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojavax.SimpleDocRefTest +[INFO] Running org.biojavax.SimpleCrossRefTest +testGetNoteSet +testGetAccession testToString -testGetAcronym testCompareTo -testGetName -testSetAuthority -testGetDescription +testGetAnnotation +testSetNoteSet +testGetVersion testHashCode -testSetAcronym +testGetDbname testEquals -testGetURI -testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNamespaceTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojavax.SimpleCrossRefTest +[INFO] Running org.biojavax.SimpleRankedDocRefTest +testGetStart +testSetLocation +testToString +testGetDocumentReference +testCompareTo +testGetRank +testHashCode +testEquals +testGetEnd +testSetRank +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.9 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.011 s - in org.biojavax.ga.impl.SimplePopulationTest +[INFO] Running org.biojavax.ga.util.WeightedSetTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 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: 0.01 s - in org.biojavax.ga.util.GAToolsTest +[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: 0.011 s - in org.biojavax.EmptyRichAnnotationTest [INFO] Running org.biojavax.ontology.SimpleComparableTermTest testSetDescription testGetRankedCrossRefs @@ -3122,7 +3207,7 @@ testRemoveSynonym testSetObsolete testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.ontology.SimpleComparableTermTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojavax.ontology.SimpleComparableTermTest [INFO] Running org.biojavax.ontology.SimpleComparableTripleTest testGetSubject testSetDescriptors @@ -3142,7 +3227,7 @@ testEquals testGetObject testRemoveSynonym -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ontology.SimpleComparableTripleTest +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.ontology.SimpleComparableTripleTest [INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest testSetTripleSet testCreateTriple @@ -3168,21 +3253,7 @@ testEquals testGetOps testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.ontology.SimpleComparableOntologyTest -[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 -testToString -testCompareTo -testGetAnnotation -testSetNoteSet -testGetVersion -testHashCode -testGetDbname -testEquals -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCrossRefTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.bio.SimpleBioEntryTest testGetNamespace testGetNoteSet @@ -3216,27 +3287,7 @@ testGetDivision testSetTaxon testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.bio.SimpleBioEntryTest -[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.bio.seq.SimpleRichFeatureTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 s - in org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Running org.biojavax.bio.seq.io.Bug2255Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.io.Bug2255Test -[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojavax.bio.seq.io.GenbankFormatTest -[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] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest Location 467: 467 Location 340..565: 340..565 @@ -3256,48 +3307,44 @@ 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.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [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] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.263 s - in org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.io.Bug2249_2248Test -[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] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.399 s - in org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Running org.biojavax.bio.seq.io.Bug2255Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.io.Bug2255Test +[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [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.RichLocationToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 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 s - in org.biojavax.bio.seq.CompoundRichLocationTest -[INFO] Running org.biojavax.SimpleDocRefTest -testGetTitle -testToString -testGetLocation -testSetCrossref -testGetCrossref -testCompareTo -testGetAuthors -testGetAuthorList -testHashCode -testSetRemark +[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals -testGetCRC -testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefTest -[INFO] Running org.biojavax.SimpleRankedCrossRefTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.SimpleRichLocationTest +[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +testGetNameClass testToString -testGetCrossRef testCompareTo -testGetRank +testSetNameClass +testGetName testHashCode testEquals -testSetRank -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedCrossRefTest +testSetName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [INFO] Running org.biojavax.SimpleNoteTest testGetValue testToString @@ -3309,19 +3356,46 @@ testSetRank testSetTerm testSetValue -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleNoteTest -[INFO] Running org.biojavax.SimpleRankedDocRefTest -testGetStart -testSetLocation +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojavax.SimpleNoteTest +[INFO] Running org.biojavax.DummyCrossReferenceResolverTest +testGetRemoteBioEntry +testGetRemoteSymbolList +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojavax.DummyCrossReferenceResolverTest +[INFO] Running org.biojavax.SimpleNamespaceTest +testGetAuthority +testSetDescription testToString -testGetDocumentReference +testGetAcronym +testCompareTo +testGetName +testSetAuthority +testGetDescription +testHashCode +testSetAcronym +testEquals +testGetURI +testSetURI +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojavax.SimpleNamespaceTest +[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.SimpleRankedCrossRefTest +testToString +testGetCrossRef testCompareTo testGetRank testHashCode 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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.SimpleRankedCrossRefTest +[INFO] Running org.biojavax.SimpleDocRefAuthorTest +testIsConsortium +testToString +testCompareTo +testGetName +testHashCode +testEquals +testGetExtendedName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote @@ -3339,27 +3413,7 @@ testRemoveProperty 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.DummyCrossReferenceResolverTest -testGetRemoteBioEntry -testGetRemoteSymbolList -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.DummyCrossReferenceResolverTest -[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: 0.002 s - in org.biojavax.EmptyRichAnnotationTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojavax.SimpleRichAnnotationTest [INFO] Running org.biojavax.SimpleCommentTest testSetComment testToString @@ -3370,227 +3424,67 @@ 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.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 s - in org.biojavax.ga.util.WeightedSetTest -[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.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.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.ga.functions.ProportionalSelectionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.ProportionalSelectionTest -[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: 0.001 s - in org.biojavax.ga.impl.SimplePopulationTest -[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.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.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.directory.SystemRegistryTest -[INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest -Reached - Attributes: No attributes -Binding: urn -> org.biojava.naming.ObdaContext@516be40f -Reached urn - Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@3c0a50da -Reached urn:open-bio.org - Attributes: {description=description: -This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed -by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the -module obda-specs in the cvs repository located at -pub.open-bio.org:/home/repository/obf-common. - } -Binding: type -> org.biojava.naming.ObdaContext@77be656f -Reached urn:open-bio.org:type - Attributes: {description=description: -The namespace for URNs that identify data types. It is expected that the types -that are given IDs will be very general in nature, such as Sequence and -File Format. All types are of type urn:open-bio.org:type:type. Any URN in the -type namespace that is not of this type is not conforming to the OBDA -specification for this namespace. - } -Binding: type -> org.biojava.naming.ObdaContext@19dc67c2 -Reached urn:open-bio.org:type:type - Attributes: {description=description: -The OBDA URN that identifies the concept of 'type'. In a given language, this -may map to the types of data structures, or objects. Alternativel, it may -map to a particular set of keys being present in a map, or a term in an -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@221af3c0 -Reached urn:open-bio.org:type:format - Attributes: {description=description: -A file format. Many file formats are used in bioinformatics. Entities of this -type identify a format. The format can be used to choose how to treat a file. -The format is not expected to be resolvable to a formal deffinition of the -file structure using OBDA-supplied functionality. Different applications may -chose to process a stream with the same format URN in different ways. This -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@62bd765 -Reached urn:open-bio.org:type:alphabet - Attributes: {description=description: -A biological sequence alphabet. Biological sequences are often represented as -strings of characters. However, in differnt circumstances, the same characters -can represent different things. For example, in DNA, the 't' character -represents tyrosine. In Protein, this same character represents tryptophan. - -Associating alphabets with these sequences disambiguates their interpretation. -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@23a5fd2 -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@78a2da20 -Reached urn:open-bio.org:format:enzyme - Attributes: {description=description: -The Enzyme database entry format. The enzyme database can be downloaded from -the ebi at: - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ - -For an example of a file in this format, see: - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat - -The format is described more fully in - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt - } -Binding: genbank -> org.biojava.naming.ObdaContext@dd3b207 -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@551bdc27 -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@58fdd99 -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@6b1274d2 -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@7bc1a03d -Reached urn:open-bio.org:alphabet:rna - Attributes: {description=description: -The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry -or genetics introductory textbook to find out more. Commonly, the nucleotides -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@70b0b186 -Reached urn:open-bio.org:alphabet:protein - Attributes: {description=description: -The protein alphabet. Proteins are composed from amino-acids. To find out more, -read a biochemistry or genetics text book. It is common for protein sequences -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@ba8d91c -Reached urn:open-bio.org:alphabet:dna - Attributes: {description=description: -The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry -or genetics introductory textbook to find out more. Commonly, the nucleotides -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@58c1c010} -My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@61d47554} -My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@69b794e2, format=org.biojava.naming.ObdaContext@3f200884, alphabet=org.biojava.naming.ObdaContext@4d339552} -My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@f0f2775, genbank=org.biojava.naming.ObdaContext@5a4aa2f2, swissprot=org.biojava.naming.ObdaContext@6591f517, embl=org.biojava.naming.ObdaContext@345965f2} -My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 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] 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.RepeatedCharSequenceTest -JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.RepeatedCharSequenceTest -[INFO] Running org.biojava.utils.process.AllTests -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 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.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.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.regex.PatternCheckerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.418 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Running org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 s - in org.biojava.utils.process.AllTests [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 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: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Increasing counter: Overlaps([20,50]) 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: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +OverlapsLocation: Overlaps([20,50]) 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: 0.021 s - in org.biojava.utils.walker.WalkerTest -[INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.393 s - in org.biojava.utils.walker.WalkerTest +[INFO] Running org.biojava.utils.RepeatedCharSequenceTest +JAM +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Running org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.016 s - in org.biojava.utils.regex.RegexTest [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] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.SmallMapTest +[INFO] Running org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.utils.automata.NfaTest +[INFO] Running org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.ListToolsTest [INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.ontology.OntologyTest [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] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.ontology.TripleImplTest -[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.program.indexdb.IndexToolsTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 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: 0.006 s - in org.biojava.bio.program.phred.PhredToolsTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest +[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.SimpleSeqSimilaritySearchHitTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 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: 0.031 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [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] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 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] 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.aaindex.SimpleSymbolPropertyTableDBTest java.lang.NullPointerException: name is null. at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) @@ -3664,7 +3558,9 @@ 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] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 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) @@ -3692,72 +3588,147 @@ 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: 0.002 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: 0.053 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[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.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 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: 0.001 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 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: 0.347 s - in org.biojava.bio.dp.DPSerializationTest [INFO] Running org.biojava.bio.dp.EmissionStateEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dp.EmissionStateEventTest -[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.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.RNAToolsTest -[INFO] Running org.biojava.bio.seq.CircularSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.CircularSequenceTest -[INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dp.EmissionStateEventTest +[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.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.bio.dist.DistSerTest +[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.dist.DistributionToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.944 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[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.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.TestSoftMaskedAlphabet +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 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: 0.212 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest +[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.UkkonenSuffixTreeTest +Adding symbol list taccaccagga$ +Adding symbol list taccaccagga$ +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest +[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: 2.14 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Running org.biojava.bio.symbol.CircularLocationTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.CircularLocationTest +[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Running org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Running org.biojava.bio.symbol.RangeLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest +[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.symbol.SymbolSerializationTest +[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.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IntegerAlphabetTest +[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.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[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.BetweenLocationTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Running org.biojava.bio.symbol.PointLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.PointLocationTest +[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.symbol.SimpleBasisSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest +[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.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.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleCodonPrefTest +[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.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.463 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest -[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] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.275 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[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.SeqIOToolsTest idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 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: 0.034 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.709 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Running org.biojava.bio.seq.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 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: 0.001 s - in org.biojava.bio.seq.ProteinToolsTest +[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Running org.biojava.bio.seq.FeatureFilterTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureFilterTest +[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 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 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 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: 0.005 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 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: 0.036 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.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.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.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.seq.SeqSerializationTest -[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.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.FilterUtilsTest [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.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.impl.ViewSeqSerializationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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} @@ -3765,98 +3736,163 @@ 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: 0.001 s - in org.biojava.bio.seq.impl.ViewSequenceTest -[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 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: 0.161 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Running org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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.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.search.SimpleSeqSimilaritySearchResultTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[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: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[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.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.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.dist.TranslatedDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.022 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: 0.014 s - in org.biojava.bio.dist.DistributionToolsTest -[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.symbol.SimpleCodonPrefTest -[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.SymbolSerializationTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.SymbolSerializationTest -[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.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.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.PointLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.PointLocationTest -[INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.BetweenLocationTest -[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.CodonPrefToolsTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Running org.biojava.bio.symbol.RangeLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest -[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.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.747 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[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.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.CircularLocationTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CircularLocationTest -[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 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest -[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.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.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 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.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.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.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.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.CompoundLocationTest -[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.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.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.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[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: 0.132 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Running org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.directory.RegistryConfigurationTest +[INFO] Running org.biojava.directory.OBDARegistryParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.directory.OBDARegistryParserTest +[INFO] Running org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.directory.SystemRegistryTest +[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: 0.002 s - in org.biojava.naming.ObdaUriParserTest +[INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest +Reached + Attributes: No attributes +Binding: urn -> org.biojava.naming.ObdaContext@2b441e56 +Reached urn + Attributes: No attributes +Binding: open-bio.org -> org.biojava.naming.ObdaContext@267891bf +Reached urn:open-bio.org + Attributes: {description=description: +This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed +by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the +module obda-specs in the cvs repository located at +pub.open-bio.org:/home/repository/obf-common. + } +Binding: type -> org.biojava.naming.ObdaContext@111a7973 +Reached urn:open-bio.org:type + Attributes: {description=description: +The namespace for URNs that identify data types. It is expected that the types +that are given IDs will be very general in nature, such as Sequence and +File Format. All types are of type urn:open-bio.org:type:type. Any URN in the +type namespace that is not of this type is not conforming to the OBDA +specification for this namespace. + } +Binding: type -> org.biojava.naming.ObdaContext@1a2773a8 +Reached urn:open-bio.org:type:type + Attributes: {description=description: +The OBDA URN that identifies the concept of 'type'. In a given language, this +may map to the types of data structures, or objects. Alternativel, it may +map to a particular set of keys being present in a map, or a term in an +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@78b0ec3a +Reached urn:open-bio.org:type:format + Attributes: {description=description: +A file format. Many file formats are used in bioinformatics. Entities of this +type identify a format. The format can be used to choose how to treat a file. +The format is not expected to be resolvable to a formal deffinition of the +file structure using OBDA-supplied functionality. Different applications may +chose to process a stream with the same format URN in different ways. This +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@46612bfc +Reached urn:open-bio.org:type:alphabet + Attributes: {description=description: +A biological sequence alphabet. Biological sequences are often represented as +strings of characters. However, in differnt circumstances, the same characters +can represent different things. For example, in DNA, the 't' character +represents tyrosine. In Protein, this same character represents tryptophan. + +Associating alphabets with these sequences disambiguates their interpretation. +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@4f213a2 +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@25699aa7 +Reached urn:open-bio.org:format:enzyme + Attributes: {description=description: +The Enzyme database entry format. The enzyme database can be downloaded from +the ebi at: + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ + +For an example of a file in this format, see: + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat + +The format is described more fully in + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt + } +Binding: genbank -> org.biojava.naming.ObdaContext@5a47730c +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@15369d73 +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@1cde374 +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@6818fd48 +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@9263c54 +Reached urn:open-bio.org:alphabet:rna + Attributes: {description=description: +The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry +or genetics introductory textbook to find out more. Commonly, the nucleotides +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@28daf506 +Reached urn:open-bio.org:alphabet:protein + Attributes: {description=description: +The protein alphabet. Proteins are composed from amino-acids. To find out more, +read a biochemistry or genetics text book. It is common for protein sequences +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@4662752a +Reached urn:open-bio.org:alphabet:dna + Attributes: {description=description: +The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry +or genetics introductory textbook to find out more. Commonly, the nucleotides +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@33bdd01} +My component is urn:open-bio.org:format:embl +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@7ac48f05} +My component is open-bio.org:format:embl +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@7af1d072, format=org.biojava.naming.ObdaContext@27ffd9f8, alphabet=org.biojava.naming.ObdaContext@642c6461} +My component is format:embl +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@3ace6346, genbank=org.biojava.naming.ObdaContext@4e48462d, swissprot=org.biojava.naming.ObdaContext@17216605, embl=org.biojava.naming.ObdaContext@10a907ec} +My component is embl +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] [INFO] Results: [INFO] @@ -3885,11 +3921,11 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 s - in org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.624 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.bio.alignment.SubstitutionMatrixTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.161 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] [INFO] Results: [INFO] @@ -3919,7 +3955,7 @@ [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: 0.033 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3947,42 +3983,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.321 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.097 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.251 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.549 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Running org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.84 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: 0.343 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.328 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.624 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.074 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.677 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.641 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.486 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: 6.428 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.488 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.983 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: 0.582 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.623 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 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: 0.027 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.526 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.735 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] [INFO] Results: [INFO] @@ -4011,31 +4047,31 @@ [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: 0.586 s - in org.biojava.bio.program.scf.SCFTest -[INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.708 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 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: 0.015 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 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: 0.021 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.bio.program.fastq.FastqToolsTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.bio.program.fastq.ConvertTest -[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] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 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: 0.036 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] [INFO] Results: [INFO] @@ -4083,7 +4119,7 @@ [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: 0.338 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.884 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -4092,20 +4128,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] -[INFO] bytecode ........................................... SUCCESS [ 0.420 s] -[INFO] core ............................................... SUCCESS [ 10.246 s] -[INFO] alignment .......................................... SUCCESS [ 10.072 s] -[INFO] biosql ............................................. SUCCESS [ 10.125 s] -[INFO] blast .............................................. SUCCESS [ 10.070 s] -[INFO] sequencing ......................................... SUCCESS [ 10.146 s] -[INFO] gui ................................................ SUCCESS [ 0.079 s] -[INFO] phylo .............................................. SUCCESS [ 10.134 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.010 s] +[INFO] bytecode ........................................... SUCCESS [ 2.631 s] +[INFO] core ............................................... SUCCESS [ 32.200 s] +[INFO] alignment .......................................... SUCCESS [ 10.720 s] +[INFO] biosql ............................................. SUCCESS [ 10.439 s] +[INFO] blast .............................................. SUCCESS [ 40.474 s] +[INFO] sequencing ......................................... SUCCESS [ 10.432 s] +[INFO] gui ................................................ SUCCESS [ 0.221 s] +[INFO] phylo .............................................. SUCCESS [ 10.361 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:01 min -[INFO] Finished at: 2025-06-19T18:23:00Z +[INFO] Total time: 01:58 min +[INFO] Finished at: 2024-05-17T12:13:30Z [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -4236,20 +4272,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.947 s] -[INFO] bytecode ........................................... SUCCESS [ 0.136 s] -[INFO] core ............................................... SUCCESS [ 0.068 s] -[INFO] alignment .......................................... SUCCESS [ 0.100 s] -[INFO] biosql ............................................. SUCCESS [ 0.086 s] -[INFO] blast .............................................. SUCCESS [ 0.041 s] -[INFO] sequencing ......................................... SUCCESS [ 0.090 s] -[INFO] gui ................................................ SUCCESS [ 0.081 s] -[INFO] phylo .............................................. SUCCESS [ 0.062 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 2.463 s] +[INFO] bytecode ........................................... SUCCESS [ 0.418 s] +[INFO] core ............................................... SUCCESS [ 0.288 s] +[INFO] alignment .......................................... SUCCESS [ 0.212 s] +[INFO] biosql ............................................. SUCCESS [ 0.238 s] +[INFO] blast .............................................. SUCCESS [ 0.213 s] +[INFO] sequencing ......................................... SUCCESS [ 0.284 s] +[INFO] gui ................................................ SUCCESS [ 0.276 s] +[INFO] phylo .............................................. SUCCESS [ 0.252 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 2.026 s -[INFO] Finished at: 2025-06-19T18:23:05Z +[INFO] Total time: 5.548 s +[INFO] Finished at: 2024-05-17T12:13:43Z [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... @@ -4334,8 +4370,8 @@ 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' 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-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4343,12 +4379,14 @@ 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/519350/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/519350/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/3683673 and its subdirectories -I: Current time: Thu Jun 19 06:24:55 -12 2025 -I: pbuilder-time-stamp: 1750357495 +I: removing directory /srv/workspace/pbuilder/519350 and its subdirectories +I: Current time: Sat May 18 02:19:10 +14 2024 +I: pbuilder-time-stamp: 1715948350