Diff of the two buildlogs: -- --- b1/build.log 2024-01-14 23:37:55.901662550 +0000 +++ b2/build.log 2024-01-14 23:45:46.703220064 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 15 17:56:19 -12 2025 -I: pbuilder-time-stamp: 1739685379 +I: Current time: Mon Jan 15 13:38:00 +14 2024 +I: pbuilder-time-stamp: 1705275480 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,85 @@ 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/118678/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 14 23:39 /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/11849/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9b36e77884a44500bac2a068c33cac50' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='118678' - PS1='# ' - PS2='> ' + INVOCATION_ID=9ae14892d89c45d5860055c2e2baeb8c + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=11849 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.o0eJwLEG/pbuilderrc_nJwY --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/b1 --logfile b1/build.log biojava-live_1.9.5+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.o0eJwLEG/pbuilderrc_n25k --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o0eJwLEG/b2 --logfile b2/build.log biojava-live_1.9.5+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin - total 6036 + total 6040 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat @@ -131,15 +163,15 @@ -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts + -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 14 23:39 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile + -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server @@ -159,7 +191,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/118678/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -483,7 +515,7 @@ Get: 268 http://deb.debian.org/debian bookworm/main i386 maven all 3.8.7-1 [18.9 kB] Get: 269 http://deb.debian.org/debian bookworm/main i386 maven-repo-helper all 1.11 [142 kB] Get: 270 http://deb.debian.org/debian bookworm/main i386 maven-debian-helper all 2.6.3 [108 kB] -Fetched 267 MB in 5s (55.9 MB/s) +Fetched 267 MB in 15s (17.8 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 ... 18156 files and directories currently installed.) @@ -1766,7 +1798,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava-live-1.9.5+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_1.9.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava-live-1.9.5+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_1.9.5+dfsg-3_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -3037,20 +3073,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 22.003 s] -[INFO] bytecode ........................................... SUCCESS [ 3.377 s] -[INFO] core ............................................... SUCCESS [ 21.971 s] -[INFO] alignment .......................................... SUCCESS [ 2.150 s] -[INFO] biosql ............................................. SUCCESS [ 2.874 s] -[INFO] blast .............................................. SUCCESS [ 2.493 s] -[INFO] sequencing ......................................... SUCCESS [ 2.667 s] -[INFO] gui ................................................ SUCCESS [ 4.143 s] -[INFO] phylo .............................................. SUCCESS [ 2.300 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 36.015 s] +[INFO] bytecode ........................................... SUCCESS [ 6.262 s] +[INFO] core ............................................... SUCCESS [ 44.010 s] +[INFO] alignment .......................................... SUCCESS [ 3.507 s] +[INFO] biosql ............................................. SUCCESS [ 4.581 s] +[INFO] blast .............................................. SUCCESS [ 3.972 s] +[INFO] sequencing ......................................... SUCCESS [ 4.509 s] +[INFO] gui ................................................ SUCCESS [ 7.489 s] +[INFO] phylo .............................................. SUCCESS [ 3.616 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:04 min -[INFO] Finished at: 2025-02-16T05:58:11Z +[INFO] Total time: 01:55 min +[INFO] Finished at: 2024-01-14T23:42:35Z [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-1.9.5\+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-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode test @@ -3113,69 +3149,389 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.ontology.OntologyTest -[INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest -[INFO] Running org.biojava.ontology.TermImplTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TermImplTest -[INFO] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.ontology.ParseOBOFileTest +[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: 0.029 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +[INFO] Running org.biojavax.bio.SimpleBioEntryTest +testGetNamespace +testGetNoteSet +testGetRankedDocRefs +testGetRelationships +testGetTaxon +testSetDescription +testGetAccession +testGetRankedCrossRefs +testToString +testCompareTo +testGetName +testRemoveComment +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation +testSetNoteSet +testRemoveRankedCrossRef +testRemoveRankedDocRef +testRemoveRelationship +testGetVersion +testGetDescription +testSetIdentifier +testGetComments +testHashCode +testEquals +testAddRankedCrossRef +testAddRankedDocRef +testAddRelationship +testSetDivision +testGetDivision +testSetTaxon +testAddComment +[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.bio.SimpleBioEntryTest +[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest +testEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest +[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +testEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 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: 0.014 s - in org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest +Location 467: 467 +Location 340..565: 340..565 +Location <345..500: <345..500 +Location <1..888: <1..888 +Location (102.110): (102.110) +Location (23.45)..600: (23.45)..600 +Location (122.133)..(204.221): (122.133)..(204.221) +Location 123^124: 123^124 +Location 145^177: 145^177 +Location join(12..78,134..202): join(12..78,134..202) +Location complement(1..23): complement(1..23) +Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) +Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) +Location complement(34..(122.126)): complement(34..(122.126)) +Location complement((122.126)..34): complement((122.126)..34) +Location J00194:100..202: J00194:100..202 +Location (8298.8300)..10206: (8298.8300)..10206 +Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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: 0.091 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: 0.006 s - in org.biojavax.bio.seq.io.Bug2255Test +[INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest +testEquals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Running org.biojavax.SimpleDocRefTest +testGetTitle +testToString +testGetLocation +testSetCrossref +testGetCrossref +testCompareTo +testGetAuthors +testGetAuthorList +testHashCode +testSetRemark +testEquals +testGetCRC +testGetRemark +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.SimpleDocRefTest +[INFO] Running org.biojavax.SimpleRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testToString +testGetNote +testSetNoteSet +testContains +testGetPropertys +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testRemoveProperty2 +testContainsProperty +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.SimpleRichAnnotationTest +[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: 0.004 s - in org.biojavax.EmptyRichAnnotationTest +[INFO] Running org.biojavax.SimpleNoteTest +testGetValue +testToString +testCompareTo +testGetRank +testGetTerm +testHashCode +testEquals +testSetRank +testSetTerm +testSetValue +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleNoteTest +[INFO] Running org.biojavax.SimpleNamespaceTest +testGetAuthority +testSetDescription +testToString +testGetAcronym +testCompareTo +testGetName +testSetAuthority +testGetDescription +testHashCode +testSetAcronym +testEquals +testGetURI +testSetURI +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNamespaceTest +[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: 0.003 s - in org.biojavax.SimpleCrossRefTest +[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.CrossReferenceResolutionExceptionTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest +[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: 0.002 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Running org.biojavax.SimpleDocRefAuthorTest +testIsConsortium +testToString +testCompareTo +testGetName +testHashCode +testEquals +testGetExtendedName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefAuthorTest +[INFO] Running org.biojavax.SimpleCommentTest +testSetComment +testToString +testCompareTo +testGetRank +testHashCode +testGetComment +testEquals +testSetRank +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleCommentTest +[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest +testGetSubject +testSetDescriptors +testToString +testGetSynonyms +testRemoveDescriptor +testCompareTo +testAddSynonym +testGetName +testGetOntology +testGetPredicate +testGetAnnotation +testGetDescription +testGetDescriptors +testHashCode +testAddDescriptor +testEquals +testGetObject +testRemoveSynonym +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ontology.SimpleComparableTripleTest +[INFO] Running org.biojavax.ontology.SimpleComparableTermTest +testSetDescription +testGetRankedCrossRefs +testToString +testGetSynonyms +testCompareTo +testAddSynonym +testGetName +testGetOntology +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation +testRemoveRankedCrossRef +testGetDescription +testSetIdentifier +testHashCode +testEquals +testAddRankedCrossRef +testRemoveSynonym +testSetObsolete +testGetObsolete +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.ontology.SimpleComparableTermTest +[INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest +testSetTripleSet +testCreateTriple +testContainsTriple +testGetTerms +testCreateVariable +testContainsTerm +testGetTermSet +testSetDescription +testToString +testGetOrCreateTerm +testCompareTo +testGetTriples +testGetName +testGetTerm +testGetOrImportTerm +testGetTripleSet +testCreateTerm +testGetDescription +testSetTermSet +testHashCode +testDeleteTerm +testEquals +testGetOps +testImportTerm +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.ontology.SimpleComparableOntologyTest +[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Running org.biojavax.ga.impl.SimplePopulationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest +[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Running org.biojavax.ga.functions.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.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.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.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.util.GAToolsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest +[INFO] Running org.biojavax.ga.util.WeightedSetTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest +[INFO] Running org.biojavax.SimpleRankedCrossRefTest +testToString +testGetCrossRef +testCompareTo +testGetRank +testHashCode +testEquals +testSetRank +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleRankedCrossRefTest +[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.molbio.RestrictionEnzymeManagerTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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.AnnotationTypeTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.AnnotationTypeTest +[INFO] Running org.biojava.bio.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 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: 0.05 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Running org.biojava.bio.dist.DistributionTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.DistributionTest +[INFO] Running org.biojava.bio.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.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: 0.004 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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.dp.EmissionStateEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dp.EmissionStateEventTest +[INFO] Running org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Running org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dp.MarkovModelEventTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.bio.program.phred.PhredToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[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.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.RNAToolsTest +[INFO] Running org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.FilterUtilsTest +[INFO] Running org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Running org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.FeatureFilterTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.FeatureFilterTest +[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[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.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[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: 0.003 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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: 0.001 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 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Running org.biojava.bio.seq.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.seq.SeqSerializationTest -[INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 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: 0.003 s - in org.biojava.bio.seq.FeatureFilterTest -[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest -idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.445 s - in org.biojava.bio.seq.io.SeqIOToolsTest -[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 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: 0.003 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 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: 0.002 s - in org.biojava.bio.seq.CircularSequenceTest -[INFO] Running org.biojava.bio.seq.FilterUtilsTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.FilterUtilsTest -[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Running org.biojava.bio.seq.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.RNAToolsTest +[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.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.impl.GappedSequenceTest -[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: 0.001 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} @@ -3185,27 +3541,36 @@ 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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Running org.biojava.bio.seq.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.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Running org.biojava.bio.dp.EmissionStateEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dp.EmissionStateEventTest -[INFO] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.dp.MarkovModelEventTest -[INFO] Running org.biojava.bio.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.dp.DPSerializationTest -[INFO] Running org.biojava.bio.AnnotationTypeTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.AnnotationTypeTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest -org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN - at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) - at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) - at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) - at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.seq.SeqSerializationTest +[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest +idb length: 79 +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.643 s - in org.biojava.bio.seq.io.SeqIOToolsTest +[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.829 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 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.project.ProjectedFeatureHolderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Running org.biojava.bio.proteomics.MassCalcTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.proteomics.MassCalcTest +[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +java.lang.NullPointerException: name is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) @@ -3227,11 +3592,9 @@ 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: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.proteomics.aaindex.AAindexTest -[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -java.lang.NullPointerException: name is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) +org.biojava.bio.seq.db.IllegalIDException: No table found with name test. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) @@ -3253,9 +3616,9 @@ 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) -org.biojava.bio.seq.db.IllegalIDException: No table found with name test. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) +java.lang.NullPointerException: table is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) @@ -3277,9 +3640,15 @@ at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -java.lang.NullPointerException: table is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 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: 0.039 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest +org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN + at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) + at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) + at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) + at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) @@ -3301,115 +3670,131 @@ 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: 0.011 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: 0.048 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Running org.biojava.bio.proteomics.MassCalcTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest -[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.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.search.SeqContentPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SeqContentPatternTest -[INFO] Running org.biojava.bio.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.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.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.SimpleSymbolListTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolListTest -[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.SimpleWobbleDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.GappedSymbolListTest -[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.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.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.IntegerAlphabetTest -[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.NameTokenizationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.NameTokenizationTest -[INFO] Running org.biojava.bio.symbol.RangeLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.RangeLocationTest -[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.PointLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest -[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest -[INFO] Running org.biojava.bio.symbol.MergeLocationTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [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.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.183 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.MergeLocationTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest +[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.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.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.532 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.IntegerAlphabetTest [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.MotifToolsTest -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.MotifToolsTest +[INFO] Running org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.036 s - in org.biojava.bio.symbol.SymbolListTest +[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.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in 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.SimpleSymbolListTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [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.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.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[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.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.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.symbol.CompoundLocationTest +[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.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.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.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.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.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Running org.biojava.bio.symbol.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 s - in org.biojava.bio.symbol.SymbolListTest -[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.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: 0.013 s - in org.biojava.bio.dist.DistributionToolsTest -[INFO] Running org.biojava.bio.dist.DistSerTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.dist.DistSerTest -[INFO] Running org.biojava.bio.MergeAnnotationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.MergeAnnotationTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Running org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest +[INFO] Running org.biojava.utils.SmallMapTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest +[INFO] Running org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 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: 0.038 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Running org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.001 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.utils.regex.RegexTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.RegexTest +[INFO] Running org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Running org.biojava.utils.walker.WalkerTest +Increasing counter: Overlaps([20,50]) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) +Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +Feature: ByClass(org.biojava.bio.seq.ComponentFeature) +Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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: 0.009 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Running org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.RegistryConfigurationTest [INFO] Running org.biojava.directory.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.directory.OBDARegistryParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.OBDARegistryParserTest -[INFO] Running org.biojava.directory.RegistryConfigurationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.RegistryConfigurationTest +[INFO] Running org.biojava.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@120f675 +Binding: urn -> org.biojava.naming.ObdaContext@12954e1 Reached urn Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@1237460 +Binding: open-bio.org -> org.biojava.naming.ObdaContext@1d8dd66 Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed @@ -3417,7 +3802,7 @@ module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } -Binding: type -> org.biojava.naming.ObdaContext@1fbc594 +Binding: type -> org.biojava.naming.ObdaContext@1f11e91 Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types @@ -3426,7 +3811,7 @@ type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } -Binding: type -> org.biojava.naming.ObdaContext@14d32bf +Binding: type -> org.biojava.naming.ObdaContext@2d192 Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this @@ -3435,7 +3820,7 @@ ontology. This is not important. The important thing is that we have unique identifiers for common types that all projects use and interact with. } -Binding: format -> org.biojava.naming.ObdaContext@14d8276 +Binding: format -> org.biojava.naming.ObdaContext@1281d19 Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this @@ -3446,7 +3831,7 @@ type of URN is purely there to identify the format of the stream, not the manner in which it should be processed. } -Binding: alphabet -> org.biojava.naming.ObdaContext@e26986 +Binding: alphabet -> org.biojava.naming.ObdaContext@ad5f2a Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as @@ -3458,14 +3843,14 @@ Alphabets do not define a mapping to or from strings, but should be used wherever the type of the content of a sequence needs to be stated. } -Binding: format -> org.biojava.naming.ObdaContext@1f2d6eb +Binding: format -> org.biojava.naming.ObdaContext@1cddaf8 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@16cd1e0 +Binding: enzyme -> org.biojava.naming.ObdaContext@1c50f52 Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from @@ -3481,29 +3866,29 @@ ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } -Binding: genbank -> org.biojava.naming.ObdaContext@a9a009 +Binding: genbank -> org.biojava.naming.ObdaContext@cc1026 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@1785903 +Binding: swissprot -> org.biojava.naming.ObdaContext@44589a 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@9349 +Binding: embl -> org.biojava.naming.ObdaContext@1e35070 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@168a7f8 +Binding: alphabet -> org.biojava.naming.ObdaContext@216f01 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@faf1f4 +Binding: rna -> org.biojava.naming.ObdaContext@901203 Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry @@ -3511,7 +3896,7 @@ are reprsented by the four letters a, g, c and u. However, this is not a formal requirement for a resource to declare this alphabet as its type. } -Binding: protein -> org.biojava.naming.ObdaContext@1811029 +Binding: protein -> org.biojava.naming.ObdaContext@721583 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, @@ -3519,7 +3904,7 @@ to be represented by characters, but this is not a formal requirement for a resource to publish an alphabet equal to this identifier. } -Binding: dna -> org.biojava.naming.ObdaContext@12b584b +Binding: dna -> org.biojava.naming.ObdaContext@1f5a6ed Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry @@ -3527,372 +3912,23 @@ 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@9aa7b2} +lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@cc9681} My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@99ca99} +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@9b3956} My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@1f0c343, format=org.biojava.naming.ObdaContext@1654f8, alphabet=org.biojava.naming.ObdaContext@bc55c4} +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@17bce6, format=org.biojava.naming.ObdaContext@a752bb, alphabet=org.biojava.naming.ObdaContext@1fc19cf} My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@958f08, genbank=org.biojava.naming.ObdaContext@1c0b742, swissprot=org.biojava.naming.ObdaContext@1bb8c16, embl=org.biojava.naming.ObdaContext@1e1ecd0} +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@3ecfef, genbank=org.biojava.naming.ObdaContext@131af02, swissprot=org.biojava.naming.ObdaContext@1b31455, embl=org.biojava.naming.ObdaContext@16528d} My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 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.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.PatternCheckerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest -[INFO] Running org.biojava.utils.regex.RegexTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.RegexTest -[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Running org.biojava.utils.automata.NfaTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.automata.NfaTest -[INFO] Running org.biojava.utils.SmallMapTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest -[INFO] Running org.biojava.utils.RepeatedCharSequenceTest -JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.RepeatedCharSequenceTest -[INFO] Running org.biojava.utils.process.ExternalProcessTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 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: 0.034 s - in org.biojava.utils.process.AllTests -[INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.utils.walker.WalkerFactoryTest -[INFO] Running org.biojava.utils.walker.WalkerTest -Increasing counter: Overlaps([20,50]) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) -Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -Feature: ByClass(org.biojava.bio.seq.ComponentFeature) -Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.utils.walker.WalkerTest -[INFO] Running org.biojavax.EmptyRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testGetNote -testSetNoteSet -testContains -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testEquals -testContainsProperty -[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.EmptyRichAnnotationTest -[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest -testGetSubject -testSetDescriptors -testToString -testGetSynonyms -testRemoveDescriptor -testCompareTo -testAddSynonym -testGetName -testGetOntology -testGetPredicate -testGetAnnotation -testGetDescription -testGetDescriptors -testHashCode -testAddDescriptor -testEquals -testGetObject -testRemoveSynonym -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ontology.SimpleComparableTripleTest -[INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest -testSetTripleSet -testCreateTriple -testContainsTriple -testGetTerms -testCreateVariable -testContainsTerm -testGetTermSet -testSetDescription -testToString -testGetOrCreateTerm -testCompareTo -testGetTriples -testGetName -testGetTerm -testGetOrImportTerm -testGetTripleSet -testCreateTerm -testGetDescription -testSetTermSet -testHashCode -testDeleteTerm -testEquals -testGetOps -testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ontology.SimpleComparableOntologyTest -[INFO] Running org.biojavax.ontology.SimpleComparableTermTest -testSetDescription -testGetRankedCrossRefs -testToString -testGetSynonyms -testCompareTo -testAddSynonym -testGetName -testGetOntology -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testRemoveRankedCrossRef -testGetDescription -testSetIdentifier -testHashCode -testEquals -testAddRankedCrossRef -testRemoveSynonym -testSetObsolete -testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableTermTest -[INFO] Running org.biojavax.SimpleRankedDocRefTest -testGetStart -testSetLocation -testToString -testGetDocumentReference -testCompareTo -testGetRank -testHashCode -testEquals -testGetEnd -testSetRank -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleRankedDocRefTest -[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.SimpleRankedCrossRefTest -testToString -testGetCrossRef -testCompareTo -testGetRank -testHashCode -testEquals -testSetRank -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedCrossRefTest -[INFO] Running org.biojavax.SimpleNamespaceTest -testGetAuthority -testSetDescription -testToString -testGetAcronym -testCompareTo -testGetName -testSetAuthority -testGetDescription -testHashCode -testSetAcronym -testEquals -testGetURI -testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleNamespaceTest -[INFO] Running org.biojavax.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: 0.001 s - in org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest -testEquals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest -[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 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: 0.004 s - in org.biojavax.bio.seq.io.Bug2255Test -[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest -Location 467: 467 -Location 340..565: 340..565 -Location <345..500: <345..500 -Location <1..888: <1..888 -Location (102.110): (102.110) -Location (23.45)..600: (23.45)..600 -Location (122.133)..(204.221): (122.133)..(204.221) -Location 123^124: 123^124 -Location 145^177: 145^177 -Location join(12..78,134..202): join(12..78,134..202) -Location complement(1..23): complement(1..23) -Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) -Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) -Location complement(34..(122.126)): complement(34..(122.126)) -Location complement((122.126)..34): complement((122.126)..34) -Location J00194:100..202: J00194:100..202 -Location (8298.8300)..10206: (8298.8300)..10206 -Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest -testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest -[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest -testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest -[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Running org.biojavax.bio.SimpleBioEntryTest -testGetNamespace -testGetNoteSet -testGetRankedDocRefs -testGetRelationships -testGetTaxon -testSetDescription -testGetAccession -testGetRankedCrossRefs -testToString -testCompareTo -testGetName -testRemoveComment -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testSetNoteSet -testRemoveRankedCrossRef -testRemoveRankedDocRef -testRemoveRelationship -testGetVersion -testGetDescription -testSetIdentifier -testGetComments -testHashCode -testEquals -testAddRankedCrossRef -testAddRankedDocRef -testAddRelationship -testSetDivision -testGetDivision -testSetTaxon -testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.SimpleBioEntryTest -[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 s - in org.biojavax.SimpleDocRefAuthorTest -[INFO] Running org.biojavax.SimpleNoteTest -testGetValue -testToString -testCompareTo -testGetRank -testGetTerm -testHashCode -testEquals -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.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] Running org.biojavax.SimpleRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testToString -testGetNote -testSetNoteSet -testContains -testGetPropertys -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testRemoveProperty2 -testContainsProperty -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRichAnnotationTest -[INFO] Running org.biojavax.SimpleDocRefTest -testGetTitle -testToString -testGetLocation -testSetCrossref -testGetCrossref -testCompareTo -testGetAuthors -testGetAuthorList -testHashCode -testSetRemark -testEquals -testGetCRC -testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleDocRefTest -[INFO] Running org.biojavax.ga.util.GAToolsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.GAToolsTest -[INFO] Running org.biojavax.ga.util.WeightedSetTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest -[INFO] Running org.biojavax.ga.impl.SimplePopulationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest -[INFO] Running org.biojavax.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.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.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.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.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.CrossReferenceResolutionExceptionTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest -[INFO] Running org.biojavax.SimpleCommentTest -testSetComment -testToString -testCompareTo -testGetRank -testHashCode -testGetComment -testEquals -testSetRank -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleCommentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.naming.ObdaInitialContextFactoryTest +[INFO] Running org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.OntologyTest +[INFO] Running org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Running org.biojava.ontology.TermImplTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TermImplTest +[INFO] Running org.biojava.ontology.TripleImplTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest [INFO] [INFO] Results: [INFO] @@ -3921,11 +3957,11 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 s - in org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.632 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: 0.006 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] [INFO] Results: [INFO] @@ -3955,7 +3991,7 @@ [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: 0.019 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3983,42 +4019,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.bio.program.sax.BlastTest -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.154 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.258 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.262 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.95 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.642 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.519 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 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: 1.127 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.194 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.145 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.232 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.441 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: 0.045 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: 0.04 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.398 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 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: 0.201 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.196 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 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: 0.05 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: 0.046 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] [INFO] Results: [INFO] @@ -4046,32 +4082,32 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.program.fastq.FastqTest -[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 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: 0.004 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 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: 0.052 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[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.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.FastqTest +[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 s - in org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.301 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: 0.009 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.scf.SCFTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] @@ -4119,7 +4155,7 @@ [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: 0.102 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.195 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -4128,20 +4164,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] -[INFO] bytecode ........................................... SUCCESS [ 0.385 s] -[INFO] core ............................................... SUCCESS [ 10.252 s] -[INFO] alignment .......................................... SUCCESS [ 10.070 s] -[INFO] biosql ............................................. SUCCESS [ 10.062 s] -[INFO] blast .............................................. SUCCESS [ 10.069 s] -[INFO] sequencing ......................................... SUCCESS [ 10.069 s] -[INFO] gui ................................................ SUCCESS [ 0.037 s] -[INFO] phylo .............................................. SUCCESS [ 10.062 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.003 s] +[INFO] bytecode ........................................... SUCCESS [ 0.720 s] +[INFO] core ............................................... SUCCESS [ 10.564 s] +[INFO] alignment .......................................... SUCCESS [ 10.164 s] +[INFO] biosql ............................................. SUCCESS [ 10.117 s] +[INFO] blast .............................................. SUCCESS [ 10.123 s] +[INFO] sequencing ......................................... SUCCESS [ 10.125 s] +[INFO] gui ................................................ SUCCESS [ 0.065 s] +[INFO] phylo .............................................. SUCCESS [ 10.113 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:01 min -[INFO] Finished at: 2025-02-16T05:59:13Z +[INFO] Total time: 01:02 min +[INFO] Finished at: 2024-01-14T23:43:39Z [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -4272,20 +4308,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.258 s] -[INFO] bytecode ........................................... SUCCESS [ 0.031 s] -[INFO] core ............................................... SUCCESS [ 0.022 s] -[INFO] alignment .......................................... SUCCESS [ 0.019 s] -[INFO] biosql ............................................. SUCCESS [ 0.018 s] -[INFO] blast .............................................. SUCCESS [ 0.018 s] -[INFO] sequencing ......................................... SUCCESS [ 0.018 s] -[INFO] gui ................................................ SUCCESS [ 0.019 s] -[INFO] phylo .............................................. SUCCESS [ 0.026 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.444 s] +[INFO] bytecode ........................................... SUCCESS [ 0.054 s] +[INFO] core ............................................... SUCCESS [ 0.042 s] +[INFO] alignment .......................................... SUCCESS [ 0.032 s] +[INFO] biosql ............................................. SUCCESS [ 0.032 s] +[INFO] blast .............................................. SUCCESS [ 0.033 s] +[INFO] sequencing ......................................... SUCCESS [ 0.033 s] +[INFO] gui ................................................ SUCCESS [ 0.034 s] +[INFO] phylo .............................................. SUCCESS [ 0.046 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.557 s -[INFO] Finished at: 2025-02-16T05:59:14Z +[INFO] Total time: 0.997 s +[INFO] Finished at: 2024-01-14T23:43:41Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/reproducible-path/biojava-live-1.9.5\+dfsg --non-explore Analysing pom.xml... @@ -4379,12 +4415,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/11849/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11849/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/118678 and its subdirectories -I: Current time: Sat Feb 15 18:00:52 -12 2025 -I: pbuilder-time-stamp: 1739685652 +I: removing directory /srv/workspace/pbuilder/11849 and its subdirectories +I: Current time: Mon Jan 15 13:45:45 +14 2024 +I: pbuilder-time-stamp: 1705275945