Diff of the two buildlogs: -- --- b1/build.log 2024-12-22 18:08:41.624712313 +0000 +++ b2/build.log 2024-12-22 20:11:51.528087159 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 22 03:36:32 -12 2024 -I: pbuilder-time-stamp: 1734881792 +I: Current time: Sun Jan 25 14:31:43 +14 2026 +I: pbuilder-time-stamp: 1769301103 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -40,52 +40,84 @@ dpkg-source: info: applying remove_tests_needing_junitx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3938538/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2406781/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 25 00:31 /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/2406781/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2406781/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='32185445ed2b4ffe9cb44de86abd8b41' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3938538' - PS1='# ' - PS2='> ' + INVOCATION_ID=c6298211227f42608af0cd4bd95b5eaa + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2406781 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.hTSKtzB9/pbuilderrc_U7ap --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hTSKtzB9/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-5.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.hTSKtzB9/pbuilderrc_EAyu --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hTSKtzB9/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3938538/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2406781/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -605,7 +637,7 @@ Get: 422 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 423 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 424 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.6 [108 kB] -Fetched 341 MB in 14s (24.2 MB/s) +Fetched 341 MB in 6s (59.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (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 ... 19967 files and directories currently installed.) @@ -1999,8 +2031,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 22 15:38:28 UTC 2024. -Universal Time is now: Sun Dec 22 15:38:28 UTC 2024. +Local time is now: Sun Jan 25 00:33:14 UTC 2026. +Universal Time is now: Sun Jan 25 00:33:14 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2548,7 +2580,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2406781/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2406781/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -3430,15 +3466,15 @@ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ -[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile -[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and -[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ +[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile +[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and +[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ @@ -5465,26 +5501,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [03:45 min] -[INFO] biojava-core ....................................... SUCCESS [ 54.423 s] -[INFO] biojava-forester ................................... SUCCESS [ 37.268 s] -[INFO] biojava-alignment .................................. SUCCESS [ 18.025 s] -[INFO] biojava-structure .................................. SUCCESS [01:03 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 11.627 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 25.848 s] -[INFO] biojava-genome ..................................... SUCCESS [ 22.727 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 20.136 s] -[INFO] biojava-ws ......................................... SUCCESS [ 15.670 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 13.481 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 19.506 s] -[INFO] biojava-survival ................................... SUCCESS [ 18.727 s] -[INFO] biojava-ontology ................................... SUCCESS [ 17.260 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 10.029 s] +[INFO] biojava ............................................ SUCCESS [ 17.676 s] +[INFO] biojava-core ....................................... SUCCESS [ 15.764 s] +[INFO] biojava-forester ................................... SUCCESS [ 11.881 s] +[INFO] biojava-alignment .................................. SUCCESS [ 3.356 s] +[INFO] biojava-structure .................................. SUCCESS [ 10.919 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.719 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 4.586 s] +[INFO] biojava-genome ..................................... SUCCESS [ 2.913 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 2.322 s] +[INFO] biojava-ws ......................................... SUCCESS [ 1.823 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 1.690 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 2.455 s] +[INFO] biojava-survival ................................... SUCCESS [ 2.488 s] +[INFO] biojava-ontology ................................... SUCCESS [ 2.373 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.192 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 09:35 min -[INFO] Finished at: 2024-12-22T03:50:33-12:00 +[INFO] Total time: 01:24 min +[INFO] Finished at: 2026-01-25T14:35:26+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dh_auto_test @@ -5548,295 +5584,295 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.search.io.HspTest +[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -getAlignment -hashCode -equals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.core.search.io.HspTest -[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.core.util.StringManipulationHelperTest +[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.core.util.CRC64ChecksumTest +[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.296 s - in org.biojava.nbio.core.search.io.SearchIOTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -createObjects +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest +[INFO] Running org.biojava.nbio.core.util.XMLHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -getFileExtensions -setFile -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.9 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -getFileExtensions +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.195 s - in org.biojava.nbio.core.util.XMLHelperTest +[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -setFile -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.062 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest + + 22 + 43.22 + some text +
2021-08-15
+
+ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.284 s - in org.biojava.nbio.core.alignment.SimpleProfileTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest +[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.61 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.SoftHashMapTest +[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.451 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.core.util.FlatFileCacheTest +[INFO] Running org.biojava.nbio.core.util.EqualsTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.core.util.EqualsTest +[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.122 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest +[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.255 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest +[INFO] Running org.biojava.nbio.core.util.HashcoderTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.util.HashcoderTest +[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.151 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest +[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.315 s - in org.biojava.nbio.core.util.SequenceToolsTest +[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.631 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.12 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.StrandTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.nbio.core.sequence.StrandTest +[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.27 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest -[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.314 s - in org.biojava.nbio.core.util.SequenceToolsTest -[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest - - 22 - 43.22 - some text -
2021-08-15
-
- +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.655 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest -[INFO] Running org.biojava.nbio.core.util.EqualsTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.509 s - in org.biojava.nbio.core.util.EqualsTest -[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.GeneSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.529 s - in org.biojava.nbio.core.util.SoftHashMapTest -[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.888 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest -[INFO] Running org.biojava.nbio.core.util.HashcoderTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.476 s - in org.biojava.nbio.core.util.HashcoderTest -[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.232 s - in org.biojava.nbio.core.util.StringManipulationHelperTest -[INFO] Running org.biojava.nbio.core.util.XMLHelperTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.327 s - in org.biojava.nbio.core.util.XMLHelperTest -[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.626 s - in org.biojava.nbio.core.util.CRC64ChecksumTest -[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.util.TestUncompressInputStream -[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.064 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest -[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.616 s - in org.biojava.nbio.core.util.FlatFileCacheTest -[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.core.fasta.TestFASTAReader -[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.514 s - in org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.514 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet -[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.425 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.084 s - in org.biojava.nbio.core.sequence.io.ABITracerTest -[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.528 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.core.sequence.ExonComparatorTest +[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.547 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.core.sequence.RNASequenceTest +[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.303 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest -[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest -[INFO] Running org.biojava.nbio.core.sequence.StrandTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 s - in org.biojava.nbio.core.sequence.StrandTest -[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.776 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.528 s - in org.biojava.nbio.core.sequence.RNASequenceTest -[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest -[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.core.sequence.location.LocationParserTest +[INFO] Running org.biojava.nbio.core.sequence.TranslationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.755 s - in org.biojava.nbio.core.sequence.GeneSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 s - in org.biojava.nbio.core.sequence.TranslationTest +[INFO] Running org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.348 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.core.sequence.DNATest +[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.427 s - in org.biojava.nbio.core.sequence.ExonSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.sequence.ExonSequenceTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.core.sequence.location.LocationTest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.039 s - in org.biojava.nbio.core.sequence.location.LocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.159 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest -[INFO] Running org.biojava.nbio.core.sequence.DNATest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.545 s - in org.biojava.nbio.core.sequence.DNATest -[INFO] Running org.biojava.nbio.core.sequence.TranslationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest +[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.396 s - in org.biojava.nbio.core.sequence.TranslationTest +[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.072 s - in org.biojava.nbio.core.alignment.SimpleProfileTest +[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.041 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.551 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 s - in org.biojava.nbio.core.sequence.ExonComparatorTest -[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.fasta.TestFASTAReader +[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.nbio.core.sequence.SequenceViewTest -[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.039 s - in org.biojava.nbio.core.search.io.SearchIOTest +[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +createObjects SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.53 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +getFileExtensions +setFile +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.613 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +getFileExtensions SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.324 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest -[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals +setFile +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.021 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +[INFO] Running org.biojava.nbio.core.search.io.HspTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.sequence.TestSequenceEquals -[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest +getAlignment +hashCode +equals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.search.io.HspTest +[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [INFO] [INFO] Results: [INFO] @@ -5885,90 +5921,90 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Running org.biojava.nbio.alignment.GuideTreeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 s - in org.biojava.nbio.phylo.TestForesterWrapper -[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 s - in org.biojava.nbio.alignment.GuideTreeTest +[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.475 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator -[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.688 s - in org.biojava.nbio.alignment.io.TestStockholmParser -[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.133 s - in org.biojava.nbio.alignment.TestSubOptimalMSA +[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.578 s - in org.biojava.nbio.alignment.LocalAlignmentTest -[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.152 s - in org.biojava.nbio.alignment.TestDNAAlignment -[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.684 s - in org.biojava.nbio.alignment.SmithWatermanTest -[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.592 s - in org.biojava.nbio.alignment.SimpleProfilePairTest -[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.342 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest [INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.575 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest -[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.252 s - in org.biojava.nbio.alignment.NeedlemanWunschTest -[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.627 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest -[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest -[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.205 s - in org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading -[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.6 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest -[INFO] Running org.biojava.nbio.alignment.GuideTreeTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.188 s - in org.biojava.nbio.alignment.GuideTreeTest -[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.863 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest -[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.972 s - in org.biojava.nbio.alignment.TestSubOptimalMSA +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [INFO] [INFO] Results: [INFO] @@ -6004,349 +6040,349 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.419 s - in org.biojava.nbio.structure.TestVeryLongFileName -[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 9.315 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles -[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Running org.biojava.nbio.structure.TestCloning +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestCloning +[INFO] Running org.biojava.nbio.structure.TestStructureImpl SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.687 s - in org.biojava.nbio.structure.io.TestMMCIFWriting -[INFO] Running org.biojava.nbio.structure.io.TestShortLines +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestStructureImpl +[INFO] Running org.biojava.nbio.structure.TestAltLocs SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.888 s - in org.biojava.nbio.structure.io.TestShortLines -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.346 s - in org.biojava.nbio.structure.TestAltLocs +[INFO] Running org.biojava.nbio.structure.HetatomImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.98 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.HetatomImplTest +[INFO] Running org.biojava.nbio.structure.TestAtomCache SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 7.708 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.043 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.37 s - in org.biojava.nbio.structure.TestAtomCache +[INFO] Running org.biojava.nbio.structure.TestAtomIterator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestAtomIterator +[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestLoadStructureFromURL +[INFO] Running org.biojava.nbio.structure.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest +[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -Using PDB_DIR=/tmp as temporary file directory -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.011 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.035 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.043 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.033 s - in org.biojava.nbio.structure.io.TestParseOnAsymId -[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.034 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.28 s - in org.biojava.nbio.structure.io.TestDBRefParsing -[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestTitleParsing -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.021 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[INFO] Running org.biojava.nbio.structure.TestURLIdentifier SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 8.036 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.044 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.137 s - in org.biojava.nbio.structure.TestURLIdentifier +[INFO] Running org.biojava.nbio.structure.ChemCompTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.896 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.03 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.243 s - in org.biojava.nbio.structure.ChemCompTest +[INFO] Running org.biojava.nbio.structure.TestStructureSerialization SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.391 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.03 s - in org.biojava.nbio.structure.TestStructureSerialization [INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestParseOnAsymId +[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing [INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.043 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestHardBioUnits -[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.743 s - in org.biojava.nbio.structure.io.TestHeaderOnly -[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestSiftsParsing -[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.039 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands -[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing -[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.737 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 4.94 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles -[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.91 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestTitleParsing +[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestHardBioUnits +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.288 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest -[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[INFO] Running org.biojava.nbio.structure.TestDNAAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.TestDNAAlignment -[INFO] Running org.biojava.nbio.structure.ChemCompTest +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.482 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.096 s - in org.biojava.nbio.structure.ChemCompTest -[INFO] Running org.biojava.nbio.structure.TestURLIdentifier +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.536 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.347 s - in org.biojava.nbio.structure.TestURLIdentifier -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.022 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster +Using PDB_DIR=/tmp as temporary file directory +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.575 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.259 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster -[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser -[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.797 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing +[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.597 s - in org.biojava.nbio.structure.PdbFileFormat30Test -[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestLoadStructureFromURL -[INFO] Running org.biojava.nbio.structure.TestStructureSerialization +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.492 s - in org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.TestSiftsParsing +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands +[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.756 s - in org.biojava.nbio.structure.TestStructureSerialization -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.127 s - in org.biojava.nbio.structure.io.TestMMCIFWriting +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.02 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 6.369 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.022 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools -[INFO] Running org.biojava.nbio.structure.TestKeywords +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.758 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.288 s - in org.biojava.nbio.structure.TestKeywords -[INFO] Running org.biojava.nbio.structure.TestAltLocs +[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.153 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[INFO] Running org.biojava.nbio.structure.io.TestShortLines SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.592 s - in org.biojava.nbio.structure.TestAltLocs -[INFO] Running org.biojava.nbio.structure.TestBond -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestBond -[INFO] Running org.biojava.nbio.structure.TestAtomIterator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestAtomIterator -[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.016 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions -[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.508 s - in org.biojava.nbio.structure.io.TestShortLines +[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 8.05 s - in org.biojava.nbio.structure.io.TestHeaderOnly [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.41 s - in org.biojava.nbio.structure.geometry.TestSuperPosition -[INFO] Running org.biojava.nbio.structure.TestChargeAdder -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.TestChargeAdder -[INFO] Running org.biojava.nbio.structure.SiteTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.058 s - in org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.059 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions +[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.SiteTest -[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier -[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.163 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.792 s - in org.biojava.nbio.structure.TestEntityHeuristics -[INFO] Running org.biojava.nbio.structure.TestPdbId -[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] -[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] -[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.structure.TestPdbId -[INFO] Running org.biojava.nbio.structure.TestAtomCache +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.059 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[INFO] Running org.biojava.nbio.structure.TestNucleotides +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestNucleotides +[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.028 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[INFO] Running org.biojava.nbio.structure.TestChargeAdder +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestChargeAdder +[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.018 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser +[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.853 s - in org.biojava.nbio.structure.TestAtomCache -[INFO] Running org.biojava.nbio.structure.TestParsingCalcium -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestParsingCalcium -[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.009 s - in org.biojava.nbio.structure.AtomPositionMapTest +Interface + - 4.0 +Interface + - 5.477225575051661 +Interface + - 5.477225575051661 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder +[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.021 s - in org.biojava.nbio.structure.contact.TestContactCalc [INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.081 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest [INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.035 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment -[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.144 s - in org.biojava.nbio.structure.align.client.TestStructureName -[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment [INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.123 s - in org.biojava.nbio.structure.align.util.AtomCacheTest +[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.053 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.structure.align.util.RotationAxisTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.008 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion -[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.032 s - in org.biojava.nbio.structure.TestStructureCrossReferences -[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.042 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[INFO] Running org.biojava.nbio.structure.Test2JA5 -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.095 s - in org.biojava.nbio.structure.Test2JA5 -[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency +[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.712 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup -[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.027 s - in org.biojava.nbio.structure.align.client.TestStructureName +[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 13.74 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering -[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.043 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo -[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.835 s - in org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor +[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 2.721 s - in org.biojava.nbio.structure.TestEntityResIndexMapping -[INFO] Running org.biojava.nbio.structure.ResidueRangeTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.102 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster +[INFO] Running org.biojava.nbio.structure.SiteTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.249 s - in org.biojava.nbio.structure.ResidueRangeTest -[INFO] Running org.biojava.nbio.structure.Test4hhb +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.nbio.structure.SiteTest +[INFO] Running org.biojava.nbio.structure.SourceCompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.787 s - in org.biojava.nbio.structure.Test4hhb -[INFO] Running org.biojava.nbio.structure.HetatomImplTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.095 s - in org.biojava.nbio.structure.SourceCompoundTest +[INFO] Running org.biojava.nbio.structure.TestPdbId +[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] +[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] +[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.structure.TestPdbId +[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 s - in org.biojava.nbio.structure.HetatomImplTest -[INFO] Running org.biojava.nbio.structure.ResidueNumberTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.structure.ResidueNumberTest -[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.808 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering +[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo +[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.171 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup [INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.023 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider -[INFO] Running org.biojava.nbio.structure.SourceCompoundTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.216 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider +[INFO] Running org.biojava.nbio.structure.TestCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.508 s - in org.biojava.nbio.structure.SourceCompoundTest -[INFO] Running org.biojava.nbio.structure.PDBStatusTest -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.03 s - in org.biojava.nbio.structure.PDBStatusTest -[INFO] Running org.biojava.nbio.structure.TestCloning -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.04 s - in org.biojava.nbio.structure.TestCloning +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.structure.TestCalc +[INFO] Running org.biojava.nbio.structure.Test4hhb +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.871 s - in org.biojava.nbio.structure.Test4hhb +[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.133 s - in org.biojava.nbio.structure.TestEntityHeuristics +[INFO] Running org.biojava.nbio.structure.TestParsingCalcium +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium +[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters -[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.059 s - in org.biojava.nbio.structure.contact.TestContactCalc -[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters +[INFO] Running org.biojava.nbio.structure.TestKeywords SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -Interface - - 4.0 -Interface - - 5.477225575051661 -Interface - - 5.477225575051661 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder -[INFO] Running org.biojava.nbio.structure.TestCalc +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.04 s - in org.biojava.nbio.structure.TestKeywords +[INFO] Running org.biojava.nbio.structure.TestBond +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBond +[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.6 s - in org.biojava.nbio.structure.TestCalc -[INFO] Running org.biojava.nbio.structure.TestStructureImpl +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.427 s - in org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Running org.biojava.nbio.structure.TestDNAAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestDNAAlignment +[INFO] Running org.biojava.nbio.structure.ResidueRangeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 s - in org.biojava.nbio.structure.TestStructureImpl -[INFO] Running org.biojava.nbio.structure.ElementTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.ElementTest -[INFO] Running org.biojava.nbio.structure.TestNucleotides -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestNucleotides -[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.031 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.052 s - in org.biojava.nbio.structure.ResidueRangeTest +[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[INFO] Running org.biojava.nbio.structure.PDBStatusTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest +[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.006 s - in org.biojava.nbio.structure.AtomPositionMapTest +[INFO] Running org.biojava.nbio.structure.Test2JA5 +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.Test2JA5 +[INFO] Running org.biojava.nbio.structure.ResidueNumberTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.nbio.structure.ResidueNumberTest [INFO] [INFO] Results: [INFO] @@ -6396,20 +6432,20 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.293 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator -[INFO] Running org.biojava.nbio.structure.gui.ViewerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.biojava.nbio.structure.gui.ViewerTest +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.058 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator +[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 s - in org.biojava.nbio.structure.gui.StructureViewerTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 s - in org.biojava.nbio.structure.gui.TestAtomInfo -[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.453 s - in org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.structure.gui.TestAtomInfo [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Running org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] [INFO] Results: [INFO] @@ -6438,51 +6474,51 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.545 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.365 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.304 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.603 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.424 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.6 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.524 s - in org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Running org.biojava.nbio.genome.TestIssue355 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.genome.TestIssue355 +[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.471 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest -[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.906 s - in org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.352 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.TestIssue355 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 s - in org.biojava.nbio.genome.TestIssue355 -[INFO] Running org.biojava.nbio.genome.TestLocation -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 s - in org.biojava.nbio.genome.TestLocation -[INFO] Running org.biojava.nbio.genome.TestGenomeMapping -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.287 s - in org.biojava.nbio.genome.TestGenomeMapping +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.531 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.FeatureListTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 s - in org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.genome.FeatureListTest [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.genome.TestChromosomeMappingTools -[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.genome.TestChromosomeMappingTools +[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.667 s - in org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.713 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Running org.biojava.nbio.genome.TestGenomeMapping +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestGenomeMapping +[INFO] Running org.biojava.nbio.genome.TestLocation +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.genome.TestLocation [INFO] [INFO] Results: [INFO] @@ -6511,20 +6547,20 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- +[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.05 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.049 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest [INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.681 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.189 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.668 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest -[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.058 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] [INFO] Results: [INFO] @@ -6554,7 +6590,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.177 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.056 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] @@ -6587,9 +6623,9 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.14 s - in org.biojava.nbio.ronn.JronnTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.275 s - in org.biojava.nbio.ronn.JronnTest [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.11 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.051 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] [INFO] Results: [INFO] @@ -6618,32 +6654,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.aaproperties.CookBookTest +[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.258 s - in org.biojava.nbio.aaproperties.CookBookTest +SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint +NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 +SequenceName,A,N,MolecularWeight +NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 +SequenceName,A,N,MolecularWeight +NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.808 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.684 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.37 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest -[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.445 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint -NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 -SequenceName,A,N,MolecularWeight -NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 -SequenceName,A,N,MolecularWeight -NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.093 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.396 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.428 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest +[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -6660,22 +6706,12 @@ SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.952 s - in org.biojava.nbio.aaproperties.CommandPromptTest -[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest -[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.852 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest -[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.4 s - in org.biojava.nbio.aaproperties.CommandPromptTest +[INFO] Running org.biojava.nbio.aaproperties.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.653 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 s - in org.biojava.nbio.aaproperties.CookBookTest [INFO] [INFO] Results: [INFO] @@ -6728,17 +6764,17 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.92 s - in org.biojava.nbio.ontology.TestParseSBO -[INFO] Running org.biojava.nbio.ontology.TestParseOBO +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.ontology.TestParseSBO +[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.nbio.ontology.TestParseOBO -[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 s - in org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Running org.biojava.nbio.ontology.TestParseOBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.351 s - in org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.ontology.TestParseOBO [INFO] [INFO] Results: [INFO] @@ -6767,26 +6803,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.021 s] -[INFO] biojava-core ....................................... SUCCESS [34:50 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.233 s] -[INFO] biojava-alignment .................................. SUCCESS [09:58 min] -[INFO] biojava-structure .................................. SUCCESS [56:08 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.120 s] -[INFO] biojava-structure-gui .............................. SUCCESS [03:16 min] -[INFO] biojava-genome ..................................... SUCCESS [09:44 min] -[INFO] biojava-modfinder .................................. SUCCESS [02:06 min] -[INFO] biojava-ws ......................................... SUCCESS [ 31.605 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [01:15 min] -[INFO] biojava-aa-prop .................................... SUCCESS [04:37 min] -[INFO] biojava-survival ................................... SUCCESS [ 0.223 s] -[INFO] biojava-ontology ................................... SUCCESS [01:38 min] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.299 s] +[INFO] biojava ............................................ SUCCESS [ 0.002 s] +[INFO] biojava-core ....................................... SUCCESS [30:29 min] +[INFO] biojava-forester ................................... SUCCESS [ 0.051 s] +[INFO] biojava-alignment .................................. SUCCESS [09:12 min] +[INFO] biojava-structure .................................. SUCCESS [52:17 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.020 s] +[INFO] biojava-structure-gui .............................. SUCCESS [03:04 min] +[INFO] biojava-genome ..................................... SUCCESS [09:13 min] +[INFO] biojava-modfinder .................................. SUCCESS [02:02 min] +[INFO] biojava-ws ......................................... SUCCESS [ 30.654 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [01:11 min] +[INFO] biojava-aa-prop .................................... SUCCESS [04:08 min] +[INFO] biojava-survival ................................... SUCCESS [ 0.029 s] +[INFO] biojava-ontology ................................... SUCCESS [01:32 min] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.167 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:04 h -[INFO] Finished at: 2024-12-22T05:54:58-12:00 +[INFO] Total time: 01:53 h +[INFO] Finished at: 2026-01-25T16:29:11+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -7018,26 +7054,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 2.649 s] -[INFO] biojava-core ....................................... SUCCESS [ 0.526 s] -[INFO] biojava-forester ................................... SUCCESS [ 0.284 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.379 s] -[INFO] biojava-structure .................................. SUCCESS [ 0.319 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.220 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 0.221 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.319 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.244 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.228 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.237 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.256 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.203 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.213 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.239 s] +[INFO] biojava ............................................ SUCCESS [ 0.349 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.040 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.028 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.027 s] +[INFO] biojava-structure .................................. SUCCESS [ 0.034 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.023 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.028 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.025 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.023 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.024 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.024 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.032 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.023 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.021 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.377 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 8.485 s -[INFO] Finished at: 2024-12-22T05:55:18-12:00 +[INFO] Total time: 1.308 s +[INFO] Finished at: 2026-01-25T16:29:13+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore Analysing pom.xml... @@ -7257,18 +7293,18 @@ dh_link jh_installlibs jh_classpath -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" Duplicate specification "V:s" for option "V" Duplicate specification "V:s" for option "V" Duplicate specification "version|V" for option "V" +Duplicate specification "version|V" for option "V" +Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" +Duplicate specification "V:s" for option "V" jh_manifest jh_depends dh_strip_nondeterminism @@ -7285,8 +7321,8 @@ dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-5_all.deb'. dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-5_all.deb'. +dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7294,12 +7330,14 @@ 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/2406781/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2406781/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/3938538 and its subdirectories -I: Current time: Sun Dec 22 06:08:40 -12 2024 -I: pbuilder-time-stamp: 1734890920 +I: removing directory /srv/workspace/pbuilder/2406781 and its subdirectories +I: Current time: Sun Jan 25 16:34:50 +14 2026 +I: pbuilder-time-stamp: 1769308490