Diff of the two buildlogs: -- --- b1/build.log 2025-11-01 04:53:35.088294919 +0000 +++ b2/build.log 2025-11-01 05:02:05.752856370 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 31 14:50:55 -12 2025 -I: pbuilder-time-stamp: 1761965455 +I: Current time: Sat Dec 5 01:16:35 +14 2026 +I: pbuilder-time-stamp: 1796382995 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -37,53 +37,85 @@ 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/1972063/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/903365/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 Dec 4 11:16 /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/903365/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/903365/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=40 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='16fb6009bf964b57831fc26819576c43' - 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='1972063' - PS1='# ' - PS2='> ' + INVOCATION_ID=bfc637134dbf4408bad2da6db28759a8 + 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=903365 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.i83CWusS/pbuilderrc_ghGv --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.i83CWusS/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-6.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - 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.i83CWusS/pbuilderrc_JzoS --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.i83CWusS/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-6.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1972063/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/903365/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -596,7 +628,7 @@ Get: 415 http://deb.debian.org/debian forky/main amd64 maven-repo-helper all 1.12 [136 kB] Get: 416 http://deb.debian.org/debian forky/main amd64 unzip amd64 6.0-29 [173 kB] Get: 417 http://deb.debian.org/debian forky/main amd64 maven-debian-helper all 2.6.9 [104 kB] -Fetched 337 MB in 22s (15.2 MB/s) +Fetched 337 MB in 4s (90.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared: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 ... 19869 files and directories currently installed.) @@ -1965,8 +1997,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 1 02:52:45 UTC 2025. -Universal Time is now: Sat Nov 1 02:52:45 UTC 2025. +Local time is now: Fri Dec 4 11:17:49 UTC 2026. +Universal Time is now: Fri Dec 4 11:17:49 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2516,7 +2548,11 @@ 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-6_source.changes +I: user script /srv/workspace/pbuilder/903365/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/903365/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-6_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -2530,7 +2566,7 @@ bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibbiojava6-java jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' @@ -3398,15 +3434,15 @@ [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] ^ @@ -5433,1329 +5469,29 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 45.407 s] -[INFO] biojava-core ....................................... SUCCESS [ 6.864 s] -[INFO] biojava-forester ................................... SUCCESS [ 12.308 s] -[INFO] biojava-alignment .................................. SUCCESS [ 4.813 s] -[INFO] biojava-structure .................................. SUCCESS [ 24.236 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 2.441 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 6.314 s] -[INFO] biojava-genome ..................................... SUCCESS [ 3.352 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 3.395 s] -[INFO] biojava-ws ......................................... SUCCESS [ 2.968 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 3.273 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 8.313 s] -[INFO] biojava-survival ................................... SUCCESS [ 9.423 s] -[INFO] biojava-ontology ................................... SUCCESS [ 3.964 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 2.011 s] +[INFO] biojava ............................................ SUCCESS [ 17.722 s] +[INFO] biojava-core ....................................... SUCCESS [ 8.569 s] +[INFO] biojava-forester ................................... SUCCESS [ 9.084 s] +[INFO] biojava-alignment .................................. SUCCESS [ 2.939 s] +[INFO] biojava-structure .................................. SUCCESS [ 9.940 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.570 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 4.471 s] +[INFO] biojava-genome ..................................... SUCCESS [ 3.025 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 2.164 s] +[INFO] biojava-ws ......................................... SUCCESS [ 1.849 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 1.846 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 2.487 s] +[INFO] biojava-survival ................................... SUCCESS [ 2.414 s] +[INFO] biojava-ontology ................................... SUCCESS [ 2.155 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.199 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:19 min -[INFO] Finished at: 2025-10-31T14:55:34-12:00 +[INFO] Total time: 01:12 min +[INFO] Finished at: 2026-12-05T01:19:37+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' - dh_auto_test - /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test -OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. -[INFO] Scanning for projects... -[WARNING] -[WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 -[WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 -[WARNING] -[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. -[WARNING] -[WARNING] For this reason, future Maven versions might no longer support building such malformed projects. -[WARNING] -[INFO] ------------------------------------------------------------------------ -[INFO] Reactor Build Order: -[INFO] -[INFO] biojava [pom] -[INFO] biojava-core [jar] -[INFO] biojava-forester [jar] -[INFO] biojava-alignment [jar] -[INFO] biojava-structure [jar] -[INFO] biojava-jcolorbrewer [jar] -[INFO] biojava-structure-gui [jar] -[INFO] biojava-genome [jar] -[INFO] biojava-modfinder [jar] -[INFO] biojava-ws [jar] -[INFO] biojava-protein-disorder [jar] -[INFO] biojava-aa-prop [jar] -[INFO] biojava-survival [jar] -[INFO] biojava-ontology [jar] -[INFO] biojava-protein-comparison-tool [jar] -[INFO] -[INFO] ------------------------< org.biojava:biojava >------------------------- -[INFO] Building biojava 6.1.0 [1/15] -[INFO] from pom.xml -[INFO] --------------------------------[ pom ]--------------------------------- -[INFO] -[INFO] ----------------------< org.biojava:biojava-core >---------------------- -[INFO] Building biojava-core 6.1.0 [2/15] -[INFO] from biojava-core/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-core --- -[INFO] Copying 24 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-core --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-core --- -[INFO] Copying 48 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-core --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-core --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -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 -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: 0.013 s - in org.biojava.nbio.core.search.io.HspTest -[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 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. -getFileExtensions -setFile -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.799 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. -setFile -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.093 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -[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. -[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.059 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. -[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest -[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest -[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] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.162 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest -[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: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest -[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. -[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.151 s - in org.biojava.nbio.core.util.SequenceToolsTest -[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 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: 0.047 s - in org.biojava.nbio.core.util.EqualsTest -[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: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.038 s - in org.biojava.nbio.core.util.SoftHashMapTest -[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 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: 0.07 s - in org.biojava.nbio.core.util.HashcoderTest -[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. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.core.util.StringManipulationHelperTest -[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. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 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: 0.065 s - in org.biojava.nbio.core.util.CRC64ChecksumTest -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.core.util.TestUncompressInputStream -[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. -[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.195 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest -[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.494 s - in org.biojava.nbio.core.util.FlatFileCacheTest -[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.fasta.TestFASTAReader -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 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: 0.013 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest -[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest -[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: 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.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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest -[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: 0.089 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest -[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 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: 0.03 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: 0.033 s - in org.biojava.nbio.core.sequence.StrandTest -[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: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest -[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.core.sequence.RNASequenceTest -[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest -[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. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.GeneSequenceTest -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest -[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest -[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: 0.038 s - in org.biojava.nbio.core.sequence.ExonSequenceTest -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in 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] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 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: 0.004 s - in org.biojava.nbio.core.sequence.location.LocationParserTest -[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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest -[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: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.core.sequence.DNATest -[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. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.238 s - in 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. -[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.ExonComparatorTest -[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.SequenceViewTest -[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. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.137 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest -[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: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.TestSequenceEquals -[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.EditSequenceTest -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 501, Failures: 0, Errors: 0, Skipped: 15 -[INFO] -[INFO] -[INFO] --------------------< org.biojava:biojava-forester >-------------------- -[INFO] Building biojava-forester 6.1.0 [3/15] -[INFO] from biojava-forester/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-forester --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-forester --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-forester --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-forester --- -[INFO] No sources to compile -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-forester --- -[INFO] No tests to run. -[INFO] -[INFO] -------------------< org.biojava:biojava-alignment >-------------------- -[INFO] Building biojava-alignment 6.1.0 [4/15] -[INFO] from biojava-alignment/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-alignment --- -[INFO] Copying 2 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-alignment --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-alignment --- -[INFO] Copying 11 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-alignment --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-alignment --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator -[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: 0.16 s - in org.biojava.nbio.alignment.io.TestStockholmParser -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.alignment.LocalAlignmentTest -[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: 1.241 s - in org.biojava.nbio.alignment.TestDNAAlignment -[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 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: 0.041 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest -[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 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: 0.146 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest -[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: 0.078 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest -[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: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.nbio.alignment.NeedlemanWunschTest -[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest -[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading -[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest -[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 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: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 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. -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.097 s - in org.biojava.nbio.alignment.TestSubOptimalMSA -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 127, Failures: 0, Errors: 0, Skipped: 1 -[INFO] -[INFO] -[INFO] -------------------< org.biojava:biojava-structure >-------------------- -[INFO] Building biojava-structure 6.1.0 [5/15] -[INFO] from biojava-structure/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-structure --- -[INFO] Copying 3 resources from src/main/resources to target/classes -[INFO] Copying 61 resources from src/main/resources to target/classes -[INFO] The encoding used to copy filtered properties files has not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-structure --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-structure --- -[INFO] Copying 55 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-structure --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-structure --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName -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: 0.033 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: 1.195 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles -[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.09 s - in org.biojava.nbio.structure.io.TestMMCIFWriting -[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.398 s - in org.biojava.nbio.structure.io.TestShortLines -[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.648 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes -[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: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.588 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: 0.004 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. -Using PDB_DIR=/tmp as temporary file directory -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.337 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: 0.004 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: 0.006 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: 0.004 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: 0.004 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 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: 0.003 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: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.782 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: 0.005 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding -[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.924 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: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[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. -[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.053 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils -[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: 0.03 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest -[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.004 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: 0.004 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: 0.008 s - in org.biojava.nbio.structure.io.TestHardBioUnits -[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: 2, Time elapsed: 4.447 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: 0.005 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: 0.004 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: 0.004 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: 0.005 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing -[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: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.628 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. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.779 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: 0.008 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: 0.004 s - in org.biojava.nbio.structure.TestDNAAlignment -[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.49 s - in org.biojava.nbio.structure.ChemCompTest -[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.081 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: 0.005 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: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.143 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: 0.009 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: 0.008 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.464 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: 0.005 s - in org.biojava.nbio.structure.TestLoadStructureFromURL -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.322 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: 0.172 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: 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.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 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: 0.004 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools -[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.078 s - in org.biojava.nbio.structure.TestKeywords -[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. -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.087 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: 0.011 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: 0.01 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: 0.021 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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.077 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP -[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: 1.961 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: 0.005 s - in org.biojava.nbio.structure.TestChargeAdder -[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. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 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: 0.005 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier -[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: 1.998 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: 0.04 s - in org.biojava.nbio.structure.TestPdbId -[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: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.266 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: 0.004 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: 0.005 s - in org.biojava.nbio.structure.AtomPositionMapTest -[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: 0.032 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: 0.004 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: 0.022 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: 0.005 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency -[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: 0.036 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: 0.017 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: 0.004 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: 0.011 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[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: 0.034 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: 0.004 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[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: 0.022 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: 0.004 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: 0.004 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: 0.004 s - in org.biojava.nbio.structure.Test2JA5 -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup -[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.994 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: 0.012 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: 0.005 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo -[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.288 s - in org.biojava.nbio.structure.TestEntityResIndexMapping -[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. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.037 s - in org.biojava.nbio.structure.ResidueRangeTest -[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: 0.644 s - in org.biojava.nbio.structure.Test4hhb -[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 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: 0.009 s - in org.biojava.nbio.structure.ResidueNumberTest -[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. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.021 s - in org.biojava.nbio.structure.asa.TestAsaCalc -[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: 0.159 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider -[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.935 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: 0.004 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: 0.004 s - in org.biojava.nbio.structure.TestCloning -[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.003 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: 0.005 s - in org.biojava.nbio.structure.contact.TestContactCalc -[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. -Interface - - 4.0 -Interface - - 5.477225575051661 -Interface - - 5.477225575051661 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder -[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: 0.039 s - in org.biojava.nbio.structure.TestCalc -[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 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: 0.01 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: 0.004 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: 0.004 s - in org.biojava.nbio.structure.TestExperimentalTechniques -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 374, Failures: 0, Errors: 0, Skipped: 188 -[INFO] -[INFO] -[INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ -[INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] -[INFO] from biojava-jcolorbrewer/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-jcolorbrewer --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-jcolorbrewer --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-jcolorbrewer --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-jcolorbrewer --- -[INFO] No sources to compile -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-jcolorbrewer --- -[INFO] No tests to run. -[INFO] -[INFO] -----------------< org.biojava:biojava-structure-gui >------------------ -[INFO] Building biojava-structure-gui 6.1.0 [7/15] -[INFO] from biojava-structure-gui/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-structure-gui --- -[INFO] Copying 49 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-structure-gui --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-structure-gui --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-structure-gui --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-structure-gui --- -[INFO] -[INFO] ------------------------------------------------------- -[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: 0.034 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: 0.035 s - in org.biojava.nbio.structure.gui.ViewerTest -[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 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: 0.04 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: 0.043 s - in org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 1 -[INFO] -[INFO] -[INFO] ---------------------< org.biojava:biojava-genome >--------------------- -[INFO] Building biojava-genome 6.1.0 [8/15] -[INFO] from biojava-genome/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-genome --- -[INFO] Copying 1 resource from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-genome --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-genome --- -[INFO] Copying 83 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-genome --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-genome --- -[INFO] -[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: 0.058 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: 0.068 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: 0.044 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: 0.042 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: 0.039 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: 0.087 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: 0.046 s - in org.biojava.nbio.genome.io.fastq.FastqTest -[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: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 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: 0.08 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: 0.059 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: 0.092 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: 0.099 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: 0.041 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: 0.043 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: 0.037 s - in org.biojava.nbio.genome.TestGenomeMapping -[INFO] Running org.biojava.nbio.genome.FeatureListTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 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: 0.039 s - in org.biojava.nbio.genome.TestChromosomeMappingTools -[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 s - in org.biojava.nbio.genome.GeneFeatureHelperTest -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 204, Failures: 0, Errors: 0, Skipped: 2 -[INFO] -[INFO] -[INFO] -------------------< org.biojava:biojava-modfinder >-------------------- -[INFO] Building biojava-modfinder 6.1.0 [9/15] -[INFO] from biojava-modfinder/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-modfinder --- -[INFO] Copying 2 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-modfinder --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-modfinder --- -[INFO] Copying 2 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-modfinder --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-modfinder --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[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: 0.139 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: 0.126 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: 0.036 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: 0.035 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 12, Failures: 0, Errors: 0, Skipped: 8 -[INFO] -[INFO] -[INFO] -----------------------< org.biojava:biojava-ws >----------------------- -[INFO] Building biojava-ws 6.1.0 [10/15] -[INFO] from biojava-ws/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-ws --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-ws --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-ws --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-ws --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-ws --- -[INFO] -[INFO] ------------------------------------------------------- -[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: 0.036 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan -[INFO] -[INFO] Results: -[INFO] -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1 -[INFO] -[INFO] -[INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- -[INFO] Building biojava-protein-disorder 6.1.0 [11/15] -[INFO] from biojava-protein-disorder/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-protein-disorder --- -[INFO] Copying 11 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-protein-disorder --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-protein-disorder --- -[INFO] Copying 2 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-protein-disorder --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-protein-disorder --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.ronn.JronnTest -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: 2.645 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: 6.045 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest -[INFO] -[INFO] Results: -[INFO] -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 -[INFO] -[INFO] -[INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- -[INFO] Building biojava-aa-prop 6.1.0 [12/15] -[INFO] from biojava-aa-prop/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-aa-prop --- -[INFO] Copying 11 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-aa-prop --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-aa-prop --- -[INFO] Copying 7 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-aa-prop --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-aa-prop --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 s - in org.biojava.nbio.aaproperties.CookBookTest -[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: 0.052 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: 0.383 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest -[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. -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: 0.253 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest -[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest -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 -SAOV_0114,53660.5723,41370.0,41370.0,4.986 -SAOV_0094,45884.0164,57760.0,57760.0,8.5193 -SAA6008_00126,95002.026,55240.0,55740.0,5.7263 -SequenceName,A,N,MolecularWeight -SAOV_0114,0.101,0.0525,53660.5723 -SAOV_0094,0.0537,0.0767,45884.0164 -SAA6008_00126,0.0955,0.0414,95002.026 -SequenceName,A,N,MolecularWeight -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: 0.276 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: 0.042 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: 0.355 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest -[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 s - in org.biojava.nbio.aaproperties.xml.ElementTest -[INFO] -[INFO] Results: -[INFO] -[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0 -[INFO] -[INFO] -[INFO] --------------------< org.biojava:biojava-survival >-------------------- -[INFO] Building biojava-survival 6.1.0 [13/15] -[INFO] from biojava-survival/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-survival --- -[INFO] Copying 1 resource from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-survival --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-survival --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-survival --- -[INFO] No sources to compile -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-survival --- -[INFO] No tests to run. -[INFO] -[INFO] --------------------< org.biojava:biojava-ontology >-------------------- -[INFO] Building biojava-ontology 6.1.0 [14/15] -[INFO] from biojava-ontology/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-ontology --- -[INFO] Copying 3 resources from src/main/resources to target/classes -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-ontology --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-ontology --- -[INFO] Copying 6 resources from src/test/resources to target/test-classes -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-ontology --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-ontology --- -[INFO] -[INFO] ------------------------------------------------------- -[INFO] T E S T S -[INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.ontology.TestParseSBO -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: 0.092 s - in org.biojava.nbio.ontology.TestParseSBO -[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: 0.066 s - in org.biojava.nbio.ontology.TestParseOBO -[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: 0.128 s - in org.biojava.nbio.ontology.TestOboFileParsing -[INFO] -[INFO] Results: -[INFO] -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 -[INFO] -[INFO] -[INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- -[INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] -[INFO] from biojava-protein-comparison-tool/pom.xml -[INFO] --------------------------------[ jar ]--------------------------------- -[INFO] -[INFO] --- resources:3.3.1:resources (default-resources) @ biojava-protein-comparison-tool --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources -[INFO] -[INFO] --- compiler:3.13.0:compile (default-compile) @ biojava-protein-comparison-tool --- -[INFO] Nothing to compile - all classes are up to date. -[INFO] -[INFO] --- resources:3.3.1:testResources (default-testResources) @ biojava-protein-comparison-tool --- -[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources -[INFO] -[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ biojava-protein-comparison-tool --- -[INFO] No sources to compile -[INFO] -[INFO] --- surefire:2.22.3:test (default-test) @ biojava-protein-comparison-tool --- -[INFO] No tests to run. -[INFO] ------------------------------------------------------------------------ -[INFO] Reactor Summary for biojava 6.1.0: -[INFO] -[INFO] biojava ............................................ SUCCESS [ 0.002 s] -[INFO] biojava-core ....................................... SUCCESS [30:34 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.278 s] -[INFO] biojava-alignment .................................. SUCCESS [09:18 min] -[INFO] biojava-structure .................................. SUCCESS [51:14 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.013 s] -[INFO] biojava-structure-gui .............................. SUCCESS [03:03 min] -[INFO] biojava-genome ..................................... SUCCESS [09:10 min] -[INFO] biojava-modfinder .................................. SUCCESS [02:02 min] -[INFO] biojava-ws ......................................... SUCCESS [ 30.554 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [01:09 min] -[INFO] biojava-aa-prop .................................... SUCCESS [04:06 min] -[INFO] biojava-survival ................................... SUCCESS [ 0.013 s] -[INFO] biojava-ontology ................................... SUCCESS [01:31 min] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.028 s] -[INFO] ------------------------------------------------------------------------ -[INFO] BUILD SUCCESS -[INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:52 h -[INFO] Finished at: 2025-10-31T16:48:17-12:00 -[INFO] ------------------------------------------------------------------------ +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -6986,26 +5722,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.280 s] -[INFO] biojava-core ....................................... SUCCESS [ 0.035 s] -[INFO] biojava-forester ................................... SUCCESS [ 0.024 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.022 s] -[INFO] biojava-structure .................................. SUCCESS [ 0.027 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.019 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 0.023 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.022 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.019 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.020 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.019 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.031 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.024 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.020 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.020 s] +[INFO] biojava ............................................ SUCCESS [ 0.299 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.040 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.026 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.027 s] +[INFO] biojava-structure .................................. SUCCESS [ 0.035 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.025 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.029 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.026 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.034 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.024 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.025 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.024 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.031 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.021 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.022 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.793 s -[INFO] Finished at: 2025-10-31T16:48:19-12:00 +[INFO] Total time: 0.892 s +[INFO] Finished at: 2026-12-05T01:19:39+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... @@ -7225,17 +5961,17 @@ dh_link jh_installlibs jh_classpath -Duplicate specification "version|V" 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 "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 "V:s" for option "V" Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" jh_manifest jh_depends @@ -7253,8 +5989,8 @@ 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-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-6_all.deb'. dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-6_all.deb'. +dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7262,12 +5998,14 @@ 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/903365/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/903365/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/1972063 and its subdirectories -I: Current time: Fri Oct 31 16:53:34 -12 2025 -I: pbuilder-time-stamp: 1761972814 +I: removing directory /srv/workspace/pbuilder/903365 and its subdirectories +I: Current time: Sat Dec 5 01:25:04 +14 2026 +I: pbuilder-time-stamp: 1796383504