Diff of the two buildlogs:
--
--- b1/build.log 2024-11-12 08:25:45.734675910 +0000
+++ b2/build.log 2024-11-12 10:44:23.801825237 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Mon Nov 11 18:12:43 -12 2024
-I: pbuilder-time-stamp: 1731391963
+I: Current time: Tue Nov 12 22:26:26 +14 2024
+I: pbuilder-time-stamp: 1731399986
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -40,52 +40,84 @@
dpkg-source: info: applying remove_tests_needing_junitx.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/22441/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/32254/tmp/hooks/D01_modify_environment starting
+debug: Running on virt64a.
+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 Nov 12 08:26 /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/32254/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/32254/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='armhf'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
- DISTRIBUTION='unstable'
- HOME='/root'
- HOST_ARCH='armhf'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
+ BASH_VERSION='5.2.32(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=armhf
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=arm
+ HOST_ARCH=armhf
IFS='
'
- INVOCATION_ID='1758827922124c21819aa53707f09d96'
- 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='22441'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=9f5a464778614f2c8bd60a3c04e2bb37
+ LANG=C
+ LANGUAGE=it_CH:it
+ LC_ALL=C
+ MACHTYPE=arm-unknown-linux-gnueabihf
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnueabihf
+ 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=32254
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.2k6ROntW/pbuilderrc_NgnR --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k6ROntW/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-5.dsc'
- SUDO_GID='110'
- SUDO_UID='103'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://10.0.0.15:3142/'
+ 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.2k6ROntW/pbuilderrc_v4t3 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k6ROntW/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-5.dsc'
+ SUDO_GID=114
+ SUDO_UID=108
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://10.0.0.15:3142/
I: uname -a
- Linux virt32z 6.1.0-27-armmp-lpae #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/22441/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/32254/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -604,7 +636,7 @@
Get: 421 http://deb.debian.org/debian unstable/main armhf maven-repo-helper all 1.11 [142 kB]
Get: 422 http://deb.debian.org/debian unstable/main armhf unzip armhf 6.0-28 [152 kB]
Get: 423 http://deb.debian.org/debian unstable/main armhf maven-debian-helper all 2.6.5 [108 kB]
-Fetched 322 MB in 13s (24.9 MB/s)
+Fetched 322 MB in 13s (25.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libapparmor1:armhf.
(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 ... 19689 files and directories currently installed.)
@@ -1994,8 +2026,8 @@
Setting up tzdata (2024b-3) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Tue Nov 12 06:15:07 UTC 2024.
-Universal Time is now: Tue Nov 12 06:15:07 UTC 2024.
+Local time is now: Tue Nov 12 08:29:03 UTC 2024.
+Universal Time is now: Tue Nov 12 08:29:03 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libxcb-present0:armhf (1.17.0-2+b1) ...
@@ -2543,7 +2575,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-5_source.changes
+I: user script /srv/workspace/pbuilder/32254/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/32254/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-5_source.changes
dpkg-buildpackage: info: source package biojava6-live
dpkg-buildpackage: info: source version 6.1.0+dfsg-5
dpkg-buildpackage: info: source distribution unstable
@@ -3059,11 +3095,11 @@
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java:[34,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:[19,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java:[36,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java:[130,19] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[69,28] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[75,22] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[76,34] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[77,40] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
-[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java:[130,19] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/BasicDescriptiveStatistics.java:[57,20] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java:[106,31] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ControlPanel.java:[494,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal
@@ -3238,8 +3274,8 @@
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
-[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Some input files use or override a deprecated API.
-[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Recompile with -Xlint:deprecation for details.
+[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Some input files use or override a deprecated API.
+[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment ---
[INFO] Tests are skipped.
@@ -3388,15 +3424,15 @@
[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/ProfileProfileAligner.java:31: warning: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
@@ -5317,26 +5353,26 @@
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
-[INFO] biojava ............................................ SUCCESS [01:03 min]
-[INFO] biojava-core ....................................... SUCCESS [ 37.655 s]
-[INFO] biojava-forester ................................... SUCCESS [ 35.651 s]
-[INFO] biojava-alignment .................................. SUCCESS [ 11.904 s]
-[INFO] biojava-structure .................................. SUCCESS [ 38.207 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 6.415 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [ 18.228 s]
-[INFO] biojava-genome ..................................... SUCCESS [ 10.319 s]
-[INFO] biojava-modfinder .................................. SUCCESS [ 8.750 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 7.158 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 6.804 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [ 8.987 s]
-[INFO] biojava-survival ................................... SUCCESS [ 9.681 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 8.229 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 4.188 s]
+[INFO] biojava ............................................ SUCCESS [01:21 min]
+[INFO] biojava-core ....................................... SUCCESS [ 51.559 s]
+[INFO] biojava-forester ................................... SUCCESS [ 44.796 s]
+[INFO] biojava-alignment .................................. SUCCESS [ 14.812 s]
+[INFO] biojava-structure .................................. SUCCESS [ 47.381 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 7.952 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 22.354 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 13.398 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 10.763 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 8.524 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 7.907 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [ 11.947 s]
+[INFO] biojava-survival ................................... SUCCESS [ 12.717 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 10.868 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 5.423 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 04:38 min
-[INFO] Finished at: 2024-11-11T18:20:58-12:00
+[INFO] Total time: 06:00 min
+[INFO] Finished at: 2024-11-12T22:36:34+14:00
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
dh_auto_test
@@ -5400,169 +5436,169 @@
SLF4J: Failed to load class "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.SimpleGenbankProxySequenceReaderTest
+[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: 0.699 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.262 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.028 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
SLF4J: Failed to load class "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: 0.153 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.sequence.SequenceViewTest
-[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.sequence.location.LocationTest
+[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: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.453 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
-[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.577 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.278 s - in org.biojava.nbio.core.sequence.RNASequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.455 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.802 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[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] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.349 s - in org.biojava.nbio.core.sequence.RNASequenceTest
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 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: 0.022 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.core.sequence.SequenceViewTest
+[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: 0.064 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
-[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[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.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.271 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
-[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.core.sequence.EditSequenceTest
+[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: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.561 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.DNATest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
+[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: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 s - in org.biojava.nbio.core.sequence.DNATest
-[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.379 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
-[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.775 s - in org.biojava.nbio.core.sequence.TranslationTest
-[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.594 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.339 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
[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: 1.434 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
-[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.624 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.StrandTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 s - in org.biojava.nbio.core.sequence.StrandTest
+[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.338 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.262 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.612 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Running org.biojava.nbio.core.sequence.DNATest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.482 s - in org.biojava.nbio.core.sequence.DNATest
+[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.281 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.014 s - in org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.StrandTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.core.sequence.StrandTest
-[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.729 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.core.sequence.EditSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.247 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
-[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
+[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: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.12 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.356 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
[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
@@ -5570,125 +5606,125 @@
getAlignment
hashCode
equals
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.core.search.io.HspTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-createObjects
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 s - in org.biojava.nbio.core.search.io.HspTest
+[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.
-getFileExtensions
setFile
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.379 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-getFileExtensions
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.084 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+[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
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.063 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.025 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
-[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
-
- 22
- 43.22
- some text
- 2021-08-15
-
-
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.168 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.362 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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
-[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.util.TestUncompressInputStream
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.253 s - in org.biojava.nbio.core.util.FlatFileCacheTest
-[INFO] Running org.biojava.nbio.core.util.EqualsTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.237 s - in org.biojava.nbio.core.util.EqualsTest
-[INFO] Running org.biojava.nbio.core.util.HashcoderTest
-[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 s - in org.biojava.nbio.core.util.HashcoderTest
-[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.334 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.759 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
[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: 0.173 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
-[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
+[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: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.903 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
-[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
+[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.048 s - in org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.976 s - in org.biojava.nbio.core.util.XMLHelperTest
-[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
+[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.108 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Running org.biojava.nbio.core.util.HashcoderTest
+[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.406 s - in org.biojava.nbio.core.util.HashcoderTest
+[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
+
+ 22
+ 43.22
+ some text
+ 2021-08-15
+
+
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.176 s - in org.biojava.nbio.core.util.SoftHashMapTest
-[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
+[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.
-[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.1 s - in org.biojava.nbio.core.util.SequenceToolsTest
-[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.801 s - in org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Running org.biojava.nbio.core.util.EqualsTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.358 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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.util.TestUncompressInputStream
-[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.189 s - in org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.85 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 s - in org.biojava.nbio.core.util.FlatFileCacheTest
+[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.
-[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.759 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[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: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.136 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.326 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
[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: 0.442 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 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: 0.804 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.924 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: 0.708 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.989 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: 0.581 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.061 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.186 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
[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: 0.105 s - in org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.nbio.core.fasta.TestFASTAReader
[INFO]
[INFO] Results:
[INFO]
@@ -5737,90 +5773,90 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
-[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.349 s - in org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.394 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
-[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.273 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.452 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
[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: 0.26 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
-[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.418 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.258 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.574 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
[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: 5.518 s - in org.biojava.nbio.alignment.TestDNAAlignment
-[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.213 s - in org.biojava.nbio.alignment.TestDNAAlignment
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.alignment.io.TestStockholmParser
-[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.357 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.651 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
-[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.446 s - in org.biojava.nbio.alignment.SmithWatermanTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.491 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
-[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.393 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.358 s - in org.biojava.nbio.alignment.GuideTreeTest
-[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.518 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.279 s - in org.biojava.nbio.alignment.LocalAlignmentTest
-[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.967 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
+[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.383 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
-[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.437 s - in org.biojava.nbio.alignment.LocalAlignmentTest
+[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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
-[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.17 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.479 s - in org.biojava.nbio.alignment.GuideTreeTest
+[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.321 s - in org.biojava.nbio.alignment.SmithWatermanTest
-[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.349 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.27 s - in org.biojava.nbio.phylo.TestForesterWrapper
-[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.436 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
[INFO]
[INFO] Results:
[INFO]
@@ -5852,353 +5888,353 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
+[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.275 s - in org.biojava.nbio.structure.SourceCompoundTest
-[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[INFO] Running org.biojava.nbio.structure.TestCalc
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.891 s - in org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Running org.biojava.nbio.structure.PDBStatusTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.025 s - in org.biojava.nbio.structure.PDBStatusTest
+[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.402 s - in org.biojava.nbio.structure.TestCalc
-[INFO] Running org.biojava.nbio.structure.TestChargeAdder
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.027 s - in org.biojava.nbio.structure.TestChargeAdder
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.127 s - in org.biojava.nbio.structure.TestEntityHeuristics
+[INFO] Running org.biojava.nbio.structure.TestBond
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.039 s - in org.biojava.nbio.structure.TestBond
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.21 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
-[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 1.48 s - in org.biojava.nbio.structure.TestAtomCache
+[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: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 9.459 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.02 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
-[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.026 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: 0.021 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[INFO] Running org.biojava.nbio.structure.Test2JA5
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.019 s - in org.biojava.nbio.structure.Test2JA5
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.978 s - in org.biojava.nbio.structure.ChemCompTest
+[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
-[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 s - in org.biojava.nbio.structure.TestVeryLongFileName
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
-[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[INFO] Running org.biojava.nbio.structure.TestStructureImpl
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.285 s - in org.biojava.nbio.structure.TestKeywords
+[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.036 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.03 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
+[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 s - in org.biojava.nbio.structure.TestStructureImpl
-[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.287 s - in org.biojava.nbio.structure.ResidueRangeTest
+[INFO] Running org.biojava.nbio.structure.TestNucleotides
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.03 s - in org.biojava.nbio.structure.TestNucleotides
+[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.221 s - in org.biojava.nbio.structure.ResidueRangeTest
-[INFO] Running org.biojava.nbio.structure.Test4hhb
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.21 s - in org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.TestDNAAlignment
+[INFO] Running org.biojava.nbio.structure.ElementTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.structure.ElementTest
+[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.151 s - in org.biojava.nbio.structure.Test4hhb
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 s - in org.biojava.nbio.structure.TestCalc
+[INFO] Running org.biojava.nbio.structure.TestChargeAdder
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.029 s - in org.biojava.nbio.structure.TestChargeAdder
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.364 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 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: 0.029 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: 0.03 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.088 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
-[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.041 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.021 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
-[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.024 s - in org.biojava.nbio.structure.TestParsingCalcium
-[INFO] Running org.biojava.nbio.structure.ChemCompTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.072 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.312 s - in org.biojava.nbio.structure.ChemCompTest
-[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
-[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.028 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.384 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: 0.048 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.456 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.069 s - in org.biojava.nbio.structure.io.TestSiftsParsing
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.001 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[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: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.279 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
-[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 6.488 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.064 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.084 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
-[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.064 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.022 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.4 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.031 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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.197 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
-[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.596 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.034 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.029 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[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: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.085 s - in org.biojava.nbio.structure.align.client.TestStructureName
-[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 5.008 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.912 s - in org.biojava.nbio.structure.TestURLIdentifier
-[INFO] Running org.biojava.nbio.structure.TestCloning
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.023 s - in org.biojava.nbio.structure.TestCloning
-[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.61 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.04 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[INFO] Running org.biojava.nbio.structure.io.TestShortLines
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.253 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
-[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.428 s - in org.biojava.nbio.structure.io.TestShortLines
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.275 s - in org.biojava.nbio.structure.TestStructureSerialization
-[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
+Using PDB_DIR=/tmp as temporary file directory
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.474 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[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.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.269 s - in org.biojava.nbio.structure.TestEntityHeuristics
-[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.019 s - in org.biojava.nbio.structure.AtomPositionMapTest
-[INFO] Running org.biojava.nbio.structure.TestAtomIterator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.021 s - in org.biojava.nbio.structure.TestAtomIterator
-[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.TestDNAAlignment
-[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.693 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 s - in org.biojava.nbio.structure.TestVeryLongFileName
-[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: 0.228 s - in org.biojava.nbio.structure.TestPdbId
-[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.059 s - in org.biojava.nbio.structure.io.TestHardBioUnits
-[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.82 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.TestTitleParsing
+[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.473 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 8.228 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.035 s - in org.biojava.nbio.structure.io.TestHardBioUnits
+[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.04 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.039 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: 0.03 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
[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: 0.425 s - in org.biojava.nbio.structure.io.TestDBRefParsing
-[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.345 s - in org.biojava.nbio.structure.io.TestDBRefParsing
+[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: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 2.881 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
-[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
-[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.022 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.023 s - in org.biojava.nbio.structure.io.TestSiftsParsing
-[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.804 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[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: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.377 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
-[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.biojava.nbio.structure.io.TestTitleParsing
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 12.547 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[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.
-Using PDB_DIR=/tmp as temporary file directory
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.96 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.745 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.036 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.035 s - in org.biojava.nbio.structure.TestParsingCalcium
+[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.039 s - in org.biojava.nbio.structure.TestStructureCrossReferences
+[INFO] Running org.biojava.nbio.structure.Test2JA5
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.034 s - in org.biojava.nbio.structure.Test2JA5
+[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: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.962 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 4.405 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Running org.biojava.nbio.structure.TestCloning
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.035 s - in org.biojava.nbio.structure.TestCloning
+[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.03 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.957 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
-[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.021 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[INFO] Running org.biojava.nbio.structure.io.TestShortLines
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.807 s - in org.biojava.nbio.structure.TestURLIdentifier
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.993 s - in org.biojava.nbio.structure.io.TestShortLines
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 s - in org.biojava.nbio.structure.TestStructureImpl
+[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: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.219 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.021 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.132 s - in org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Running org.biojava.nbio.structure.SiteTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.266 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.023 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.nbio.structure.SiteTest
+[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.034 s - in org.biojava.nbio.structure.TestExperimentalTechniques
+[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.036 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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.122 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
+Interface
+ - 4.0
+Interface
+ - 5.477225575051661
+Interface
+ - 5.477225575051661
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.396 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
+[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: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.807 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
+[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.32 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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.707 s - in org.biojava.nbio.structure.io.TestHeaderOnly
-[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
+[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: 0.14 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: 0.02 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.065 s - in org.biojava.nbio.structure.TestStructureCrossReferences
-[INFO] Running org.biojava.nbio.structure.TestKeywords
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.033 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.176 s - in org.biojava.nbio.structure.TestKeywords
-[INFO] Running org.biojava.nbio.structure.TestNucleotides
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.026 s - in org.biojava.nbio.structure.TestNucleotides
-[INFO] Running org.biojava.nbio.structure.PDBStatusTest
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.027 s - in org.biojava.nbio.structure.PDBStatusTest
-[INFO] Running org.biojava.nbio.structure.TestAltLocs
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.032 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.029 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
+[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.436 s - in org.biojava.nbio.structure.TestAltLocs
-[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.129 s - in org.biojava.nbio.structure.align.client.TestStructureName
+[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.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.731 s - in org.biojava.nbio.structure.PdbFileFormat30Test
-[INFO] Running org.biojava.nbio.structure.TestBond
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.027 s - in org.biojava.nbio.structure.TestBond
-[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.03 s - in org.biojava.nbio.structure.TestExperimentalTechniques
-[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.396 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: 0.03 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.033 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.structure.ResidueNumberTest
+[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.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.692 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-[INFO] Running org.biojava.nbio.structure.ElementTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.nbio.structure.ElementTest
-[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.027 s - in org.biojava.nbio.structure.contact.TestContactCalc
-[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 s - in org.biojava.nbio.structure.HetatomImplTest
+[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.
-Interface
- - 4.0
-Interface
- - 5.477225575051661
-Interface
- - 5.477225575051661
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
-[INFO] Running org.biojava.nbio.structure.TestAtomCache
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.189 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
+[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: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 1.534 s - in org.biojava.nbio.structure.TestAtomCache
-[INFO] Running org.biojava.nbio.structure.SiteTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.124 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.057 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[INFO] Running org.biojava.nbio.structure.TestAltLocs
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.SiteTest
-[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 2.108 s - in org.biojava.nbio.structure.TestAltLocs
+[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.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.106 s - in org.biojava.nbio.structure.asa.TestAsaCalc
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.43 s - in org.biojava.nbio.structure.SourceCompoundTest
+[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: 2, Time elapsed: 0.6 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.032 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[INFO] Running org.biojava.nbio.structure.HetatomImplTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.923 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 s - in org.biojava.nbio.structure.HetatomImplTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.399 s - in org.biojava.nbio.structure.Test4hhb
+[INFO] Running org.biojava.nbio.structure.TestAtomIterator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.034 s - in org.biojava.nbio.structure.TestAtomIterator
+[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.033 s - in org.biojava.nbio.structure.AtomPositionMapTest
+[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: 0.289 s - in org.biojava.nbio.structure.TestPdbId
[INFO]
[INFO] Results:
[INFO]
@@ -6247,21 +6283,21 @@
[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: 0.447 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 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: 0.206 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s - in org.biojava.nbio.structure.gui.ViewerTest
[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: 0.396 s - in org.biojava.nbio.structure.gui.TestAtomInfo
-[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.166 s - in org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.217 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[INFO]
[INFO] Results:
[INFO]
@@ -6290,51 +6326,51 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.genome.FeatureListTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.nbio.genome.FeatureListTest
[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: 1.88 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.25 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Running org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.genome.TestLocation
[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: 0.185 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
-[INFO] Running org.biojava.nbio.genome.TestIssue355
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 s - in org.biojava.nbio.genome.TestIssue355
-[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.453 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.495 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.332 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.342 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.256 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.477 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.401 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.232 s - in org.biojava.nbio.genome.io.fastq.FastqTest
[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.439 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.39 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Running org.biojava.nbio.genome.TestLocation
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.928 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.593 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.606 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in org.biojava.nbio.genome.FeatureListTest
[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.26 s - in org.biojava.nbio.genome.TestGenomeMapping
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.215 s - in org.biojava.nbio.genome.TestGenomeMapping
+[INFO] Running org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 s - in org.biojava.nbio.genome.TestIssue355
[INFO]
[INFO] Results:
[INFO]
@@ -6367,16 +6403,16 @@
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.055 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.884 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: 0.252 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.736 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
-[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.217 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 2.039 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.32 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.291 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
[INFO]
[INFO] Results:
[INFO]
@@ -6406,7 +6442,7 @@
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.169 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.36 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
[INFO]
[INFO] Results:
[INFO]
@@ -6435,13 +6471,13 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.16 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
[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: 8.609 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.132 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: 6.299 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
[INFO]
[INFO] Results:
[INFO]
@@ -6470,27 +6506,31 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
+[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: 2.666 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
[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: 1.219 s - in org.biojava.nbio.aaproperties.CookBookTest
-[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.799 s - in org.biojava.nbio.aaproperties.CookBookTest
+[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.
-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: 1.365 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
-[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.972 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: 1.878 s - in org.biojava.nbio.aaproperties.xml.ElementTest
[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -6507,27 +6547,23 @@
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: 1.387 s - in org.biojava.nbio.aaproperties.CommandPromptTest
-[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: 2.119 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-[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: 1.527 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.903 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[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: 0.24 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.466 s - in org.biojava.nbio.aaproperties.xml.ElementTest
+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: 1.774 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
[INFO]
[INFO] Results:
[INFO]
@@ -6580,17 +6616,17 @@
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 s - in org.biojava.nbio.ontology.TestParseOBO
-[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 s - in org.biojava.nbio.ontology.TestParseOBO
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.777 s - in org.biojava.nbio.ontology.TestOboFileParsing
-[INFO] Running org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.69 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.062 s - in org.biojava.nbio.ontology.TestOboFileParsing
[INFO]
[INFO] Results:
[INFO]
@@ -6619,26 +6655,26 @@
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
-[INFO] biojava ............................................ SUCCESS [ 0.006 s]
-[INFO] biojava-core ....................................... SUCCESS [31:52 min]
-[INFO] biojava-forester ................................... SUCCESS [ 0.194 s]
-[INFO] biojava-alignment .................................. SUCCESS [09:27 min]
-[INFO] biojava-structure .................................. SUCCESS [54:02 min]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.192 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [03:15 min]
-[INFO] biojava-genome ..................................... SUCCESS [09:26 min]
-[INFO] biojava-modfinder .................................. SUCCESS [02:11 min]
-[INFO] biojava-ws ......................................... SUCCESS [ 31.303 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [01:16 min]
-[INFO] biojava-aa-prop .................................... SUCCESS [04:18 min]
-[INFO] biojava-survival ................................... SUCCESS [ 0.071 s]
-[INFO] biojava-ontology ................................... SUCCESS [01:34 min]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.142 s]
+[INFO] biojava ............................................ SUCCESS [ 0.007 s]
+[INFO] biojava-core ....................................... SUCCESS [32:18 min]
+[INFO] biojava-forester ................................... SUCCESS [ 0.209 s]
+[INFO] biojava-alignment .................................. SUCCESS [09:38 min]
+[INFO] biojava-structure .................................. SUCCESS [56:11 min]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.065 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [03:08 min]
+[INFO] biojava-genome ..................................... SUCCESS [09:35 min]
+[INFO] biojava-modfinder .................................. SUCCESS [02:10 min]
+[INFO] biojava-ws ......................................... SUCCESS [ 32.344 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [01:28 min]
+[INFO] biojava-aa-prop .................................... SUCCESS [04:22 min]
+[INFO] biojava-survival ................................... SUCCESS [ 0.070 s]
+[INFO] biojava-ontology ................................... SUCCESS [01:35 min]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.159 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 01:57 h
-[INFO] Finished at: 2024-11-11T20:19:00-12:00
+[INFO] Total time: 02:01 h
+[INFO] Finished at: 2024-11-13T00:37:40+14:00
[INFO] ------------------------------------------------------------------------
create-stamp debian/debhelper-build-stamp
dh_prep
@@ -6870,26 +6906,26 @@
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
-[INFO] biojava ............................................ SUCCESS [ 1.086 s]
-[INFO] biojava-core ....................................... SUCCESS [ 0.124 s]
-[INFO] biojava-forester ................................... SUCCESS [ 0.099 s]
-[INFO] biojava-alignment .................................. SUCCESS [ 0.088 s]
-[INFO] biojava-structure .................................. SUCCESS [ 0.105 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.073 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [ 0.083 s]
-[INFO] biojava-genome ..................................... SUCCESS [ 0.075 s]
-[INFO] biojava-modfinder .................................. SUCCESS [ 0.073 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 0.100 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.077 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [ 0.077 s]
-[INFO] biojava-survival ................................... SUCCESS [ 0.070 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 0.068 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.077 s]
+[INFO] biojava ............................................ SUCCESS [ 1.323 s]
+[INFO] biojava-core ....................................... SUCCESS [ 0.141 s]
+[INFO] biojava-forester ................................... SUCCESS [ 0.145 s]
+[INFO] biojava-alignment .................................. SUCCESS [ 0.111 s]
+[INFO] biojava-structure .................................. SUCCESS [ 0.116 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.080 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 0.080 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 0.084 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 0.074 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 0.071 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.073 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [ 0.073 s]
+[INFO] biojava-survival ................................... SUCCESS [ 0.077 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 0.083 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.089 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 2.931 s
-[INFO] Finished at: 2024-11-11T20:19:06-12:00
+[INFO] Total time: 3.422 s
+[INFO] Finished at: 2024-11-13T00:37:48+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...
@@ -7109,18 +7145,18 @@
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 "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
+Duplicate specification "V:s" for option "V"
+Duplicate specification "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 "version|V" for option "V"
-Duplicate specification "V:s" for option "V"
jh_manifest
jh_depends
dh_strip_nondeterminism
@@ -7146,12 +7182,14 @@
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/32254/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/32254/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/22441 and its subdirectories
-I: Current time: Mon Nov 11 20:25:40 -12 2024
-I: pbuilder-time-stamp: 1731399940
+I: removing directory /srv/workspace/pbuilder/32254 and its subdirectories
+I: Current time: Wed Nov 13 00:44:16 +14 2024
+I: pbuilder-time-stamp: 1731408256