[Debian-med-packaging] Bug#768710: biojava3-live: FTBFS in jessie: dh_install: libbiojava3-java-doc missing files (doc/biojava/*), aborting
Andreas Tille
andreas at an3as.eu
Thu Nov 13 06:52:30 UTC 2014
Hi folks,
is anybody up for fixing this one? As I said in my previous mail I'm
busy with real life and release team will probably simply kick the
package out from testing if this bug is not closed and no unblock
request will be filed. Everybody in the team can work on this!
Thanks
Andreas.
On Sun, Nov 09, 2014 at 08:07:04AM +0100, Lucas Nussbaum wrote:
> Source: biojava3-live
> Version: 3.1.0+dfsg-1
> Severity: serious
> Tags: jessie sid
> User: debian-qa at lists.debian.org
> Usertags: qa-ftbfs-20141108 qa-ftbfs
> Justification: FTBFS in jessie on amd64
>
> Hi,
>
> During a rebuild of all packages in jessie (in a jessie chroot, not a
> sid chroot), your package failed to build on amd64.
>
> Relevant part (hopefully):
> > make[1]: Entering directory '/«BUILDDIR»/biojava3-live-3.1.0+dfsg'
> > cd biojava3-forester && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-forester/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-forester/classes
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-forester/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 332 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-forester/classes
> > [javac] Note: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java uses or overrides a deprecated API.
> > [javac] Note: Recompile with -Xlint:deprecation for details.
> > [javac] Note: Some input files use unchecked or unsafe operations.
> > [javac] Note: Recompile with -Xlint:unchecked for details.
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-forester/src/main/resources does not exist.
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-forester.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 12 seconds
> > cd biojava3-core && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-core/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-core/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-core/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 140 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-core/classes
> > [copy] Copying 1 file to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-core/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-core.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 5 seconds
> > cd biojava3-phylo && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-phylo/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-phylo/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-phylo/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 10 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-phylo/classes
> > [copy] Copying 1 file to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-phylo/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-phylo.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > cd biojava3-alignment && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-alignment/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-alignment/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-alignment/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 66 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-alignment/classes
> > [copy] Copying 20 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-alignment/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-alignment.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 4 seconds
> > cd biojava3-aa-prop && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-aa-prop/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-aa-prop/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 31 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/xml/package-info.class
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/convertor/package-info.class
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/package-info.class
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/package-info.class
> > [copy] Copying 10 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-aa-prop/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-aa-prop.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 3 seconds
> > cd biojava3-genome && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-genome/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-genome/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-genome/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 27 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-genome/classes
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-genome/src/main/resources does not exist.
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-genome.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 3 seconds
> > cd biojava3-sequencing && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-sequencing/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-sequencing/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 19 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes/org/biojava3/sequencing/io/fastq/package-info.class
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-sequencing/src/main/resources does not exist.
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-sequencing.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > cd biojava3-structure && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 342 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
> > [javac] Note: Some input files use or override a deprecated API.
> > [javac] Note: Recompile with -Xlint:deprecation for details.
> > [javac] Note: Some input files use unchecked or unsafe operations.
> > [javac] Note: Recompile with -Xlint:unchecked for details.
> > [copy] Copying 63 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-structure.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 10 seconds
> > cd biojava3-structure-gui && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure-gui/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 109 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure-gui/classes
> > [javac] Note: Some input files use unchecked or unsafe operations.
> > [javac] Note: Recompile with -Xlint:unchecked for details.
> > [copy] Copying 48 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-structure-gui/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-structure-gui.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 6 seconds
> > cd biojava3-modfinder && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-modfinder/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-modfinder/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-modfinder/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 21 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-modfinder/classes
> > [copy] Copying 1 file to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-modfinder/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-modfinder.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > cd biojava3-protein-disorder && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-protein-disorder/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-protein-disorder/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-protein-disorder/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 13 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-protein-disorder/classes
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/data/sequence/package-info.class
> > [javac] Creating empty /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/ronn/package-info.class
> > [copy] Copying 10 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-protein-disorder/classes
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-protein-disorder.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > cd biojava3-ws && ant jar
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-ws/build.xml
> >
> > compile:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-ws/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-ws/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 20 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/build/biojava3-ws/classes
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-ws/src/main/resources does not exist.
> >
> > jar:
> > [jar] Building jar: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/dist/biojava3-ws.jar
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > # make doc
> > rm -rf biojavadoc
> > mkdir biojavadoc
> > cp -r biojava3-*/src biojavadoc/
> > sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
> > cd biojavadoc && ant javadocs
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/build.xml
> >
> > javadocs:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/javadoc
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/doc/biojava
> > [javadoc] Generating Javadoc
> > [javadoc] Javadoc execution
> > [javadoc] Loading source files for package org.biojava.bio.structure...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.ce...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.client...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.events...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.fatcat...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.fatcat.calc...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.gui...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.aligpanel...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.autosuggest...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.gui.jmol...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.helper...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.model...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.pairwise...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.seq...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.util...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.webstart...
> > [javadoc] Loading source files for package org.biojava.bio.structure.align.xml...
> > [javadoc] Loading source files for package org.biojava.bio.structure.asa...
> > [javadoc] Loading source files for package org.biojava.bio.structure.cath...
> > [javadoc] Loading source files for package org.biojava.bio.structure.domain...
> > [javadoc] Loading source files for package org.biojava.bio.structure.domain.pdp...
> > [javadoc] Loading source files for package org.biojava.bio.structure.gui...
> > [javadoc] Loading source files for package org.biojava.bio.structure.gui.events...
> > [javadoc] Loading source files for package org.biojava.bio.structure.gui.util...
> > [javadoc] Loading source files for package org.biojava.bio.structure.gui.util.color...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif.chem...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io.mmcif.model...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io.sifts...
> > [javadoc] Loading source files for package org.biojava.bio.structure.io.util...
> > [javadoc] Loading source files for package org.biojava.bio.structure.jama...
> > [javadoc] Loading source files for package org.biojava.bio.structure.math...
> > [javadoc] Loading source files for package org.biojava.bio.structure.quaternary...
> > [javadoc] Loading source files for package org.biojava.bio.structure.quaternary.io...
> > [javadoc] Loading source files for package org.biojava.bio.structure.rcsb...
> > [javadoc] Loading source files for package org.biojava.bio.structure.scop...
> > [javadoc] Loading source files for package org.biojava.bio.structure.scop.server...
> > [javadoc] Loading source files for package org.biojava.bio.structure.secstruc...
> > [javadoc] Loading source files for package org.biojava.bio.structure.server...
> > [javadoc] Loading source files for package org.biojava3.aaproperties...
> > [javadoc] Loading source files for package org.biojava3.aaproperties.profeat...
> > [javadoc] Loading source files for package org.biojava3.aaproperties.profeat.convertor...
> > [javadoc] Loading source files for package org.biojava3.aaproperties.xml...
> > [javadoc] Loading source files for package org.biojava3.alignment...
> > [javadoc] Loading source files for package org.biojava3.alignment.aaindex...
> > [javadoc] Loading source files for package org.biojava3.alignment.io...
> > [javadoc] Loading source files for package org.biojava3.alignment.routines...
> > [javadoc] Loading source files for package org.biojava3.alignment.template...
> > [javadoc] Loading source files for package org.biojava3.core.exceptions...
> > [javadoc] Loading source files for package org.biojava3.core.sequence...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.compound...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.edits...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.features...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.io...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.io.template...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.io.util...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.loader...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.location...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.location.template...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.storage...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.template...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.transcription...
> > [javadoc] Loading source files for package org.biojava3.core.sequence.views...
> > [javadoc] Loading source files for package org.biojava3.core.util...
> > [javadoc] Loading source files for package org.biojava3.data.sequence...
> > [javadoc] Loading source files for package org.biojava3.genome...
> > [javadoc] Loading source files for package org.biojava3.genome.homology...
> > [javadoc] Loading source files for package org.biojava3.genome.parsers.cytoband...
> > [javadoc] Loading source files for package org.biojava3.genome.parsers.geneid...
> > [javadoc] Loading source files for package org.biojava3.genome.parsers.genename...
> > [javadoc] Loading source files for package org.biojava3.genome.parsers.gff...
> > [javadoc] Loading source files for package org.biojava3.genome.query...
> > [javadoc] Loading source files for package org.biojava3.genome.uniprot...
> > [javadoc] Loading source files for package org.biojava3.genome.util...
> > [javadoc] Loading source files for package org.biojava3.ontology...
> > [javadoc] Loading source files for package org.biojava3.ontology.io...
> > [javadoc] Loading source files for package org.biojava3.ontology.obo...
> > [javadoc] Loading source files for package org.biojava3.ontology.utils...
> > [javadoc] Loading source files for package org.biojava3.phylo...
> > [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
> > [javadoc] * @author Kalle N???slund (docs)
> > [javadoc] ^
> > [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
> > [javadoc] * @author Kalle N???slund (docs)
> > [javadoc] ^
> > [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
> > [javadoc] * @author Kalle N???slund (docs)
> > [javadoc] ^
> > [javadoc] Loading source files for package org.biojava3.protmod...
> > [javadoc] Loading source files for package org.biojava3.protmod.io...
> > [javadoc] Loading source files for package org.biojava3.protmod.structure...
> > [javadoc] Loading source files for package org.biojava3.ronn...
> > [javadoc] Loading source files for package org.biojava3.sequencing.io.fastq...
> > [javadoc] Loading source files for package org.biojava3.structure...
> > [javadoc] Loading source files for package org.biojava3.structure.gui...
> > [javadoc] Loading source files for package org.biojava3.structure.validation...
> > [javadoc] Loading source files for package org.biojava3.survival.cox...
> > [javadoc] Loading source files for package org.biojava3.survival.cox.comparators...
> > [javadoc] Loading source files for package org.biojava3.survival.cox.matrix...
> > [javadoc] Loading source files for package org.biojava3.survival.cox.stats...
> > [javadoc] Loading source files for package org.biojava3.survival.data...
> > [javadoc] Loading source files for package org.biojava3.survival.kaplanmeier.figure...
> > [javadoc] Loading source files for package org.biojava3.survival.kaplanmeier.metadata...
> > [javadoc] Loading source files for package org.biojava3.ws.alignment...
> > [javadoc] Loading source files for package org.biojava3.ws.alignment.qblast...
> > [javadoc] Loading source files for package org.biojava3.ws.hmmer...
> > [javadoc] Loading source files for package org.forester.analysis...
> > [javadoc] Loading source files for package org.forester.application...
> > [javadoc] Loading source files for package org.forester.archaeopteryx...
> > [javadoc] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
> > [javadoc] Loading source files for package org.forester.archaeopteryx.tools...
> > [javadoc] Loading source files for package org.forester.archaeopteryx.webservices...
> > [javadoc] Loading source files for package org.forester.datastructures...
> > [javadoc] Loading source files for package org.forester.development...
> > [javadoc] Loading source files for package org.forester.evoinference...
> > [javadoc] Loading source files for package org.forester.evoinference.distance...
> > [javadoc] Loading source files for package org.forester.evoinference.matrix.character...
> > [javadoc] Loading source files for package org.forester.evoinference.matrix.distance...
> > [javadoc] Loading source files for package org.forester.evoinference.parsimony...
> > [javadoc] Loading source files for package org.forester.evoinference.tools...
> > [javadoc] Loading source files for package org.forester.go...
> > [javadoc] Loading source files for package org.forester.go.etc...
> > [javadoc] Loading source files for package org.forester.io.parsers...
> > [javadoc] Loading source files for package org.forester.io.parsers.nexus...
> > [javadoc] Loading source files for package org.forester.io.parsers.nhx...
> > [javadoc] Loading source files for package org.forester.io.parsers.phyloxml...
> > [javadoc] Loading source files for package org.forester.io.parsers.phyloxml.data...
> > [javadoc] Loading source files for package org.forester.io.parsers.tol...
> > [javadoc] Loading source files for package org.forester.io.parsers.util...
> > [javadoc] Loading source files for package org.forester.io.writers...
> > [javadoc] Loading source files for package org.forester.msa...
> > [javadoc] Loading source files for package org.forester.pccx...
> > [javadoc] Loading source files for package org.forester.phylogeny...
> > [javadoc] Loading source files for package org.forester.phylogeny.data...
> > [javadoc] Loading source files for package org.forester.phylogeny.factories...
> > [javadoc] Loading source files for package org.forester.phylogeny.iterators...
> > [javadoc] Loading source files for package org.forester.protein...
> > [javadoc] Loading source files for package org.forester.sdi...
> > [javadoc] Loading source files for package org.forester.sequence...
> > [javadoc] Loading source files for package org.forester.species...
> > [javadoc] Loading source files for package org.forester.surfacing...
> > [javadoc] Loading source files for package org.forester.test...
> > [javadoc] Loading source files for package org.forester.test.examples...
> > [javadoc] Loading source files for package org.forester.tools...
> > [javadoc] Loading source files for package org.forester.util...
> > [javadoc] Loading source files for package org.forester.ws.hmmer...
> > [javadoc] Loading source files for package org.forester.ws.seqdb...
> > [javadoc] Loading source files for package org.forester.ws.uniprot...
> > [javadoc] Loading source files for package org.forester.ws.wabi...
> > [javadoc] 3 errors
> >
> > BUILD SUCCESSFUL
> > Total time: 4 seconds
> > rm -rf biojavadoc
> > make[1]: Leaving directory '/«BUILDDIR»/biojava3-live-3.1.0+dfsg'
> > jh_build
> > debian/rules override_dh_auto_test
> > make[1]: Entering directory '/«BUILDDIR»/biojava3-live-3.1.0+dfsg'
> > cd biojava3-core && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-core/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-core/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-core/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 17 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-core/classes
> > [copy] Copying 8 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-core/classes
> > [copy] Copying 140 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-core/classes
> >
> > test:
> > [junit] Running org.biojava3.core.sequence.DNATest
> > [junit] Testsuite: org.biojava3.core.sequence.DNATest
> > [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 sec
> > [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 sec
> > [junit]
> > [junit] Testcase: sequenceEquality took 0.013 sec
> > [junit] Testcase: subSequence took 0.004 sec
> > [junit] Testcase: singleCompoundSequence took 0.002 sec
> > [junit] Testcase: translateToRna took 0.037 sec
> > [junit] Testcase: kmerNonOverlap took 0.002 sec
> > [junit] Testcase: twoBit took 0 sec
> > [junit] Testcase: composition took 0.001 sec
> > [junit] Testcase: fourBit took 0.004 sec
> > [junit] Testcase: complement took 0.001 sec
> > [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.001 sec
> > [junit] Testcase: at took 0 sec
> > [junit] Testcase: gc took 0 sec
> > [junit] Testcase: basesEqual took 0 sec
> > [junit] Testcase: bogusSequence took 0 sec
> > [junit] Testcase: kmerOverlap took 0 sec
> > [junit] Testcase: reverseComplement took 0.001 sec
> > [junit] Testcase: reverse took 0.001 sec
> > [junit] Testcase: respectCase took 0 sec
> > [junit] Testcase: basesEquivalent took 0 sec
> > [junit] Testcase: badTwoBit took 0 sec
> > [junit] Running org.biojava3.core.sequence.EditSequenceTest
> > [junit] Testsuite: org.biojava3.core.sequence.EditSequenceTest
> > [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
> > [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
> > [junit]
> > [junit] Testcase: badSubstitute took 0.015 sec
> > [junit] Testcase: delete took 0.004 sec
> > [junit] Testcase: insert took 0 sec
> > [junit] Testcase: substitute took 0 sec
> > [junit] Running org.biojava3.core.sequence.JoiningSequenceReaderTest
> > [junit] Testsuite: org.biojava3.core.sequence.JoiningSequenceReaderTest
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec
> > [junit]
> > [junit] Testcase: empty took 0.014 sec
> > [junit] Testcase: canScan took 0 sec
> > [junit] Running org.biojava3.core.sequence.MultipleSequenceAlignmentTest
> > [junit] Testsuite: org.biojava3.core.sequence.MultipleSequenceAlignmentTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec
> > [junit]
> > [junit] Testcase: testGetCompoundsAt took 0.017 sec
> > [junit] Running org.biojava3.core.sequence.SequenceViewTest
> > [junit] Testsuite: org.biojava3.core.sequence.SequenceViewTest
> > [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec
> > [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec
> > [junit]
> > [junit] Testcase: testLastIndexOf took 0.016 sec
> > [junit] Testcase: testGetCompoundAt took 0 sec
> > [junit] Testcase: testInverse took 0 sec
> > [junit] Running org.biojava3.core.sequence.TranslationTest
> > [junit] Testsuite: org.biojava3.core.sequence.TranslationTest
> > [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec
> > [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec
> > [junit]
> > [junit] Testcase: translateN took 0.045 sec
> > [junit] Testcase: basicTranslation took 0.002 sec
> > [junit] Testcase: translateBrca2 took 0.356 sec
> > [junit] Testcase: getUniversal took 0.001 sec
> > [junit] Testcase: translateInternalStops took 0.016 sec
> > [junit] Testcase: multiFrameTranslation took 0.004 sec
> > [junit] Testcase: translateInitMet took 0 sec
> > [junit] Testcase: lowerCases took 0 sec
> > [junit] Testcase: testHashCollision took 0.006 sec
> > [junit] Testcase: translateBrca2ExonOne took 0 sec
> > [junit] Running org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest
> > [junit] Testsuite: org.biojava3.core.sequence.compound.AmbiguityDNACompoundTest
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec
> > [junit]
> > [junit] Testcase: testAmbiguity took 0.002 sec
> > [junit] Testcase: testBasicAmbiguity took 0 sec
> > [junit] Running org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreatorTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec
> > [junit]
> > [junit] Testcase: testConstructor took 0.012 sec
> > [junit] Running org.biojava3.core.sequence.io.FastaReaderTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.FastaReaderTest
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 sec
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 sec
> > [junit] ------------- Standard Output ---------------
> > [junit] process
> > [junit] process(int)
> > [junit] ------------- ---------------- ---------------
> > [junit]
> > [junit] Testcase: testProcess took 0.174 sec
> > [junit] Testcase: processIntTest took 0.042 sec
> > [junit] Running org.biojava3.core.sequence.io.FastaWriterTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.FastaWriterTest
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
> > [junit]
> > [junit] Testcase: writeBasicFasta took 0.02 sec
> > [junit] Testcase: writeFastaEqualToLineLength took 0 sec
> > [junit] Running org.biojava3.core.sequence.io.GenbankCookbookTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.GenbankCookbookTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec
> > [junit] ------------- Standard Output ---------------
> > [junit] AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
> > [junit] MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS
> > [junit] {NM_000266=AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA}
> > [junit] {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS}
> > [junit] ------------- ---------------- ---------------
> > [junit]
> > [junit] Testcase: testProcess took 0.154 sec
> > [junit] Running org.biojava3.core.sequence.io.GenbankReaderTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.GenbankReaderTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec
> > [junit] ------------- Standard Output ---------------
> > [junit] process protein
> > [junit] process DNA
> > [junit] ------------- ---------------- ---------------
> > [junit]
> > [junit] Testcase: testProcess took 0.112 sec
> > [junit] Running org.biojava3.core.sequence.io.GenbankWriterTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.GenbankWriterTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 sec
> > [junit] ------------- Standard Output ---------------
> > [junit] DIVISION:UNK linear
> > [junit] ------------- ---------------- ---------------
> > [junit]
> > [junit] Testcase: testProcess took 0.157 sec
> > [junit] Running org.biojava3.core.sequence.io.GenericFastaHeaderParserTest
> > [junit] Testsuite: org.biojava3.core.sequence.io.GenericFastaHeaderParserTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec
> > [junit] ------------- Standard Output ---------------
> > [junit] parseHeader
> > [junit] ------------- ---------------- ---------------
> > [junit]
> > [junit] Testcase: testParseHeader took 0.013 sec
> > [junit] Running org.biojava3.core.sequence.location.LocationParserTest
> > [junit] Testsuite: org.biojava3.core.sequence.location.LocationParserTest
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec
> > [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec
> > [junit]
> > [junit] Testcase: moreComplex took 0.009 sec
> > [junit] Testcase: basicLocationTests took 0.002 sec
> > [junit] Running org.biojava3.core.sequence.location.LocationTest
> > [junit] Testsuite: org.biojava3.core.sequence.location.LocationTest
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec
> > [junit]
> > [junit] Testcase: testWithStrandSwitch took 0.02 sec
> > [junit] Testcase: modulateCircular took 0.001 sec
> > [junit] Testcase: testStrandFlip took 0 sec
> > [junit] Testcase: testBasicCircularLocation took 0.001 sec
> > [junit] Testcase: badLocations took 0.001 sec
> > [junit] Testcase: completePasses took 0 sec
> > [junit] Testcase: testSubLocations took 0.002 sec
> >
> > BUILD SUCCESSFUL
> > Total time: 10 seconds
> > cd biojava3-alignment && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-alignment/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-alignment/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-alignment/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 24 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-alignment/classes
> > [copy] Copying 9 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-alignment/classes
> > [copy] Copying 66 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-alignment/classes
> >
> > test:
> > [junit] Running org.biojava3.alignment.FractionalIdentityScorerTest
> > [junit] Testsuite: org.biojava3.alignment.FractionalIdentityScorerTest
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec
> > [junit]
> > [junit] Testcase: testGetQuery took 0.026 sec
> > [junit] Testcase: testGetScore took 0.019 sec
> > [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec
> > [junit] Testcase: testGetMinScore took 0 sec
> > [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec
> > [junit] Testcase: testGetTarget took 0 sec
> > [junit] Testcase: testGetMaxScore took 0.001 sec
> > [junit] Running org.biojava3.alignment.FractionalSimilarityScorerTest
> > [junit] Testsuite: org.biojava3.alignment.FractionalSimilarityScorerTest
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec
> > [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec
> > [junit]
> > [junit] Testcase: testGetQuery took 0.026 sec
> > [junit] Testcase: testGetScore took 0.019 sec
> > [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec
> > [junit] Testcase: testGetMinScore took 0.001 sec
> > [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec
> > [junit] Testcase: testGetTarget took 0 sec
> > [junit] Testcase: testGetMaxScore took 0.002 sec
> > [junit] Running org.biojava3.alignment.GuideTreeTest
> > [junit] Testsuite: org.biojava3.alignment.GuideTreeTest
> > [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec
> > [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec
> > [junit]
> > [junit] Testcase: testGuideTree took 0.078 sec
> > [junit] Testcase: testToString took 0.003 sec
> > [junit] Testcase: testGetScoreMatrix took 0.004 sec
> > [junit] Testcase: testGetRoot took 0.018 sec
> > [junit] Testcase: testGetSequences took 0.003 sec
> > [junit] Testcase: testGetDistanceMatrix took 0.003 sec
> > [junit] Testcase: testGetAllPairsScores took 0.004 sec
> > [junit] Testcase: testIterator took 0.003 sec
> > [junit] Running org.biojava3.alignment.LocalAlignmentTest
> > [junit] Testsuite: org.biojava3.alignment.LocalAlignmentTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec
> > [junit]
> > [junit] Testcase: shouldAllowZeroLengthMatches took 0.066 sec
> > [junit] Running org.biojava3.alignment.NeedlemanWunschTest
> > [junit] Testsuite: org.biojava3.alignment.NeedlemanWunschTest
> > [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec
> > [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec
> > [junit]
> > [junit] Testcase: testGetSubstitutionMatrix took 0.025 sec
> > [junit] Testcase: testGetGapPenalty took 0 sec
> > [junit] Testcase: testGetComputationTime took 0.019 sec
> > [junit] Testcase: should_align_middle_anchor took 0.029 sec
> > [junit] Testcase: testGetQuery took 0.001 sec
> > [junit] Testcase: testGetScore took 0.001 sec
> > [junit] Testcase: testNeedlemanWunsch took 0.001 sec
> > [junit] Testcase: should_align_all_anchored took 0.001 sec
> > [junit] Testcase: testGetScoreMatrix took 0.001 sec
> > [junit] Testcase: testGetPair took 0.001 sec
> > [junit] Testcase: should_align_multiple_anchors took 0.001 sec
> > [junit] Testcase: testAnchoredDNAAlignment took 0.003 sec
> > [junit] Testcase: testGetProfile took 0.001 sec
> > [junit] Testcase: testGetMinScore took 0 sec
> > [junit] Testcase: should_align_ending_anchor took 0.001 sec
> > [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec
> > [junit] Testcase: testGetScoreMatrixAsString took 0.015 sec
> > [junit] Testcase: should_align_starting_anchor took 0.001 sec
> > [junit] Testcase: anchors_should_not_change_score took 0 sec
> > [junit] Testcase: testGetTarget took 0 sec
> > [junit] Testcase: testGetMaxScore took 0.001 sec
> > [junit] Running org.biojava3.alignment.SimpleAlignedSequenceTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleAlignedSequenceTest
> > [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 sec
> > [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 sec
> > [junit]
> > [junit] Testcase: testGetIndexOf took 0.012 sec
> > [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec
> > [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec
> > [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec
> > [junit] Testcase: testGetNumGaps took 0 sec
> > [junit] Testcase: testGetStart took 0 sec
> > [junit] Testcase: testGetSequenceIndexAt took 0 sec
> > [junit] Testcase: testGetAccession took 0 sec
> > [junit] Testcase: testToString took 0.001 sec
> > [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec
> > [junit] Testcase: testCountCompounds took 0.001 sec
> > [junit] Testcase: testGetAlignmentIndexAt took 0 sec
> > [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec
> > [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetSubSequence took 0 sec
> > [junit] SKIPPED
> > [junit] Testcase: testGetAsList took 0.001 sec
> > [junit] Testcase: testGetOriginalSequence took 0 sec
> > [junit] Testcase: testGetCompoundAt took 0.001 sec
> > [junit] Testcase: testGetLength took 0 sec
> > [junit] Testcase: testIsCircular took 0 sec
> > [junit] Testcase: testGetEnd took 0 sec
> > [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec
> > [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec
> > [junit] Testcase: testGetOverlapCount took 0 sec
> > [junit] Testcase: testGetCompoundSet took 0 sec
> > [junit] Testcase: testGetLocationInAlignment took 0.001 sec
> > [junit] Testcase: testIterator took 0.001 sec
> > [junit] Testcase: testGetSequenceAsString took 0 sec
> > [junit] Testcase: testGetLastIndexOf took 0 sec
> > [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 sec
> > [junit] Running org.biojava3.alignment.SimpleGapPenaltyTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleGapPenaltyTest
> > [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec
> > [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec
> > [junit]
> > [junit] Testcase: testOpenPenalty took 0.003 sec
> > [junit] Testcase: testType took 0 sec
> > [junit] Testcase: testExtensionPenalty took 0 sec
> > [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec
> > [junit] Testcase: testSimpleGapPenalty took 0 sec
> > [junit] Running org.biojava3.alignment.SimpleProfilePairTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleProfilePairTest
> > [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec
> > [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec
> > [junit]
> > [junit] Testcase: testGetQuery took 0.049 sec
> > [junit] Testcase: testGetTarget took 0.001 sec
> > [junit] Testcase: testSimpleProfilePair took 0.004 sec
> > [junit] Running org.biojava3.alignment.SimpleProfileProfileAlignerTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleProfileProfileAlignerTest
> > [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 sec
> > [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 sec
> > [junit]
> > [junit] Testcase: testGetSubstitutionMatrix took 0.048 sec
> > [junit] Testcase: testGetGapPenalty took 0.005 sec
> > [junit] Testcase: testGetComputationTime took 0.006 sec
> > [junit] Testcase: testGetQuery took 0.004 sec
> > [junit] Testcase: testGetScore took 0.006 sec
> > [junit] Testcase: testGetScoreMatrix took 0.004 sec
> > [junit] Testcase: testGetPair took 0.005 sec
> > [junit] Testcase: testGetProfile took 0.003 sec
> > [junit] Testcase: testGetMinScore took 0.002 sec
> > [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec
> > [junit] Testcase: testGetScoreMatrixAsString took 0.028 sec
> > [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec
> > [junit] Testcase: testSimpleProfileProfileAligner took 0.003 sec
> > [junit] Testcase: testGetTarget took 0.002 sec
> > [junit] Testcase: testGetMaxScore took 0.002 sec
> > [junit] Running org.biojava3.alignment.SimpleProfileTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleProfileTest
> > [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.149 sec
> > [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.149 sec
> > [junit]
> > [junit] Testcase: testGetIndexOf took 0.032 sec
> > [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0 sec
> > [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec
> > [junit] Testcase: testToStringInt took 0.011 sec
> > [junit] Testcase: testToString took 0.001 sec
> > [junit] Testcase: testToStringFormatted took 0.037 sec
> > [junit] Testcase: testSimpleProfile took 0 sec
> > [junit] Testcase: testGetSize took 0 sec
> > [junit] Testcase: testGetAlignedSequenceS took 0 sec
> > [junit] Testcase: testGetAlignedSequences took 0 sec
> > [junit] Testcase: testGetOriginalSequences took 0 sec
> > [junit] Testcase: testGetSubProfile took 0 sec
> > [junit] SKIPPED
> > [junit] Testcase: testGetCompoundAtSInt took 0.001 sec
> > [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec
> > [junit] Testcase: testGetIndicesAt took 0.002 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0 sec
> > [junit] Testcase: testGetAlignedSequencesIntArray took 0.002 sec
> > [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec
> > [junit] Testcase: testGetLength took 0 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec
> > [junit] Testcase: testIsCircular took 0 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec
> > [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec
> > [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec
> > [junit] Testcase: testGetCompoundSet took 0 sec
> > [junit] Testcase: testGetCompoundsAt took 0 sec
> > [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec
> > [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec
> > [junit] Testcase: testIterator took 0.001 sec
> > [junit] Testcase: testGetLastIndexOf took 0.002 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec
> > [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec
> > [junit] Testcase: testGetIndicesAtOutOfBounds took 0 sec
> > [junit] Running org.biojava3.alignment.SimpleSequencePairTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleSequencePairTest
> > [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec
> > [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec
> > [junit]
> > [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.031 sec
> > [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetQuery took 0 sec
> > [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec
> > [junit] Testcase: testGetIndexInTargetAt took 0 sec
> > [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec
> > [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec
> > [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec
> > [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.001 sec
> > [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec
> > [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec
> > [junit] Testcase: testGetNumIdenticals took 0 sec
> > [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec
> > [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec
> > [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetCompoundInTargetAt took 0 sec
> > [junit] Testcase: testGetIndexInQueryAt took 0.001 sec
> > [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec
> > [junit] Testcase: testGetTarget took 0 sec
> > [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec
> > [junit] Testcase: testGetNumSimilars took 0.002 sec
> > [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec
> > [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec
> > [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec
> > [junit] Running org.biojava3.alignment.SimpleSubstitutionMatrixTest
> > [junit] Testsuite: org.biojava3.alignment.SimpleSubstitutionMatrixTest
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.07 sec
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.07 sec
> > [junit]
> > [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.006 sec
> > [junit] Testcase: testSetDescription took 0.013 sec
> > [junit] Testcase: testToString took 0.008 sec
> > [junit] Testcase: testCaseEquivalence took 0.001 sec
> > [junit] Testcase: testSimpleSubstitutionMatrix took 0.008 sec
> > [junit] Testcase: testSimpleSubstitutionMatrixWrong took 0 sec
> > [junit] SKIPPED
> > [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.002 sec
> > [junit] Testcase: testSetName took 0.007 sec
> > [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.003 sec
> > [junit] Running org.biojava3.alignment.SmithWatermanTest
> > [junit] Testsuite: org.biojava3.alignment.SmithWatermanTest
> > [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec
> > [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec
> > [junit]
> > [junit] Testcase: testGetSubstitutionMatrix took 0.026 sec
> > [junit] Testcase: testGetGapPenalty took 0 sec
> > [junit] Testcase: testGetComputationTime took 0.018 sec
> > [junit] Testcase: testGetQuery took 0.001 sec
> > [junit] Testcase: testGetScore took 0.002 sec
> > [junit] Testcase: testGetScoreMatrix took 0.002 sec
> > [junit] Testcase: testGetPair took 0.004 sec
> > [junit] Testcase: testSmithWaterman took 0.001 sec
> > [junit] Testcase: testGetProfile took 0.002 sec
> > [junit] Testcase: testGetMinScore took 0.001 sec
> > [junit] Testcase: testIsStoringScoreMatrix took 0 sec
> > [junit] Testcase: testGetScoreMatrixAsString took 0.036 sec
> > [junit] Testcase: testSetStoringScoreMatrix took 0 sec
> > [junit] Testcase: testGetTarget took 0 sec
> > [junit] Testcase: testGetMaxScore took 0.001 sec
> > [junit] Running org.biojava3.alignment.routines.AlignerHelperTest
> > [junit] Testsuite: org.biojava3.alignment.routines.AlignerHelperTest
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec
> > [junit]
> > [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.003 sec
> > [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.002 sec
> > [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec
> > [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec
> > [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec
> > [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec
> > [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec
> > [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec
> > [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec
> > [junit] Running org.biojava3.alignment.routines.GuanUberbacherTest
> > [junit] Testsuite: org.biojava3.alignment.routines.GuanUberbacherTest
> > [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec
> > [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec
> > [junit]
> > [junit] Testcase: testGetComputationTime took 0.043 sec
> > [junit] Testcase: testGuanUberbacher took 0 sec
> > [junit] Testcase: testGetScore took 0.001 sec
> > [junit] Testcase: testGetPair took 0.004 sec
> > [junit] Testcase: testGetProfile took 0.001 sec
> > [junit] Testcase: testGetMinScore took 0.001 sec
> > [junit] Testcase: should_align_shorter_target took 0.025 sec
> > [junit] Testcase: should_align_multiple_cuts took 0 sec
> > [junit] Testcase: testGetMaxScore took 0 sec
> > [junit] Testcase: should_align_shorter_query took 0.001 sec
> >
> > BUILD SUCCESSFUL
> > Total time: 9 seconds
> > cd biojava3-aa-prop && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-aa-prop/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-aa-prop/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-aa-prop/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 9 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-aa-prop/classes
> > [javac] Note: Some input files use or override a deprecated API.
> > [javac] Note: Recompile with -Xlint:deprecation for details.
> > [copy] Copying 12 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-aa-prop/classes
> > [copy] Copying 31 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-aa-prop/classes
> >
> > test:
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > # Skip, missing dependency
> > #cd biojava3-genome && ant test
> > cd biojava3-phylo && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-phylo/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-phylo/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-phylo/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 1 source file to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-phylo/classes
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-phylo/src/test/resources does not exist.
> > [copy] Copying 10 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-phylo/classes
> >
> > test:
> > [junit] Running org.biojava3.phylo.AppTest
> > [junit] Testsuite: org.biojava3.phylo.AppTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
> > [junit]
> > [junit] Testcase: testApp took 0.001 sec
> >
> > BUILD SUCCESSFUL
> > Total time: 2 seconds
> > # Native errors may cause issue on NFS...; skipping
> > #cd biojava3-sequencing && ant test
> > #cd biojava3-modfinder && ant test
> > cd biojava3-protein-disorder && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-protein-disorder/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-protein-disorder/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-protein-disorder/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 3 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-protein-disorder/classes
> > [copy] Copying 1 file to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-protein-disorder/classes
> > [copy] Copying 14 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-protein-disorder/classes
> >
> > test:
> > [junit] Running org.biojava3.ronn.JronnTest
> > [junit] Testsuite: org.biojava3.ronn.JronnTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.032 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.032 sec
> > [junit]
> > [junit] Testcase: verifyRanges took 2.017 sec
> > [junit] Running org.biojava3.ronn.NonstandardProteinCompoundTest
> > [junit] Testsuite: org.biojava3.ronn.NonstandardProteinCompoundTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.02 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.02 sec
> > [junit]
> > [junit] Testcase: test took 6.002 sec
> >
> > BUILD SUCCESSFUL
> > Total time: 10 seconds
> > # Requires remote access and tmp directory write access
> > #cd biojava3-structure && ant test
> > cd biojava3-structure-gui && ant test
> > Buildfile: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml
> >
> > compile-test:
> > [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-structure-gui/classes
> > [javac] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml:81: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > [javac] Compiling 6 source files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-structure-gui/classes
> > [copy] Warning: /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/src/test/resources does not exist.
> > [copy] Copying 115 files to /«BUILDDIR»/biojava3-live-3.1.0+dfsg/buildtest/biojava3-structure-gui/classes
> >
> > test:
> > [junit] Running org.biojava.structure.gui.JmolViewerImplTest
> > [junit] Testsuite: org.biojava.structure.gui.JmolViewerImplTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec
> > [junit]
> > [junit] Testcase: testMe took 0.001 sec
> > [junit] Running org.biojava.structure.gui.RenderStyleTest
> > [junit] Testsuite: org.biojava.structure.gui.RenderStyleTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
> > [junit]
> > [junit] Testcase: testSomeMethod took 0.001 sec
> > [junit] Running org.biojava.structure.gui.StructureViewerTest
> > [junit] Testsuite: org.biojava.structure.gui.StructureViewerTest
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec
> > [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec
> > [junit]
> > [junit] Testcase: testGetColor took 0.003 sec
> > [junit] Testcase: testSetStructure took 0 sec
> > [junit] Testcase: testClear took 0 sec
> > [junit] Testcase: testGetSelection took 0.003 sec
> > [junit] Testcase: testRepaint took 0 sec
> > [junit] Testcase: testSetSelection took 0 sec
> > [junit] Testcase: testSetZoom took 0 sec
> > [junit] Testcase: testSetColor took 0.001 sec
> > [junit] Testcase: testSetStyle took 0 sec
> > [junit] Running org.biojava.structure.gui.ViewerTest
> > [junit] Testsuite: org.biojava.structure.gui.ViewerTest
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
> > [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
> > [junit]
> > [junit] Testcase: testStructureLoad took 0.001 sec
> >
> > BUILD SUCCESSFUL
> > Total time: 3 seconds
> > #No test in biojava-ws available
> > #cd biojava3-ws && ant test
> > make[1]: Leaving directory '/«BUILDDIR»/biojava3-live-3.1.0+dfsg'
> > fakeroot debian/rules binary
> > dh binary --with javahelper
> > dh_testroot
> > dh_prep
> > dh_auto_install
> > dh_install
> > dh_install: libbiojava3-java-doc missing files (doc/biojava/*), aborting
> > make: *** [binary] Error 2
>
> The full build log is available from:
> http://aws-logs.debian.net/ftbfs-logs/2014/11/08/biojava3-live_3.1.0+dfsg-1_jessie.log
>
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
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