[Debian-med-packaging] Bug#768710: biojava3-live: FTBFS in jessie: dh_install: libbiojava3-java-doc missing files (doc/biojava/*), aborting
Lucas Nussbaum
lucas at lucas-nussbaum.net
Sun Nov 9 07:07:04 UTC 2014
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.
More information about the Debian-med-packaging
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