Reading package lists... Building dependency tree... Reading state information... NOTICE: 'biojava-live' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/biojava/trunk/ Need to get 11.1 MB of source archives. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main biojava-live 1:1.7.1-5 (dsc) [2,486 B] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main biojava-live 1:1.7.1-5 (tar) [11.0 MB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main biojava-live 1:1.7.1-5 (diff) [8,604 B] gpgv: keyblock resource `/tmp/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue 20 May 2014 01:10:09 PM UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./biojava-live_1.7.1-5.dsc dpkg-source: info: extracting biojava-live in biojava-live-1.7.1 dpkg-source: info: unpacking biojava-live_1.7.1.orig.tar.gz dpkg-source: info: unpacking biojava-live_1.7.1-5.debian.tar.xz dpkg-source: info: applying buildxml.patch Fetched 11.1 MB in 1s (6,907 kB/s) Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libbytecode-java 0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded. Need to get 87.7 kB of archives. After this operation, 137 kB of additional disk space will be used. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main libbytecode-java all 0.92.svn.20090106-1.1 [87.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 87.7 kB in 0s (6,983 kB/s) Selecting previously unselected package libbytecode-java. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82591 files and directories currently installed.) Preparing to unpack .../libbytecode-java_0.92.svn.20090106-1.1_all.deb ... Unpacking libbytecode-java (0.92.svn.20090106-1.1) ... Processing triggers for man-db (2.7.2-1) ... Setting up libbytecode-java (0.92.svn.20090106-1.1) ... Killed old client process Internet Systems Consortium DHCP Client 4.3.2 Copyright 2004-2015 Internet Systems Consortium. All rights reserved. For info, please visit https://www.isc.org/software/dhcp/ Listening on LPF/eth0/c6:90:b4:03:59:09 Sending on LPF/eth0/c6:90:b4:03:59:09 Sending on Socket/fallback DHCPRELEASE on eth0 to 10.0.3.1 port 67 dpkg-buildpackage: source package biojava-live dpkg-buildpackage: source version 1:1.7.1-5 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Olivier Sallou dpkg-source --before-build biojava-live-1.7.1 dpkg-buildpackage: host architecture amd64 debian/rules clean dh_testdir dh_testroot rm -f build-stamp # Add here commands to clean up after the build process. ant clean Buildfile: /biojava-live-1.7.1/build.xml init: [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true clean: BUILD SUCCESSFUL Total time: 0 seconds dh_clean dpkg-source -b biojava-live-1.7.1 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building biojava-live using existing ./biojava-live_1.7.1.orig.tar.gz dpkg-source: info: building biojava-live in biojava-live_1.7.1-5.debian.tar.xz dpkg-source: info: building biojava-live in biojava-live_1.7.1-5.dsc debian/rules build dh_testdir find . -name "*.java" -o -name ReadMe -o -name "*.fa" -o -name "*.html" | xargs -r chmod 644 # circumvent Debian's difficulties with libjgrapht - deleting all usage of that library rm -rf src/org/biojavax/bio/phylo/io/nexus/ \ src/org/biojavax/bio/phylo/DistanceBasedTreeMethod.java \ src/org/biojavax/bio/phylo/ParsimonyTreeMethod.java # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /biojava-live-1.7.1/build.xml init: [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: [mkdir] Created dir: /biojava-live-1.7.1/ant-build prepare-biojava: [mkdir] Created dir: /biojava-live-1.7.1/ant-build/classes/biojava [mkdir] Created dir: /biojava-live-1.7.1/ant-build/docs/biojava [mkdir] Created dir: /biojava-live-1.7.1/ant-build/docs/check/biojava compile-biojava: [javac] /biojava-live-1.7.1/build.xml:246: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1444 source files to /biojava-live-1.7.1/ant-build/classes/biojava [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:37: warning: '_' used as an identifier [javac] private static final AtomicSymbol _; [javac] ^ [javac] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javac] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:53: warning: '_' used as an identifier [javac] _ = (AtomicSymbol) sTok.parseToken(" "); [javac] ^ [javac] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javac] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:72: warning: '_' used as an identifier [javac] return _; [javac] ^ [javac] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javac] /biojava-live-1.7.1/src/org/biojava/bio/structure/PDBHeader.java:10: warning: GetEndPointInfoAgainException is internal proprietary API and may be removed in a future release [javac] import com.sun.corba.se.spi.legacy.connection.GetEndPointInfoAgainException; [javac] ^ [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. [javac] 8 warnings [javac] Creating empty /biojava-live-1.7.1/ant-build/classes/biojava/org/biojava/bio/program/fastq/package-info.class package-biojava: [jar] Building jar: /biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL Total time: 18 seconds #ant compile-demos ant javadocs-biojava Buildfile: /biojava-live-1.7.1/build.xml init: [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: prepare-biojava: javadocs-biojava: [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.bibliography... [javadoc] Loading source files for package org.biojava.bio... [javadoc] Loading source files for package org.biojava.bio.alignment... [javadoc] Loading source files for package org.biojava.bio.annodb... [javadoc] Loading source files for package org.biojava.bio.chromatogram... [javadoc] Loading source files for package org.biojava.bio.chromatogram.graphic... [javadoc] Loading source files for package org.biojava.bio.dist... [javadoc] Loading source files for package org.biojava.bio.dp... [javadoc] Loading source files for package org.biojava.bio.dp.onehead... [javadoc] Loading source files for package org.biojava.bio.dp.twohead... [javadoc] Loading source files for package org.biojava.bio.gui... [javadoc] Loading source files for package org.biojava.bio.gui.glyph... [javadoc] Loading source files for package org.biojava.bio.gui.sequence... [javadoc] Loading source files for package org.biojava.bio.gui.sequence.tracklayout... [javadoc] Loading source files for package org.biojava.bio.molbio... 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[javadoc] Loading source files for package org.biojava.bio.program.indexdb... [javadoc] Loading source files for package org.biojava.bio.program.phred... [javadoc] Loading source files for package org.biojava.bio.program.sax... [javadoc] Loading source files for package org.biojava.bio.program.sax.blastxml... [javadoc] Loading source files for package org.biojava.bio.program.scf... [javadoc] Loading source files for package org.biojava.bio.program.ssaha... [javadoc] Loading source files for package org.biojava.bio.program.ssbind... [javadoc] Loading source files for package org.biojava.bio.program.tagvalue... [javadoc] Loading source files for package org.biojava.bio.program.unigene... [javadoc] Loading source files for package org.biojava.bio.program.xff... [javadoc] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:37: warning: '_' used as an identifier [javadoc] private static final AtomicSymbol _; [javadoc] ^ [javadoc] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javadoc] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:53: warning: '_' used as an identifier [javadoc] _ = (AtomicSymbol) sTok.parseToken(" "); [javadoc] ^ [javadoc] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javadoc] /biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:72: warning: '_' used as an identifier [javadoc] return _; [javadoc] ^ [javadoc] (use of '_' as an identifier might not be supported in releases after Java SE 8) [javadoc] Loading source files for package org.biojava.bio.program.xml... [javadoc] Loading source files for package org.biojava.bio.proteomics... [javadoc] Loading source files for package org.biojava.bio.proteomics.aaindex... [javadoc] Loading source files for package org.biojava.bio.search... [javadoc] Loading source files for package org.biojava.bio.seq... [javadoc] Loading source files for package org.biojava.bio.seq.db... [javadoc] Loading source files for package org.biojava.bio.seq.db.biofetch... [javadoc] Loading source files for package org.biojava.bio.seq.db.biosql... [javadoc] Loading source files for package org.biojava.bio.seq.db.emblcd... [javadoc] Loading source files for package org.biojava.bio.seq.db.flat... [javadoc] Loading source files for package org.biojava.bio.seq.distributed... [javadoc] Loading source files for package org.biojava.bio.seq.filter... [javadoc] Loading source files for package org.biojava.bio.seq.homol... [javadoc] Loading source files for package org.biojava.bio.seq.impl... [javadoc] Loading source files for package org.biojava.bio.seq.io... 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[javadoc] Loading source files for package org.biojava.stats.svm... [javadoc] Loading source files for package org.biojava.stats.svm.tools... [javadoc] Loading source files for package org.biojava.utils... [javadoc] Loading source files for package org.biojava.utils.automata... [javadoc] Loading source files for package org.biojava.utils.cache... [javadoc] Loading source files for package org.biojava.utils.candy... [javadoc] Loading source files for package org.biojava.utils.io... [javadoc] Loading source files for package org.biojava.utils.lsid... [javadoc] Loading source files for package org.biojava.utils.math... [javadoc] Loading source files for package org.biojava.utils.net... [javadoc] Loading source files for package org.biojava.utils.process... [javadoc] Loading source files for package org.biojava.utils.regex... [javadoc] Loading source files for package org.biojava.utils.stax... [javadoc] Loading source files for package org.biojava.utils.walker... [javadoc] Loading source files for package org.biojava.utils.xml... [javadoc] Loading source files for package org.biojavax... [javadoc] Loading source files for package org.biojavax.bio... [javadoc] Loading source files for package org.biojavax.bio.db... [javadoc] Loading source files for package org.biojavax.bio.db.biosql... [javadoc] Loading source files for package org.biojavax.bio.db.ncbi... [javadoc] Loading source files for package org.biojavax.bio.phylo... [javadoc] Loading source files for package org.biojavax.bio.phylo.io.phylip... [javadoc] Loading source files for package org.biojavax.bio.seq... [javadoc] Loading source files for package org.biojavax.bio.seq.io... [javadoc] Loading source files for package org.biojavax.bio.taxa... [javadoc] Loading source files for package org.biojavax.bio.taxa.io... [javadoc] Loading source files for package org.biojavax.ga... [javadoc] Loading source files for package org.biojavax.ga.exception... [javadoc] Loading source files for package org.biojavax.ga.functions... [javadoc] Loading source files for package org.biojavax.ga.impl... [javadoc] Loading source files for package org.biojavax.ga.util... [javadoc] Loading source files for package org.biojavax.ontology... [javadoc] Loading source files for package org.biojavax.utils... [javadoc] Constructing Javadoc information... [javadoc] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.5.0/docs/api/ [javadoc] Standard Doclet version 1.8.0_66-internal [javadoc] Building tree for all the packages and classes... [javadoc] Generating /biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/package-summary.html... [javadoc] Copying file /biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_corba.jpg to directory /biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg to directory /biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg to directory /biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/bibobjects_java.jpg to directory /biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Generating /biojava-live-1.7.1/ant-build/docs/biojava/help-doc.html... [javadoc] 4 warnings BUILD SUCCESSFUL Total time: 27 seconds touch build-stamp debian/rules binary dh_testdir dh_testroot dh_prep dh_installdirs cp ant-build/biojava.jar /biojava-live-1.7.1/debian/libbiojava1.7-java/usr/share/java/biojava1.7.1.jar d=/biojava-live-1.7.1/debian/libbiojava-java-doc/usr/share/doc/libbiojava-java/api; \ [ -d $d ] || mkdir -p $d ; \ cp -r ant-build/docs/biojava/* $d for i in /biojava-live-1.7.1/debian/libbiojava-java*; do \ if [ -d "" ]; then \ find -name ".svn" | xargs -r rm -r ; \ fi ; \ done ant runtests Buildfile: /biojava-live-1.7.1/build.xml init: [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: prepare-tests: [mkdir] Created dir: /biojava-live-1.7.1/ant-build/classes/tests [mkdir] Created dir: /biojava-live-1.7.1/ant-build/docs/tests [mkdir] Created dir: /biojava-live-1.7.1/reports/tests prepare-biojava: compile-biojava: [javac] /biojava-live-1.7.1/build.xml:246: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds package-biojava: compile-tests: [javac] /biojava-live-1.7.1/build.xml:264: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 184 source files to /biojava-live-1.7.1/ant-build/classes/tests [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [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. [javac] 4 warnings runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec [junit] Running org.biojava.bio.MergeAnnotationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.dist.DistSerTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec [junit] Running org.biojava.bio.dist.DistributionTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.dp.DPSerializationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.fastq.FastqTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.program.sax.BlastTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.71 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.606 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.689 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.714 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.39 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.681 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.125 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.456 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.879 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.659 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] Running org.biojava.bio.seq.DNAToolsTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.RNAToolsTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 1.48 sec [junit] Test org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest FAILED [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.218 sec [junit] Test org.biojava.bio.seq.io.SeqIOToolsTest FAILED [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.656 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.structure.MMcifTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.332 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 2.044 sec [junit] Test org.biojava.bio.structure.StructurePairAlignerTest FAILED [junit] Running org.biojava.bio.structure.StructureTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] Running org.biojava.bio.structure.StructureToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.88 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.symbol.GappedSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.PointLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SymbolListTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.TranslationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec [junit] Running org.biojava.directory.OBDARegistryParserTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.directory.RegistryConfigurationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.directory.SystemRegistryTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.naming.ObdaUriParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.ontology.OntologyTest [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.ontology.ParseOBOFileTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 sec [junit] Running org.biojava.ontology.TermImplTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.ontology.TripleImplTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.ListToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.SmallMapTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.utils.automata.NfaTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.process.ExternalProcessTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.329 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.utils.regex.RegexTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] Running org.biojava.utils.walker.WalkerTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.EmptyRichAnnotationTest [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleCommentTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.SimpleCrossRefTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleDocRefTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.SimpleNamespaceTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.SimpleNoteTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleRankedDocRefTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.SimpleRichAnnotationTest [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.bio.SimpleBioEntryTest [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec [junit] Test org.biojavax.bio.SimpleBioEntryTest FAILED [junit] Running org.biojavax.bio.seq.CompoundRichLocationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.util.GAToolsTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.ga.util.WeightedSetTest [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.ontology.SimpleComparableOntologyTest [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.ontology.SimpleComparableTermTest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec BUILD SUCCESSFUL Total time: 44 seconds dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installexamples -plibbiojava-java-demos demos/* #dh_installman dh_link -p libbiojava-java /usr/share/java/biojava1.7.1.jar /usr/share/java/biojava.jar # thinking about svn snapshots if [ "1.7" != "1.7.1" ]; then \ dh_link -p libbiojava1.7-java \ /usr/share/java/biojava1.7.1.jar \ /usr/share/java/biojava1.7.jar; \ fi dh_link # use .link files for version independant linking dh_compress dh_fixperms dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libbiojava1.7-java: unknown substitution variable ${shlibs:Depends} dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-5_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-5_all.deb'. dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-5_all.deb'. dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.7.1-5_all.deb'. dpkg-genchanges >../biojava-live_1.7.1-5_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build biojava-live-1.7.1 dpkg-buildpackage: binary and diff upload (original source NOT included)