Started by upstream project "dsutils" build number 48 originally caused by: Started by user David Soergel Started by upstream project "stats" build number 30 originally caused by: Started by upstream project "dsutils" build number 48 originally caused by: Started by user David Soergel Building in workspace /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace > git rev-parse --is-inside-work-tree Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/davidsoergel/sequtils.git Fetching upstream changes from https://github.com/davidsoergel/sequtils.git > git --version > git fetch --tags --progress https://github.com/davidsoergel/sequtils.git +refs/heads/*:refs/remotes/origin/* > git rev-parse origin/master^{commit} Checking out Revision 5571a5790bfbb5de8aebfe6ed926e38b33ac6939 (origin/master) > git config core.sparsecheckout > git checkout -f 5571a5790bfbb5de8aebfe6ed926e38b33ac6939 > git rev-list 5571a5790bfbb5de8aebfe6ed926e38b33ac6939 Parsing POMs [workspace] $ java -Xmx1024M -XX:MaxPermSize=256M -cp /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven31-agent-1.5.jar:/usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/boot/plexus-classworlds-2.5.1.jar:/usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/conf/logging jenkins.maven3.agent.Maven31Main /usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1 /usr/share/apache-tomcat-7.0.22/webapps/jenkins/WEB-INF/lib/remoting-2.43.jar /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven31-interceptor-1.5.jar /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven3-interceptor-commons-1.5.jar 40749 <===[JENKINS REMOTING CAPACITY]===>channel started Executing Maven: -B -f /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/pom.xml -U -e clean source:jar package jar:test-jar javadoc:jar [INFO] Error stacktraces are turned on. [WARNING] [WARNING] Some problems were encountered while building the effective settings [WARNING] Unrecognised tag: 'scmVersionType' (position: START_TAG seen ...</username>\n <scmVersionType>... @22:21) @ /usr/share/apache-tomcat-7.0.22/.m2/settings.xml, line 22, column 21 [WARNING] [INFO] Scanning for projects... [INFO] Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/mojo/maven-metadata.xml [INFO] Downloading: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml [INFO] Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml (13 KB at 21.9 KB/sec) [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/mojo/maven-metadata.xml (20 KB at 31.9 KB/sec) [INFO] Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml (20 KB at 61.5 KB/sec) [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml (13 KB at 18.4 KB/sec) [INFO] Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml (692 B at 4.5 KB/sec) [INFO] Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml (692 B at 4.3 KB/sec) [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-javadoc-plugin/maven-metadata.xml [INFO] Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-javadoc-plugin/maven-metadata.xml [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-javadoc-plugin/maven-metadata.xml (782 B at 12.9 KB/sec) [INFO] Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-javadoc-plugin/maven-metadata.xml (782 B at 5.4 KB/sec) [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building sequtils 0.92-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ sequtils --- [INFO] Deleting /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ sequtils --- [INFO] [INFO] >>> maven-source-plugin:2.2.1:jar (default-cli) @ sequtils >>> [WARNING] Failed to getClass for org.apache.maven.plugin.source.SourceJarMojo [INFO] [INFO] <<< maven-source-plugin:2.2.1:jar (default-cli) @ sequtils <<< [INFO] [INFO] --- maven-source-plugin:2.2.1:jar (default-cli) @ sequtils --- [INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ sequtils --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils --- [INFO] Compiling 66 source files to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ sequtils --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ sequtils --- [INFO] Compiling 11 source files to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ sequtils --- [INFO] Surefire report directory: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running TestSuite 2014-07-08 12:59:51,608 [main] WARN edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA 2014-07-08 12:59:51,610 [main] WARN edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA 2014-07-08 12:59:51,615 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS 2014-07-08 12:59:51,621 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS] 2014-07-08 12:59:51,626 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,627 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346 2014-07-08 12:59:51,630 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,702 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346 2014-07-08 12:59:51,704 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,705 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346 2014-07-08 12:59:51,724 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,730 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,733 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,733 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,735 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,736 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,739 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,740 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,741 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,741 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,744 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,744 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,747 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,748 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,750 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,750 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,814 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,815 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,816 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,817 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 2014-07-08 12:59:51,818 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/test-classes/Test_Genome true 2014-07-08 12:59:51,819 [main] INFO edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346 Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.322 sec Results : Tests run: 52, Failures: 0, Errors: 0, Skipped: 0 [JENKINS] Recording test results log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ sequtils --- [INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ sequtils --- [INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-tests.jar [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ sequtils --- [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ sequtils --- [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (default-cli) @ sequtils --- [INFO] Loading source files for package edu.berkeley.compbio.sequtils... Loading source files for package edu.berkeley.compbio.sequtils.sequencefragmentiterator... Loading source files for package edu.berkeley.compbio.sequtils.strings... Loading source files for package edu.berkeley.compbio.sequtils.sequencereader... Loading source files for package edu.berkeley.compbio.sequtils.sequencereader.fasta... Constructing Javadoc information... Standard Doclet version 1.7.0_60 Building tree for all the packages and classes... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/AffineSubstitutionMatrix.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/ByteArraySequenceReader.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/DnaDist.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.TracebackBegin.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.TracebackEnd.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/FilterException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/FilteringSequenceReader.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/GapFrequency.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/IndelFilter.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/LogOddsSubstitutionMatrix.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/NotEnoughSequenceException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/PairAlignedDnaDist.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayUtils.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceError.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceFragmentMetadata.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceReader.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SequenceRuntimeException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SimpleSubstitutionMatrix.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/SubstitutionFilter.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/TranslatingSequenceReader.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/TranslationException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/AbstractSequenceFragmentIterator.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelProvidingSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelSelectableSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSectionSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSequentialMatePairSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ScanningSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionDecomposingSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionListBasedSequenceFragmentIterator.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequenceFragmentIterator.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequentialMatePairSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ShuffledSectionSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/StubSFI.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/AggregateSequenceFragment.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/DoubleKcount.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/DoublePseudocountAdder.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/FirstWordProvider.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/HierarchicalSpectrum.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/InferredMixturePST.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/IntKcount.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/IntPseudocountAdder.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/Kcount.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/KcountScanner.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/KneserNeyPSASmoother.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/LairdSaulPST.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSA.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSANode.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSASmoother.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPST.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTNode.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTSmoother.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceFragment.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumRuntimeException.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumScanner.html... Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/SimplexVectorTargetAndProportion.html... 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[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/SequenceFragmentMetadata.java:210: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequenceFragmentIterator.java:43: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceFragment.java:189: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceFragment.java:899: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:61: warning - Tag @see: can't find fragmentLogProbability(SequenceFragment) in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:116: warning - Tag @see: can't find addUnknown() in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:123: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/Kcount.java:64: warning - Tag @link: can't find getNumberOfSamples() in edu.berkeley.compbio.sequtils.strings.Kcount [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.java:549: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.java:1152: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSANode.java:24: warning - @Author is an unknown tag -- same as a known tag except for case. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSANode.java:24: warning - @Version is an unknown tag -- same as a known tag except for case. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:41: warning - @Author is an unknown tag -- same as a known tag except for case. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:635: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:116: warning - Tag @link: can't find getNumberOfSamples() in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:635: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSTNode.java:34: warning - @Author is an unknown tag -- same as a known tag except for case. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSTNode.java:310: warning - @returns is an unknown tag. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:35: warning - @inheritDoc used but clone() does not override or implement any method. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:35: warning - @inheritDoc used but clone() does not override or implement any method. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/sequencereader/SectionList.java:67: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.java:675: warning - @return tag has no arguments. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.java:566: warning - @return tag cannot be used in method with void return type. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:35: warning - @inheritDoc used but clone() does not override or implement any method. [WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:635: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-javadoc.jar [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 49.043s [INFO] Finished at: Tue Jul 08 13:00:20 EDT 2014 [INFO] Final Memory: 21M/51M [INFO] ------------------------------------------------------------------------ [JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/pom.xml to edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT.pom [JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT.jar to edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT.jar [JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-sources.jar to edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT-sources.jar [JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-tests.jar to edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT-tests.jar [JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/sequtils-0.92-SNAPSHOT-javadoc.jar to edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT-javadoc.jar channel stopped Maven RedeployPublisher use remote maven settings from : /usr/share/apache-tomcat-7.0.22/.m2/settings.xml [ERROR] uniqueVersion == false is not anymore supported in maven 3 [INFO] Deployment in dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots (id=dev.davidsoergel.com.snapshot,uniqueVersion=false) Deploying the main artifact sequtils-0.92-SNAPSHOT.jar Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml Downloaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml (2 KB at 4.0 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9.jar Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9.jar (119 KB at 250.2 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9.pom Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9.pom (3 KB at 11.8 KB/sec) Downloading: 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dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-sources.jar Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-sources.jar (115 KB at 505.0 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml (2 KB at 15.5 KB/sec) Deploying the main artifact sequtils-0.92-SNAPSHOT-tests.jar Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-tests.jar Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-tests.jar (30 KB at 228.8 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/maven-metadata.xml (2 KB at 10.6 KB/sec) Deploying the main artifact sequtils-0.92-SNAPSHOT-javadoc.jar Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-javadoc.jar Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-20140708.170021-9-javadoc.jar (463 KB at 1364.0 KB/sec) Uploading: 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