SuccessConsole Output

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...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/FilteringSectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/RandomSectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/SectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaFileSet.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParserSet.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/overview-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/constant-values.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/serialized-form.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceRuntimeException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackBegin.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackEnd.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/GapFrequency.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceReader.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DnaDist.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/LogOddsSubstitutionMatrix.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceError.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/FilteringSequenceReader.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SubstitutionFilter.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/AffineSubstitutionMatrix.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslationException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/NotEnoughSequenceException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceFragmentMetadata.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayUtils.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/IndelFilter.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslatingSequenceReader.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/FilterException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/ByteArraySequenceReader.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/PairAlignedDnaDist.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SimpleSubstitutionMatrix.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/StubSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionDecomposingSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/AbstractSequenceFragmentIterator.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ShuffledSectionSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelSelectableSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSequentialMatePairSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequenceFragmentIterator.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelProvidingSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequentialMatePairSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionListBasedSequenceFragmentIterator.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ScanningSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSectionSFI.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSASmoother.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPST.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoublePseudocountAdder.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/AggregateSequenceFragment.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/LairdSaulPST.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/Kcount.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/HierarchicalSpectrum.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumRuntimeException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSA.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTSmoother.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoubleKcount.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/InferredMixturePST.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntKcount.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumScanner.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/FirstWordProvider.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntPseudocountAdder.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSANode.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KneserNeyPSASmoother.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SimplexVectorTargetAndProportion.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/MarkovTreeNode.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrum.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTNode.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KcountScanner.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceFragment.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/FilteringSectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/SectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/RandomSectionList.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParser.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParserSet.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaFileSet.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/package-use.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-use.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-use.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-use.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-use.html...
Building index for all the packages and classes...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/overview-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/index-all.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/allclasses-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/allclasses-noframe.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/index.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/overview-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/target/apidocs/help-doc.html...
28 warnings
[WARNING] Javadoc Warnings
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace/src/main/java/edu/berkeley/compbio/sequtils/IndelFilter.java:20: 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/SequenceArrayUtils.java:550: 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/SequenceArrayUtils.java:623: 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/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: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/maven-metadata.xml (346 B at 2.4 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 22.6 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/maven-metadata.xml (346 B at 1.9 KB/sec)
Deploying the main artifact sequtils-0.92-SNAPSHOT-sources.jar
Uploading: 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: 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 0.9 KB/sec)
[INFO] Deployment done in 4.3 sec
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of msensr
Triggering a new build of sequtils-docs-deploy
Finished: SUCCESS