SuccessConsole Output

Started by upstream project "dsutils" build number 45
originally caused by:
 Started by GitHub push by davidsoergel
Started by upstream project "stats" build number 27
originally caused by:
 Started by upstream project "dsutils" build number 45
 originally caused by:
  Started by GitHub push by davidsoergel
Building in workspace /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace
Cloning the remote Git repository
Cloning repository https://github.com/davidsoergel/sequtils.git
 > git init /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/workspace
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 config remote.origin.url https://github.com/davidsoergel/sequtils.git
 > git config remote.origin.fetch +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/davidsoergel/sequtils.git
Fetching upstream changes from https://github.com/davidsoergel/sequtils.git
 > 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
First time build. Skipping changelog.
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 57382
<===[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
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[INFO] ------------------------------------------------------------------------
[INFO] Building sequtils 0.92-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ sequtils ---
[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
2014-07-06 17:22:33,747 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
2014-07-06 17:22:33,749 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
2014-07-06 17:22:33,755 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
2014-07-06 17:22:33,760 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
2014-07-06 17:22:33,764 [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
2014-07-06 17:22:33,765 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
2014-07-06 17:22:33,767 [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
2014-07-06 17:22:33,768 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
2014-07-06 17:22:33,769 [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
2014-07-06 17:22:33,799 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
2014-07-06 17:22:33,816 [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
2014-07-06 17:22:33,822 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,825 [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
2014-07-06 17:22:33,826 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,828 [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
2014-07-06 17:22:33,828 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,831 [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
2014-07-06 17:22:33,832 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,833 [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
2014-07-06 17:22:33,833 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,835 [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
2014-07-06 17:22:33,836 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,838 [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
2014-07-06 17:22:33,839 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,841 [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
2014-07-06 17:22:33,841 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,843 [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
2014-07-06 17:22:33,843 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,847 [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
2014-07-06 17:22:33,853 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
2014-07-06 17:22:33,855 [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
2014-07-06 17:22:33,855 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.023 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.
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Constructing Javadoc information...
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[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] Fixed Javadoc frame injection vulnerability (CVE-2013-1571) in 1 files.
[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
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[INFO] Total time: 49.080s
[INFO] Finished at: Sun Jul 06 17:23:01 EDT 2014
[INFO] Final Memory: 16M/41M
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