SuccessConsole Output

Started by user soergel
Building remotely on i-aefcc9c0 in workspace /media/ephemeral0/workspace/sequtils
[sequtils] $ hg showconfig paths.default
[sequtils] $ hg pull --rev default
[sequtils] $ hg update --clean --rev default
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
[sequtils] $ hg --config extensions.purge= clean --all
[sequtils] $ hg log --rev . --template {node}
[sequtils] $ hg log --rev . --template {rev}
[sequtils] $ hg log --rev 293ef9a874ad54c6393bf304d9aa370fb3be551f
[sequtils] $ hg log --template "<changeset node='{node}' author='{author|xmlescape}' rev='{rev}' date='{date}'><msg>{desc|xmlescape}</msg><added>{file_adds|stringify|xmlescape}</added><deleted>{file_dels|stringify|xmlescape}</deleted><files>{files|stringify|xmlescape}</files><parents>{parents}</parents></changeset>\n" --rev default:0 --follow --prune 293ef9a874ad54c6393bf304d9aa370fb3be551f
Parsing POMs
[sequtils] $ java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 47032
<===[JENKINS REMOTING CAPACITY]===>channel started
log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
Executing Maven:  -B -f /media/ephemeral0/workspace/sequtils/pom.xml -DdevelopmentVersion=0.92-SNAPSHOT -DreleaseVersion=0.911 -U -e clean -Dresume=false release:prepare release:perform
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building sequtils 0.92-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ sequtils ---
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ sequtils ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building sequtils 0.92-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-release-plugin:2.0:prepare (default-cli) @ sequtils ---
[INFO] Verifying that there are no local modifications...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg status
[INFO] [release.properties:unknown]
[INFO] Checking dependencies and plugins for snapshots ...
[INFO] Transforming 'sequtils'...
[INFO] Not generating release POMs
[INFO] Executing goals 'clean verify'...
[INFO] [INFO] Scanning for projects...
[INFO] [INFO]                                                                         
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Building sequtils 0.911
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] 
[INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ sequtils ---
[INFO] [INFO] 
[INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ sequtils ---
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Compiling 66 source files to /media/ephemeral0/workspace/sequtils/target/classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 3 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ sequtils ---
[INFO] [INFO] Compiling 11 source files to /media/ephemeral0/workspace/sequtils/target/test-classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ sequtils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/sequtils/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 02:13:35,451 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2013-03-21 02:13:35,459 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2013-03-21 02:13:35,565 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2013-03-21 02:13:35,575 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2013-03-21 02:13:35,593 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,594 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:13:35,602 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,603 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:13:35,607 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,608 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:13:35,718 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,721 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,726 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,741 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,743 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,743 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,746 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,746 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,747 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,748 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,754 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,759 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,761 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,761 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,856 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,861 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,866 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,866 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,872 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,873 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:13:35,879 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:13:35,880 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.065 sec
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/sequtils-0.911.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/sequtils-0.911-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ sequtils ---
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] BUILD SUCCESS
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Total time: 56.629s
[INFO] [INFO] Finished at: Thu Mar 21 02:13:48 UTC 2013
[INFO] [INFO] Final Memory: 11M/27M
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] Checking in modified POMs...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg commit --message '[maven-release-plugin] prepare release sequtils-0.911' /media/ephemeral0/workspace/sequtils/pom.xml
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg push ssh://dev.davidsoergel.com//home/hg/sequtils
[INFO] Tagging release with the label sequtils-0.911...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg tag --message '[maven-release-plugin]  copy for tag sequtils-0.911' sequtils-0.911
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg push ssh://dev.davidsoergel.com//home/hg/sequtils
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg locate
[INFO] Transforming 'sequtils'...
[INFO] Not removing release POMs
[INFO] Checking in modified POMs...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg commit --message '[maven-release-plugin] prepare for next development iteration' /media/ephemeral0/workspace/sequtils/pom.xml
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg push ssh://dev.davidsoergel.com//home/hg/sequtils
[INFO] Release preparation complete.
[INFO] 
[INFO] --- maven-release-plugin:2.0:perform (default-cli) @ sequtils ---
[INFO] Checking out the project to perform the release ...
[INFO] Removing /media/ephemeral0/workspace/sequtils/target/checkout
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils/target && hg clone -r sequtils-0.911 ssh://dev.davidsoergel.com//home/hg/sequtils /media/ephemeral0/workspace/sequtils/target/checkout
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils/target/checkout && hg locate
[INFO] Executing goals 'deploy site-deploy'...
[INFO] [INFO] Scanning for projects...
[INFO] [WARNING] 
[INFO] [WARNING] Some problems were encountered while building the effective model for edu.berkeley.compbio:sequtils:jar:0.911
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing.
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-deploy-plugin is missing.
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-source-plugin is missing.
[INFO] [WARNING] 
[INFO] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[INFO] [WARNING] 
[INFO] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[INFO] [WARNING] 
[INFO] [INFO]                                                                         
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Building sequtils 0.911
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/target/checkout/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Compiling 66 source files to /media/ephemeral0/workspace/sequtils/target/checkout/target/classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 3 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ sequtils ---
[INFO] [INFO] Compiling 11 source files to /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ sequtils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/sequtils/target/checkout/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 02:15:19,549 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2013-03-21 02:15:19,555 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2013-03-21 02:15:19,561 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2013-03-21 02:15:19,633 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2013-03-21 02:15:19,656 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,657 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:15:19,666 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,670 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:15:19,676 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,677 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:15:19,789 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,804 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,807 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,809 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,816 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,817 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,819 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,825 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,827 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,828 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,947 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,951 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,955 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,962 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,968 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,976 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:19,979 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:19,980 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:20,080 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:20,082 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:15:20,087 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:15:20,090 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.069 sec
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911.jar
[INFO] [INFO] 
[INFO] [INFO] >>> maven-source-plugin:2.2.1:jar (attach-sources) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-source-plugin:2.2.1:jar (attach-sources) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] --- maven-source-plugin:2.2.1:jar (attach-sources) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-sources.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-javadoc-plugin:2.9:jar (attach-javadocs) @ sequtils ---
[INFO] [INFO] 
[INFO] Loading source files for package edu.berkeley.compbio.sequtils...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.strings...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader.fasta...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencefragmentiterator...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.6.0_37
[INFO] Building tree for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//AffineSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//ByteArraySequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//DnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//DynamicProgrammingPairwiseAligner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//DynamicProgrammingPairwiseAligner.TracebackBegin.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//DynamicProgrammingPairwiseAligner.TracebackEnd.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//FilterException.html...
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[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings//InferredMixturePST.html...
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[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings//RonPSA.html...
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[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils//class-use/DynamicProgrammingPairwiseAligner.html...
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[INFO] Building index for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/overview-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/index-all.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/deprecated-list.html...
[INFO] Building index for all classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/allclasses-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/allclasses-noframe.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/overview-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/help-doc.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/stylesheet.css...
[INFO] 27 warnings
[INFO] [WARNING] Javadoc Warnings
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/IndelFilter.java:14: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/SequenceArrayUtils.java:617: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/SequenceArrayUtils.java:544: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/SequenceFragmentMetadata.java:236: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/Kcount.java:90: warning - Tag @link: can't find getNumberOfSamples() in edu.berkeley.compbio.sequtils.strings.Kcount
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:149: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:87: warning - Tag @see: can't find fragmentLogProbability(SequenceFragment) in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.java:575: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.java:1178: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:142: warning - Tag @see: can't find addUnknown() in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSANode.java:50: warning - @Author is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSANode.java:50: warning - @Version is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:67: warning - @Author is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:661: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:142: warning - Tag @link: can't find getNumberOfSamples() in edu.berkeley.compbio.sequtils.strings.SequenceSpectrum
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:661: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSTNode.java:60: warning - @Author is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPSTNode.java:336: warning - @returns is an unknown tag.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceFragment.java:215: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceFragment.java:925: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:61: warning - @inheritDoc used but clone() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:61: warning - @inheritDoc used but clone() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/sequencereader/SectionList.java:93: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.java:592: warning - @return tag cannot be used in method with void return type.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequenceFragmentIterator.java:37: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.java:61: warning - @inheritDoc used but clone() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/main/java/edu/berkeley/compbio/sequtils/strings/RonPST.java:661: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-javadoc.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ sequtils ---
[INFO] [INFO] 
[INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ sequtils ---
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/pom.xml to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.pom
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-sources.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-sources.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-javadoc.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-javadoc.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.911-tests.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ sequtils ---
[INFO] WAGON_VERSION: 1.0-beta-2
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.jar (120 KB at 7.3 KB/sec)
[INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.pom
[INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911.pom (5 KB at 1.1 KB/sec)
[INFO] Downloading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/maven-metadata.xml
[INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/maven-metadata.xml (360 B at 0.7 KB/sec)
[INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/maven-metadata.xml
[INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/maven-metadata.xml (392 B at 0.3 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-sources.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-sources.jar (151 KB at 50.9 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-javadoc.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-javadoc.jar (460 KB at 202.1 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-tests.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.911/sequtils-0.911-tests.jar (31 KB at 16.0 KB/sec)
[INFO] [INFO] 
[INFO] [INFO] --- maven-site-plugin:3.1:site (default-site) @ sequtils ---
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-javadoc-plugin:2.8.1
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-aggregate (report:test-aggregate) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/target/checkout/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:test-aggregate (report:test-aggregate) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/target/checkout/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ sequtils <<<
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-jxr-plugin:2.3
[INFO] [INFO] configuring report plugin org.codehaus.mojo:cobertura-maven-plugin:2.5.1
[INFO] [INFO] 
[INFO] [INFO] >>> cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/target/checkout/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- cobertura-maven-plugin:2.5.1:instrument (report:cobertura) @ sequtils ---
[INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file
[INFO] Instrumenting 70 files to /media/ephemeral0/workspace/sequtils/target/checkout/target/generated-classes/cobertura
[INFO] Cobertura: Saved information on 70 classes.
[INFO] Instrument time: 6939ms
[INFO] 
[INFO] [INFO] Instrumentation was successful.
[INFO] [INFO] NOT adding cobertura ser file to attached artifacts list.
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 3 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ sequtils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/sequtils/target/checkout/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 02:17:57,140 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2013-03-21 02:17:57,390 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2013-03-21 02:17:57,393 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2013-03-21 02:17:57,405 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2013-03-21 02:17:57,423 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,429 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:17:57,440 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,442 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:17:57,445 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,446 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2013-03-21 02:17:57,550 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,551 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,556 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,556 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,561 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,561 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,670 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,670 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,672 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,672 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,677 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,677 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,680 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,680 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,687 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,687 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,779 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,780 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,784 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,787 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2013-03-21 02:17:57,798 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/checkout/target/test-classes/Test_Genome true
[INFO] 2013-03-21 02:17:57,799 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.655 sec
[INFO] Flushing results...
[INFO] Flushing results done
[INFO] Cobertura: Loaded information on 70 classes.
[INFO] Cobertura: Saved information on 70 classes.
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] <<< cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ sequtils <<<
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-surefire-report-plugin:2.12
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report (report:report) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/sequtils/target/checkout/src/main/resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ sequtils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 3 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ sequtils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ sequtils ---
[INFO] [INFO] Skipping execution of surefire because it has already been run for this configuration
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report (report:report) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report-only (report:report-only) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report-only (report:report-only) @ sequtils <<<
[INFO] [WARNING] Report plugin org.apache.maven.plugins:maven-project-info-reports-plugin has an empty version.
[INFO] [WARNING] 
[INFO] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[INFO] [WARNING] 
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[INFO] [INFO] Total time: 7:38.955s
[INFO] [INFO] Finished at: Thu Mar 21 02:21:44 UTC 2013
[INFO] [INFO] Final Memory: 29M/83M
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[INFO] Total time: 9:29.465s
[INFO] Finished at: Thu Mar 21 02:21:47 UTC 2013
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[JENKINS] Archiving /media/ephemeral0/workspace/sequtils/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/sequtils/modules/edu.berkeley.compbio$sequtils/builds/2013-03-20_22-12-08/archive/edu.berkeley.compbio/sequtils/0.92-SNAPSHOT/sequtils-0.92-SNAPSHOT.pom
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[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.pom
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Triggering a new build of msensr #17
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