SuccessConsole Output

Started by user soergel
Building remotely on i-b4b502cc 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 bd9f4b72edd5a8a244b18a36380c7283ae37ccdf
[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 bd9f4b72edd5a8a244b18a36380c7283ae37ccdf
 your Apache Maven build is setup to use a config with id org.jenkinsci.plugins.configfiles.maven.MavenSettingsConfig1337980147845 but cannot find the config
Parsing POMs
[sequtils] $ /usr/java/default/bin/java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/Maven/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/Maven/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 58752
<===[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=0.91 -U -e clean -Dresume=false release:prepare release:perform
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
Projects to build: [MavenProject: edu.berkeley.compbio:sequtils:0.91-SNAPSHOT @ /media/ephemeral0/workspace/sequtils/pom.xml]
projectStarted edu.berkeley.compbio:sequtils:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building sequtils 0.91-SNAPSHOT
[INFO] ------------------------------------------------------------------------
mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ sequtils ---
mojoSucceeded org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)
mojoStarted org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean)
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ sequtils ---
mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean)
projectSucceeded edu.berkeley.compbio:sequtils:0.91-SNAPSHOT
projectStarted edu.berkeley.compbio:sequtils:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building sequtils 0.91-SNAPSHOT
[INFO] ------------------------------------------------------------------------
mojoStarted org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
[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 0.91
[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] 2012-07-09 03:30:50,910 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2012-07-09 03:30:50,917 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2012-07-09 03:30:50,931 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2012-07-09 03:30:51,016 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2012-07-09 03:30:51,129 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,134 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:30:51,153 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,153 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:30:51,161 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,162 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:30:51,253 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,260 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,268 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,268 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,276 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,277 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,289 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,291 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,358 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,359 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,367 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,378 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,382 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,382 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,393 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,394 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,405 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,405 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,475 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,475 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:30:51,490 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Loading test genome: /media/ephemeral0/workspace/sequtils/target/test-classes/Test_Genome true
[INFO] 2012-07-09 03:30:51,491 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 37.882 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-0.91.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/sequtils-0.91-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: 1:40.743s
[INFO] [INFO] Finished at: Mon Jul 09 03:31:23 UTC 2012
[INFO] [INFO] Final Memory: 14M/34M
[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-0.91' /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-0.91...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && hg tag --message '[maven-release-plugin]  copy for tag sequtils-0.91' sequtils-0.91
[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.
mojoSucceeded org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
mojoStarted org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
[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-0.91 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:0.91
[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 0.91
[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] 2012-07-09 03:32:31,631 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2012-07-09 03:32:31,639 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2012-07-09 03:32:31,644 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2012-07-09 03:32:31,723 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2012-07-09 03:32:31,745 [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] 2012-07-09 03:32:31,748 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:32:31,757 [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] 2012-07-09 03:32:31,759 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:32:31,766 [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] 2012-07-09 03:32:31,767 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:32:31,850 [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] 2012-07-09 03:32:31,851 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,854 [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] 2012-07-09 03:32:31,858 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,861 [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] 2012-07-09 03:32:31,865 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,867 [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] 2012-07-09 03:32:31,869 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,872 [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] 2012-07-09 03:32:31,874 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,879 [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] 2012-07-09 03:32:31,884 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,886 [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] 2012-07-09 03:32:31,891 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,893 [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] 2012-07-09 03:32:31,895 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,897 [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] 2012-07-09 03:32:31,899 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,961 [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] 2012-07-09 03:32:31,961 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:32:31,963 [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] 2012-07-09 03:32:31,963 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.368 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-0.91.jar
[INFO] [INFO] 
[INFO] [INFO] >>> maven-source-plugin:2.1.2:jar (attach-sources) @ sequtils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-source-plugin:2.1.2:jar (attach-sources) @ sequtils <<<
[INFO] [INFO] 
[INFO] [INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ sequtils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.91-sources.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-javadoc-plugin:2.8.1: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.sequencefragmentiterator...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.strings...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader.fasta...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.7.0_04
[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...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/FilteringSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/GapFrequency.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/IndelFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/LogOddsSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/NotEnoughSequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/PairAlignedDnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayUtils.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceError.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceFragmentMetadata.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SequenceRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SimpleSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/SubstitutionFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/TranslatingSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/TranslationException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/AbstractSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelProvidingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelSelectableSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ScanningSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionDecomposingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionListBasedSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ShuffledSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/StubSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/AggregateSequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/DoubleKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/DoublePseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/FirstWordProvider.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/HierarchicalSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/InferredMixturePST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/IntKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/IntPseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/Kcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/KcountScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/KneserNeyPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/LairdSaulPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSA.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSANode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTSmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/SimplexVectorTargetAndProportion.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/FilteringSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/RandomSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/SectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaFileSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParserSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/overview-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/serialized-form.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackBegin.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackEnd.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/FilteringSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/GapFrequency.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/IndelFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceError.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SimpleSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslationException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/NotEnoughSequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayUtils.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceFragmentMetadata.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/LogOddsSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/PairAlignedDnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/ByteArraySequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/FilterException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/SubstitutionFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/AffineSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/DnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslatingSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionDecomposingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/AbstractSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelSelectableSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ScanningSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ShuffledSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelProvidingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionListBasedSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/StubSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/Kcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SimplexVectorTargetAndProportion.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/HierarchicalSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KcountScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoublePseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoubleKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/FirstWordProvider.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSANode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/InferredMixturePST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/MarkovTreeNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/AggregateSequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KneserNeyPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTSmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSA.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/LairdSaulPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntPseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/FilteringSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/SectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/RandomSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParserSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaFileSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParser.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/apidocs/edu/berkeley/compbio/sequtils/strings/package-use.html...
[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] 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/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/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/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-0.91-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-0.91-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-0.91.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/pom.xml to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91.pom
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.91-sources.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-sources.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.91-javadoc.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-javadoc.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/sequtils/target/checkout/target/sequtils-0.91-tests.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-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/0.91/sequtils-0.91.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91.jar (120 KB at 96.2 KB/sec)
[INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91.pom
[INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91.pom (5 KB at 5.4 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 (350 B at 0.6 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 (360 B at 0.1 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-sources.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-sources.jar (151 KB at 129.7 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-javadoc.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-javadoc.jar (460 KB at 313.5 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-tests.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/sequtils/0.91/sequtils-0.91-tests.jar (31 KB at 45.7 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: 5433ms
[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] 2012-07-09 03:34:06,192 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2012-07-09 03:34:06,194 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2012-07-09 03:34:06,201 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2012-07-09 03:34:06,295 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2012-07-09 03:34:06,339 [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] 2012-07-09 03:34:06,349 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:34:06,431 [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] 2012-07-09 03:34:06,432 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:34:06,434 [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] 2012-07-09 03:34:06,435 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:34:06,457 [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] 2012-07-09 03:34:06,458 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,549 [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] 2012-07-09 03:34:06,551 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,566 [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] 2012-07-09 03:34:06,570 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,808 [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] 2012-07-09 03:34:06,809 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,817 [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] 2012-07-09 03:34:06,818 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,897 [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] 2012-07-09 03:34:06,900 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:06,912 [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] 2012-07-09 03:34:06,936 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:07,025 [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] 2012-07-09 03:34:07,026 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:07,033 [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] 2012-07-09 03:34:07,039 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:07,067 [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] 2012-07-09 03:34:07,132 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:34:07,159 [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] 2012-07-09 03:34:07,163 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 29.471 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] 
[INFO] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-project-info-reports-plugin:2.4
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0
[INFO] [WARNING] Unable to find a URL to the parent project. The parent menu will NOT be added.
[INFO] [INFO] Relativizing decoration links with respect to project URL: http://dev.davidsoergel.com/sequtils
[INFO] [INFO] Rendering site with org.apache.maven.skins:maven-default-skin:jar:1.0 skin.
[INFO] [INFO] Skipped "Test JavaDocs" report, file "testapidocs/index.html" already exists for the English version.
[INFO] [INFO] Skipped "JavaDocs" report, file "apidocs/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Source Xref" report, file "xref/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Test Source Xref" report, file "xref-test/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Surefire Report" report, file "surefire-report.html" already exists for the English version.
[INFO] [INFO] Generating "Test JavaDocs" report    --- maven-javadoc-plugin:2.8.1
[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] Constructing Javadoc information...
[INFO] Standard Doclet version 1.7.0_04
[INFO] Building tree for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAlignerTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/SequenceArrayUtilsTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/DoubleKcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/IntKcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/KcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/MarkovTreeNodeTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/RonPSTNodeTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/RonPSTTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/RonPSTTest.StubSequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumInterfaceTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaFileSetTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParserTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/overview-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAlignerTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayUtilsTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoubleKcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTNodeTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntKcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTTest.StubSequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/KcountAbstractTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumInterfaceTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/class-use/MarkovTreeNodeTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParserTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaFileSetTest.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/sequtils/strings/package-use.html...
[INFO] Building index for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/overview-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/index-all.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/deprecated-list.html...
[INFO] Building index for all classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/allclasses-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/allclasses-noframe.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/overview-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/testapidocs/help-doc.html...
[INFO] 6 warnings
[INFO] [WARNING] Javadoc Warnings
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:612: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:642: warning - @inheritDoc used but getSumOfCounts() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:612: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:642: warning - @inheritDoc used but getSumOfCounts() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:612: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method.
[INFO] [WARNING] /media/ephemeral0/workspace/sequtils/target/checkout/src/test/java/edu/berkeley/compbio/sequtils/strings/RonPSTTest.java:642: warning - @inheritDoc used but getSumOfCounts() does not override or implement any method.
[INFO] [INFO] Generating "JavaDocs" report    --- maven-javadoc-plugin:2.8.1
[INFO] [INFO] 
[INFO] Loading source files for package edu.berkeley.compbio.sequtils...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencefragmentiterator...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.strings...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader...
[INFO] Loading source files for package edu.berkeley.compbio.sequtils.sequencereader.fasta...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.7.0_04
[INFO] Building tree for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/AffineSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/ByteArraySequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/DnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.TracebackBegin.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/DynamicProgrammingPairwiseAligner.TracebackEnd.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/FilterException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/FilteringSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/GapFrequency.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/IndelFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/LogOddsSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/NotEnoughSequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/PairAlignedDnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceArrayUtils.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceError.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceFragmentMetadata.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SequenceRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SimpleSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/SubstitutionFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/TranslatingSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/TranslationException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/AbstractSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelProvidingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/LabelSelectableSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/RandomSequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ScanningSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionDecomposingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionListBasedSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/SequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/ShuffledSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/StubSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/AggregateSequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/DoubleKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/DoublePseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/FirstWordProvider.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/HierarchicalSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/InferredMixturePST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/IntKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/IntPseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/Kcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/KcountScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/KneserNeyPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/LairdSaulPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/MarkovTreeNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSA.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSANode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/RonPSTSmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SequenceSpectrumScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/SimplexVectorTargetAndProportion.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/FilteringSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/RandomSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/SectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaFileSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParser.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/FastaParserSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/overview-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/serialized-form.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackBegin.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/DynamicProgrammingPairwiseAligner.TracebackEnd.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/FilteringSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/GapFrequency.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/IndelFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceError.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SimpleSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslationException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/NotEnoughSequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceArrayUtils.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceFragmentMetadata.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/LogOddsSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SequenceException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/PairAlignedDnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/ByteArraySequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/FilterException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/SubstitutionFilter.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/AffineSubstitutionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/DnaDist.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/class-use/TranslatingSequenceReader.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionDecomposingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/AbstractSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelSelectableSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ScanningSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/ShuffledSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/LabelProvidingSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSectionSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/RandomSequentialMatePairSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/SectionListBasedSequenceFragmentIterator.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/class-use/StubSFI.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/Kcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SimplexVectorTargetAndProportion.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/HierarchicalSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KcountScanner.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoublePseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/DoubleKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/FirstWordProvider.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSANode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/InferredMixturePST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrum.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/MarkovTreeNode.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/AggregateSequenceFragment.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/KneserNeyPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSTSmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSA.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntKcount.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/SequenceSpectrumException.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/RonPSASmoother.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/LairdSaulPST.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/class-use/IntPseudocountAdder.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/FilteringSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/SectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/class-use/RandomSectionList.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParserSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaFileSet.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/class-use/FastaParser.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencefragmentiterator/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/sequencereader/fasta/package-use.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/edu/berkeley/compbio/sequtils/strings/package-use.html...
[INFO] Building index for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/overview-tree.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/index-all.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/deprecated-list.html...
[INFO] Building index for all classes...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/allclasses-frame.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/allclasses-noframe.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/overview-summary.html...
[INFO] Generating /media/ephemeral0/workspace/sequtils/target/checkout/target/site/apidocs/help-doc.html...
[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/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/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/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] Generating "Source Xref" report    --- maven-jxr-plugin:2.3
[INFO] [INFO] Generating "Test Source Xref" report    --- maven-jxr-plugin:2.3
[INFO] [INFO] Generating "Cobertura Test Coverage" report    --- cobertura-maven-plugin:2.5.1
[INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file
[INFO] Cobertura: Loaded information on 70 classes.
[INFO] Report time: 14165ms
[INFO] 
[INFO] [INFO] Cobertura Report generation was successful.
[INFO] [INFO] Generating "Surefire Report" report    --- maven-surefire-report-plugin:2.12
[INFO] [INFO] Generating "Distribution Management" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "About" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Dependencies" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Issue Tracking" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Project Plugins" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Continuous Integration" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Project License" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Mailing Lists" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Project Team" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Source Repository" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Plugin Management" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] Generating "Project Summary" report    --- maven-project-info-reports-plugin:2.4
[INFO] [INFO] 
[INFO] [INFO] --- maven-site-plugin:3.1:deploy (default-deploy) @ sequtils ---
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0
[INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/sequtils/ - Session: Opened  
[INFO] [INFO] Pushing /media/ephemeral0/workspace/sequtils/target/checkout/target/site
[INFO] [INFO]    >>> to scpexe://dev.davidsoergel.com/home/build/mavensites/sequtils/./
[INFO] Executing command: mkdir -p /home/build/mavensites/sequtils/./
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "mkdir -p /home/build/mavensites/sequtils/./"'
[INFO] 
[INFO] 
[INFO] Executing command: mkdir -p /home/build/mavensites/sequtils//.
[INFO] 
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "mkdir -p /home/build/mavensites/sequtils//.
[INFO] "'
[INFO] 
[INFO] 
[INFO] Uploading: ./wagon6544702965428933333.zip to scpexe://dev.davidsoergel.com/home/build/mavensites/sequtils/
[INFO] 
[INFO] Executing command: /bin/bash -c 'cd /tmp && scp -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" wagon6544702965428933333.zip jenkins@dev.davidsoergel.com:/home/build/mavensites/sequtils//./wagon6544702965428933333.zip'
[INFO] ##############################################################################################################################################################################################################################################################################################################################################
[INFO] Transfer finished. 1366546 bytes copied in 0.863 seconds
[INFO] Executing command: cd /home/build/mavensites/sequtils/./; unzip -q -o wagon6544702965428933333.zip; rm -f wagon6544702965428933333.zip
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "cd /home/build/mavensites/sequtils/./; unzip -q -o wagon6544702965428933333.zip; rm -f wagon6544702965428933333.zip"'
[INFO] 
[INFO] 
[INFO] Executing command: chmod -Rf g+w,a+rX /home/build/mavensites/sequtils/
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "chmod -Rf g+w,a+rX /home/build/mavensites/sequtils/"'
[INFO] 
[INFO] 
[INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/sequtils/ - Session: Disconnecting  
[INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/sequtils/ - Session: Disconnected
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] BUILD SUCCESS
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Total time: 5:20.249s
[INFO] [INFO] Finished at: Mon Jul 09 03:37:05 UTC 2012
[INFO] [INFO] Final Memory: 29M/85M
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] Cleaning up after release...
mojoSucceeded org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
projectSucceeded edu.berkeley.compbio:sequtils:0.91-SNAPSHOT
sessionEnded
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8:11.989s
[INFO] Finished at: Mon Jul 09 03:37:06 UTC 2012
[INFO] Final Memory: 11M/28M
[INFO] ------------------------------------------------------------------------
Projects to build: [MavenProject: edu.berkeley.compbio:sequtils:0.91-SNAPSHOT @ /media/ephemeral0/workspace/sequtils/pom.xml]
[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/2012-07-08_23-28-34/archive/edu.berkeley.compbio/sequtils/0.91-SNAPSHOT/sequtils-0.91-SNAPSHOT.pom
Waiting for Jenkins to finish collecting data
channel stopped
[M2Release] marking build to keep until the next release build
 your Apache Maven build is setup to use a config with id org.jenkinsci.plugins.configfiles.maven.MavenSettingsConfig1337980147845 but cannot find the config
Maven RedeployPublished use remote i-b4b502cc maven settings from : /home/ec2-user/.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-0.91-SNAPSHOT.pom
Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/maven-metadata.xml
Downloaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/maven-metadata.xml (2 KB at 8.5 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/sequtils-0.91-20120709.033711-10.pom
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/sequtils-0.91-20120709.033711-10.pom (5 KB at 1.5 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 (287 B at 5.4 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/sequtils/0.91-SNAPSHOT/maven-metadata.xml (2 KB at 6.6 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 (287 B at 2.0 KB/sec)
[INFO] Deployment done in 4 sec
pmax #17 is already in the queue
Finished: SUCCESS