FailedConsole 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 81e8a00e502dba7b2befb865f9c47adb3077467e
[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 81e8a00e502dba7b2befb865f9c47adb3077467e
 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 56562
<===[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 ---
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Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/jdom/jdom/1.1/jdom-1.1.jar (150 KB at 799.6 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-utils/1.5.6/plexus-utils-1.5.6.jar (245 KB at 556.1 KB/sec)
[INFO] Verifying that there are no local modifications...
[INFO] Executing: /bin/sh -c cd /media/ephemeral0/workspace/sequtils && svn --non-interactive status
[INFO] Working directory: /media/ephemeral0/workspace/sequtils
[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 03:20:54,558 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GAATTCAGTTA
[INFO] 2012-07-09 03:20:54,563 [main] WARN  edu.berkeley.compbio.sequtils.DynamicProgrammingPairwiseAlignerTest - GGA-TC---GA
[INFO] 2012-07-09 03:20:54,572 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtils - Bad char '71' in pattern: AC-GTRS
[INFO] 2012-07-09 03:20:54,583 [main] ERROR edu.berkeley.compbio.sequtils.SequenceArrayUtilsTest - [.-]*A[.-]*C[.-]*G[.-]*T[.-]*[AGR][.-]*[CGS]
[INFO] 2012-07-09 03:20:54,661 [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 03:20:54,667 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:20:54,673 [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 03:20:54,674 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:20:54,681 [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 03:20:54,681 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaFileSetTest - Got FastaFileSet: 3346
[INFO] 2012-07-09 03:20:54,694 [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 03:20:54,695 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,700 [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 03:20:54,701 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,704 [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 03:20:54,706 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,773 [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 03:20:54,774 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,776 [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 03:20:54,776 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,779 [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 03:20:54,783 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,785 [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 03:20:54,788 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,790 [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 03:20:54,793 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,795 [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 03:20:54,796 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,800 [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 03:20:54,801 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] 2012-07-09 03:20:54,803 [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 03:20:54,806 [main] INFO  edu.berkeley.compbio.sequtils.sequencereader.fasta.FastaParserTest - Got FastaParser: 3346
[INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.26 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: 43.428s
[INFO] [INFO] Finished at: Mon Jul 09 03:21:05 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 && svn --non-interactive commit --file /tmp/maven-scm-1659356024.commit --targets /tmp/maven-scm-8100329356711571016-targets
[INFO] Working directory: /media/ephemeral0/workspace/sequtils
mojoFailed org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
projectFailed edu.berkeley.compbio:sequtils:0.91-SNAPSHOT
sessionEnded
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:17.174s
[INFO] Finished at: Mon Jul 09 03:21:05 UTC 2012
[INFO] Final Memory: 12M/32M
[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_23-19-36/archive/edu.berkeley.compbio/sequtils/0.91-SNAPSHOT/sequtils-0.91-SNAPSHOT.pom
Waiting for Jenkins to finish collecting data
mavenExecutionResult exceptions not empty
message : Failed to execute goal org.apache.maven.plugins:maven-release-plugin:2.0:prepare (default-cli) on project sequtils: Unable to commit files
Provider message:
The svn command failed.
Command output:
svn: '/media/ephemeral0/workspace/sequtils' is not a working copy

cause : Unable to commit files
Provider message:
The svn command failed.
Command output:
svn: '/media/ephemeral0/workspace/sequtils' is not a working copy

Stack trace : 
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-release-plugin:2.0:prepare (default-cli) on project sequtils: Unable to commit files
Provider message:
The svn command failed.
Command output:
svn: '/media/ephemeral0/workspace/sequtils' is not a working copy

	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
	at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:601)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239)
	at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:98)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:64)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
	at java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
	at java.lang.Thread.run(Thread.java:722)
Caused by: org.apache.maven.plugin.MojoFailureException: Unable to commit files
Provider message:
The svn command failed.
Command output:
svn: '/media/ephemeral0/workspace/sequtils' is not a working copy

	at org.apache.maven.plugins.release.PrepareReleaseMojo.prepareRelease(PrepareReleaseMojo.java:219)
	at org.apache.maven.plugins.release.PrepareReleaseMojo.execute(PrepareReleaseMojo.java:181)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
	... 27 more
Caused by: org.apache.maven.shared.release.scm.ReleaseScmCommandException: Unable to commit files
Provider message:
The svn command failed.
Command output:
svn: '/media/ephemeral0/workspace/sequtils' is not a working copy

	at org.apache.maven.shared.release.phase.ScmCommitPhase.checkin(ScmCommitPhase.java:133)
	at org.apache.maven.shared.release.phase.ScmCommitPhase.execute(ScmCommitPhase.java:109)
	at org.apache.maven.shared.release.DefaultReleaseManager.prepare(DefaultReleaseManager.java:203)
	at org.apache.maven.shared.release.DefaultReleaseManager.prepare(DefaultReleaseManager.java:140)
	at org.apache.maven.shared.release.DefaultReleaseManager.prepare(DefaultReleaseManager.java:103)
	at org.apache.maven.plugins.release.PrepareReleaseMojo.prepareRelease(PrepareReleaseMojo.java:211)
	... 30 more
channel stopped
Sending e-mails to: dev@davidsoergel.com
Finished: FAILURE