See <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/171/changes>
Changes: [kono] To avoid crash, an exception handler had been added. ------------------------------------------ [...truncated 23718 lines...] [INFO] Instrumentation was successful. [INFO] [resources:testResources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/src/test/resources> [INFO] [compiler:testCompile] [INFO] Nothing to compile - all classes are up to date [INFO] [surefire:test] [INFO] Surefire report directory: <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/surefire-reports> ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.cytoscape.coreplugin.cpath.test.protocol.TestCPathProtocol Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.401 sec Running org.cytoscape.coreplugin.cpath.test.task.TestCPathTimeEstimator Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Results : Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 26 classes. Report time: 484ms [INFO] Cobertura Report generation was successful. [INFO] Execute maven plugin cobertura-maven-plugin done: 7826 ms [INFO] Sensor CoberturaSensor... [INFO] parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/site/cobertura/coverage.xml> [INFO] Sensor CoberturaSensor done: 77 ms [INFO] Sensor CpdSensor... [INFO] Sensor CpdSensor done: 25 ms [INFO] Execute maven plugin taglist-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building cPath [INFO] task-segment: [org.codehaus.mojo:taglist-maven-plugin:2.4:taglist] [INFO] ------------------------------------------------------------------------ [WARNING] DEPRECATED [tags]: No reason given [INFO] [taglist:taglist] [WARNING] Using legacy tag format. This is not recommended. [INFO] Execute maven plugin taglist-maven-plugin done: 1375 ms [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@481dbd8b... [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@481dbd8b done: 12 ms [INFO] Sensor SurefireSensor... [INFO] parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/surefire-reports> [INFO] Sensor SurefireSensor done: 41 ms [INFO] Execute decorators... [INFO] ------------- Analyzing cPath2 [INFO] Selected quality profile : Cytoscape, language=java [INFO] Configure maven plugins... [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 241 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 0 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 326 ms [INFO] Java bytecode scan... [INFO] Java bytecode scan done: 169 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 41 ms [INFO] Squid extraction done: 448 ms [INFO] Sensor SquidSensor done: 988 ms [INFO] Sensor ProfileSensor... [INFO] Sensor ProfileSensor done: 25 ms [INFO] Sensor ProjectLinksSensor... [INFO] Sensor ProjectLinksSensor done: 2 ms [INFO] Sensor VersionEventsSensor... [INFO] Sensor VersionEventsSensor done: 23 ms [INFO] Sensor Maven dependencies... [INFO] Sensor Maven dependencies done: 75 ms [INFO] Execute maven plugin findbugs-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building cPath2 [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:2.3.1:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [jaxb2:generate {execution: SearchResponse}] [INFO] Started execution. [INFO] JAXB API is loaded from the [jar:file:/R1/tools/java/jdk1.6.0_20/jre/lib/rt.jar!]. [INFO] Detected JAXB API version [2.1]. 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Using java.util.ServiceLoader [INFO] Parsing input schema(s)... [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc].> [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/BasicRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/DataSourceType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ErrorType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ExtendedRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ObjectFactory.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/OrganismType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/PathwayListType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/PathwayType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/SearchResponseType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/XRefType.java [INFO] Finished execution. [INFO] [jaxb2:generate {execution: SummaryResponse}] [INFO] Started execution. [INFO] JAXB API is loaded from the [jar:file:/R1/tools/java/jdk1.6.0_20/jre/lib/rt.jar!]. [INFO] Detected JAXB API version [2.1]. 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/home/bturner/.m2/repository/cytoscape/corelibs/phoebe-dnd/2.8.0-beta3-SNAPSHOT/phoebe-dnd-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/geom-rtree/2.8.0-beta3-SNAPSHOT/geom-rtree-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/undo-support/2.8.0-beta3-SNAPSHOT/undo-support-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/equations/2.8.0-beta3-SNAPSHOT/equations-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/task/2.8.0-beta3-SNAPSHOT/task-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/ding/2.8.0-beta3-SNAPSHOT/ding-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/obo/2.8.0-beta3-SNAPSHOT/obo-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/cytoscape/corelibs/commons-cli-1-x-cytocape-custom/2.8.0-beta3-SNAPSHOT/commons-cli-1-x-cytocape-custom-2.8.0-beta3-SNAPSHOT.jar, /home/bturner/.m2/repository/commons-lang/commons-lang/2.4/commons-lang-2.4.jar, /home/bturner/.m2/repository/org/cytoscape/wrappers/com.l2fprod.common.sheet/7.3/com.l2fprod.common.sheet-7.3.jar, /home/bturner/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/0.9.7/org.swinglabs.swingx-0.9.7.jar, /home/bturner/.m2/repository/org/cytoscape/wrappers/com.l2fprod.common.shared/7.3/com.l2fprod.common.shared-7.3.jar, /home/bturner/.m2/repository/org/cytoscape/wrappers/com.l2fprod.common.fontchooser/7.3/com.l2fprod.common.fontchooser-7.3.jar, /home/bturner/.m2/repository/javax/help/javahelp/2.0.02/javahelp-2.0.02.jar, /home/bturner/.m2/repository/com/lowagie/itext/2.0.8/itext-2.0.8.jar, /home/bturner/.m2/repository/bouncycastle/bcmail-jdk14/138/bcmail-jdk14-138.jar, /home/bturner/.m2/repository/bouncycastle/bcprov-jdk14/138/bcprov-jdk14-138.jar, /home/bturner/.m2/repository/colt/colt/1.2.0/colt-1.2.0.jar, /home/bturner/.m2/repository/concurrent/concurrent/1.3.4/concurrent-1.3.4.jar, /home/bturner/.m2/repository/cytoscape-temp/biojava/1.4/biojava-1.4.jar, /home/bturner/.m2/repository/org/jdom/jdom/1.1/jdom-1.1.jar, /home/bturner/.m2/repository/org/swinglabs/swing-layout/1.0.3/swing-layout-1.0.3.jar, /home/bturner/.m2/repository/com/jgoodies/looks/2.1.4/looks-2.1.4.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-export/2.1.1/freehep-export-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-graphics2d/2.1.1/freehep-graphics2d-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-graphicsio/2.1.1/freehep-graphicsio-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-graphicsio-ps/2.1.1/freehep-graphicsio-ps-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-graphicsio-svg/2.1.1/freehep-graphicsio-svg-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-graphicsio-java/2.1.1/freehep-graphicsio-java-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-io/2.0.2/freehep-io-2.0.2.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-swing/2.0.3/freehep-swing-2.0.3.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-util/2.0.2/freehep-util-2.0.2.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-xml/2.1.1/freehep-xml-2.1.1.jar, /home/bturner/.m2/repository/cytoscape-temp/freehep-jas-plotter/2.2/freehep-jas-plotter-2.2.jar, /home/bturner/.m2/repository/org/apache/lucene/lucene-core/3.0.1/lucene-core-3.0.1.jar, /home/bturner/.m2/repository/cytoscape-temp/tclib/1.0/tclib-1.0.jar, /home/bturner/.m2/repository/cytoscape-temp/violinstrings/1.0.2/violinstrings-1.0.2.jar, /home/bturner/.m2/repository/cytoscape-temp/install4j/4.0/install4j-4.0.jar, /home/bturner/.m2/repository/cytoscape-sun/jaxb-api/1.0/jaxb-api-1.0.jar, /home/bturner/.m2/repository/cytoscape-sun/jaxb-impl/1.0/jaxb-impl-1.0.jar] [INFO] plugins:null [INFO] episodes:null [INFO] xjcPlugins:null [INFO] episodes:null [INFO] specVersion:2.1 [INFO] schemaFiles (calculated):[<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd/SummaryResponse.xsd]> [INFO] bindingFiles (calculated):[] [INFO] xjcPluginArtifacts (resolved):[] [INFO] xjcPluginFiles (resolved):[] [INFO] xjcPluginURLs (resolved):[] [INFO] episodeArtifacts (resolved):[] [INFO] episodeFiles (resolved):[] [INFO] The schemaLanguage setting was not defined, assuming 'AUTODETECT'. Using java.util.ServiceLoader [INFO] Parsing input schema(s)... [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc].> [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/BasicRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/DataSourceType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ErrorType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ExtendedRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ObjectFactory.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/OrganismType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/PathwayListType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/PathwayType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/SummaryResponseType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/XRefType.java [INFO] Finished execution. [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 12 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [compiler:compile] [INFO] Compiling 20 source files to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/classes> [INFO] ------------------------------------------------------------------------ [ERROR] FATAL ERROR [INFO] ------------------------------------------------------------------------ [INFO] PermGen space [INFO] ------------------------------------------------------------------------ [INFO] Trace java.lang.OutOfMemoryError: PermGen space at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632) at java.lang.ClassLoader.defineClass(ClassLoader.java:616) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141) at java.net.URLClassLoader.defineClass(URLClassLoader.java:283) at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at org.codehaus.classworlds.RealmClassLoader.loadClassDirect(RealmClassLoader.java:195) at org.codehaus.classworlds.DefaultClassRealm.loadClass(DefaultClassRealm.java:255) at org.codehaus.classworlds.RealmClassLoader.loadClass(RealmClassLoader.java:214) at java.lang.ClassLoader.loadClass(ClassLoader.java:248) at org.apache.maven.execution.ReactorManager.registerBuildFailure(ReactorManager.java:188) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.handleExecutionFailure(DefaultLifecycleExecutor.java:396) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:377) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:332) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:181) at org.sonar.maven2.Maven2PluginExecutor.execute(Maven2PluginExecutor.java:65) at org.sonar.maven2.Maven2PluginExecutor.execute(Maven2PluginExecutor.java:47) at org.sonar.batch.SensorsExecutor.executeMavenPlugin(SensorsExecutor.java:69) at org.sonar.batch.SensorsExecutor.execute(SensorsExecutor.java:55) at org.sonar.batch.ProjectBatch.execute(ProjectBatch.java:53) at org.sonar.batch.Batch.analyzeProject(Batch.java:112) at org.sonar.batch.Batch.analyzeProject(Batch.java:109) at org.sonar.batch.Batch.analyzeProject(Batch.java:109) at org.sonar.batch.Batch.analyzeProjects(Batch.java:81) at org.sonar.batch.Batch.execute(Batch.java:57) at org.sonar.maven2.BatchMojo.executeBatch(BatchMojo.java:142) at org.sonar.maven2.BatchMojo.execute(BatchMojo.java:133) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:483) [INFO] ------------------------------------------------------------------------ [INFO] Total time: 18 minutes 52 seconds [INFO] Finished at: Tue Nov 02 02:48:46 EDT 2010 [INFO] Final Memory: 125M/1784M [INFO] ------------------------------------------------------------------------ -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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