See <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/169/>
------------------------------------------ [...truncated 23542 lines...] [INFO] Sensor FindbugsSensor done: 41 ms [INFO] Sensor CheckstyleSensor... [INFO] Execute Checkstyle 5.1... [INFO] Checkstyle output report: <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/sonar/checkstyle-result.xml> [INFO] Checkstyle configuration: <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/sonar/checkstyle.xml> [INFO] Execute Checkstyle 5.1 done: 307 ms [INFO] Sensor CheckstyleSensor done: 365 ms [INFO] Sensor PmdSensor... [INFO] Execute PMD 4.2.5... [INFO] Java version: 1.6 [INFO] PMD configuration: <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/sonar/pmd.xml> [INFO] PMD output report: <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/sonar/pmd-result.xml> [INFO] Execute PMD 4.2.5 done: 867 ms [INFO] Sensor PmdSensor done: 905 ms [INFO] Execute maven plugin cobertura-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building cPath [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin:2.4:cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Preparing cobertura:cobertura [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [cobertura:instrument] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 26 files to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath/target/generated-classes/cobertura> Cobertura: Saved information on 26 classes. Instrument time: 667ms [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: 5.581 sec Running org.cytoscape.coreplugin.cpath.test.task.TestCPathTimeEstimator Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 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: 531ms [INFO] Cobertura Report generation was successful. [INFO] Execute maven plugin cobertura-maven-plugin done: 8203 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: 72 ms [INFO] Sensor CpdSensor... [INFO] Sensor CpdSensor done: 24 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: 939 ms [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@e21581d... [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@e21581d done: 9 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: 31 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: 184 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 0 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 213 ms [INFO] Java bytecode scan... [INFO] Java bytecode scan done: 123 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 27 ms [INFO] Squid extraction done: 459 ms [INFO] Sensor SquidSensor done: 838 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: 58 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]. [INFO] pluginArtifacts:[org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.3:runtime, org.codehaus.plexus:plexus-utils:jar:1.1:runtime, org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1:runtime, com.sun.xml.bind:jaxb-impl:jar:2.1.12:runtime, javax.xml.bind:jaxb-api:jar:2.1:runtime, javax.xml.stream:stax-api:jar:1.0-2:runtime, javax.activation:activation:jar:1.1:runtime, org.jvnet.jaxb2_commons:jaxb2-basics-jaxb-xjc:jar:2.1.12:runtime, com.sun.codemodel:codemodel:jar:2.2:runtime, com.sun.xml.dtd-parser:dtd-parser:jar:1.0:runtime, com.sun.istack:istack-commons-tools:jar:1.1:runtime, relaxngDatatype:relaxngDatatype:jar:20020414:runtime, com.sun.org.apache.xml.internal:resolver:jar:20050927:runtime, org.kohsuke.rngom:rngom:jar:20061207:runtime, com.sun.xsom:xsom:jar:20081112:runtime] [INFO] schemaLanguage:null [INFO] schemaDirectory:<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd> [INFO] schemaIncludes:[Ljava.lang.String;@26ae1613 [INFO] schemaExcludes:null [INFO] bindingDirectory:<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd> [INFO] bindingIncludes:[Ljava.lang.String;@6f2b4d3b [INFO] bindingExcludes:null [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:com.sun.org.apache.xml.internal.resolver.tools.CatalogResolver [INFO] generatePackage:org.cytoscape.coreplugin.cpath2.schemas.search_response [INFO] generateDirectory:<http://cytoscape.wodaklab.org/hudson/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc> [INFO] readOnly:false [INFO] extension:false [INFO] strict:true [INFO] writeCode:true [INFO] verbose:true [INFO] debug:false [INFO] args:[] [INFO] forceRegenerate:true [INFO] removeOldOutput:false [INFO] otherDepends:null [INFO] 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/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 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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] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Can not execute Sonar Embedded error: PicoLifecycleException: method 'public void org.sonar.api.database.AbstractDatabaseConnector.stop()', instance 'org.sonar.api.database.driverdatabaseconnec...@3b4f6d5f, java.lang.RuntimeException: wrapper PermGen space [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 18 minutes 45 seconds [INFO] Finished at: Mon Nov 01 17:12:39 EDT 2010 [INFO] Final Memory: 127M/1850M [INFO] ------------------------------------------------------------------------ -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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