See <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/17/>
------------------------------------------ [...truncated 3161 lines...] [INFO] [findbugs:findbugs] [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using FindBugs Version: 1.3.2 [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Using the xdoc format [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Debugging is Off [INFO] Using bug include filter <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/AutomaticLayout/target/sonar/findbugs-include.xml> [INFO] No bug exclude filter. [INFO] Printing Errors [INFO] Printing Missing classes [INFO] Printing Source Roots [INFO] Automatic Layout Executing org.apache.maven.plugins:maven-checkstyle-plugin:[checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] Building Automatic Layout [INFO] task-segment: [org.apache.maven.plugins:maven-checkstyle-plugin:2.2:checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] [checkstyle:checkstyle] [INFO] There are 677 checkstyle errors. [INFO] Automatic Layout Executing org.apache.maven.plugins:maven-pmd-plugin:[pmd] [INFO] ------------------------------------------------------------------------ [INFO] Building Automatic Layout [INFO] task-segment: [org.apache.maven.plugins:maven-pmd-plugin:2.4:pmd] [INFO] ------------------------------------------------------------------------ [INFO] [pmd:pmd] [INFO] Automatic Layout Executing org.codehaus.mojo:javancss-maven-plugin:[report] [INFO] ------------------------------------------------------------------------ [INFO] Building Automatic Layout [INFO] task-segment: [org.codehaus.mojo:javancss-maven-plugin:2.0-beta-2:report] [INFO] ------------------------------------------------------------------------ [INFO] [javancss:report] [INFO] Automatic Layout Executing org.codehaus.mojo:cobertura-maven-plugin:[cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Building Automatic Layout [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin:2.2: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 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 188 files to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/AutomaticLayout/target/generated-classes/cobertura> [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class csplugins.layout.algorithms.graphPartition.AttributeCircleLayout$1. Perhaps you need to compile with debug=true? [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class org.jgraph.plaf.basic.BasicGraphUI$1. Perhaps you need to compile with debug=true? [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class org.jgraph.layout.MoenLayoutAlgorithm$1. Perhaps you need to compile with debug=true? Cobertura: Saved information on 188 classes. Instrument time: 7255ms [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%202.X%20coreplugins/ws/trunk/AutomaticLayout/src/test/resources> [INFO] [compiler:testCompile] [INFO] No sources to compile [INFO] [surefire:test] [INFO] No tests to run. [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 188 classes. Report time: 3027ms [INFO] Cobertura Report generation was successful. [INFO] Automatic Layout Executing org.apache.maven.plugins:maven-surefire-plugin:[] [INFO] Automatic Layout [class org.sonar.plugins.findbugs.FindbugsMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.cpd.CpdMavenCollector] executing [INFO] Automatic Layout Collecting duplications... [INFO] Automatic Layout File suffixes : java [INFO] Automatic Layout Exclusions : {} [INFO] Automatic Layout [class org.sonar.plugins.checkstyle.CheckstyleMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.pmd.PmdMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.core.SaveProfileMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.core.sources.ImportJavaSourcesMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.core.SaveProjectLinksFromPom] executing [INFO] Automatic Layout [class org.sonar.plugins.javancss.JavaNcssMavenCollector] executing [INFO] Automatic Layout [class org.sonar.plugins.cobertura.CoberturaMavenCollector] executing [INFO] Automatic Layout parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/AutomaticLayout/target/site/cobertura/coverage.xml> [INFO] Automatic Layout [class org.sonar.plugins.surefire.SurefireMavenCollector] executing [INFO] Automatic Layout parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/AutomaticLayout/target/surefire-reports> [INFO] BioMart Client Selected quality profile : Cytoscape, language=java [INFO] BioMart Client Executing org.codehaus.mojo:findbugs-maven-plugin:[findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Building BioMart Client [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:1.2:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [findbugs:findbugs] [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using FindBugs Version: 1.3.2 [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Using the xdoc format [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Debugging is Off [INFO] Using bug include filter <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioMartClient/target/sonar/findbugs-include.xml> [INFO] No bug exclude filter. [INFO] Printing Errors [INFO] Printing Missing classes [INFO] Printing Source Roots [INFO] BioMart Client Executing org.apache.maven.plugins:maven-checkstyle-plugin:[checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] Building BioMart Client [INFO] task-segment: [org.apache.maven.plugins:maven-checkstyle-plugin:2.2:checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] [checkstyle:checkstyle] [INFO] There are 15 checkstyle errors. [INFO] BioMart Client Executing org.apache.maven.plugins:maven-pmd-plugin:[pmd] [INFO] ------------------------------------------------------------------------ [INFO] Building BioMart Client [INFO] task-segment: [org.apache.maven.plugins:maven-pmd-plugin:2.4:pmd] [INFO] ------------------------------------------------------------------------ [INFO] [pmd:pmd] [INFO] BioMart Client Executing org.codehaus.mojo:javancss-maven-plugin:[report] [INFO] ------------------------------------------------------------------------ [INFO] Building BioMart Client [INFO] task-segment: [org.codehaus.mojo:javancss-maven-plugin:2.0-beta-2:report] [INFO] ------------------------------------------------------------------------ [INFO] [javancss:report] [INFO] BioMart Client Executing org.codehaus.mojo:cobertura-maven-plugin:[cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Building BioMart Client [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin:2.2:cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Preparing cobertura:cobertura [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [cobertura:instrument] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 17 files to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioMartClient/target/generated-classes/cobertura> [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class edu.ucsd.bioeng.idekerlab.biomartclient.ui.BiomartMainDialog$1. Perhaps you need to compile with debug=true? Cobertura: Saved information on 17 classes. Instrument time: 451ms [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%202.X%20coreplugins/ws/trunk/BioMartClient/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%202.X%20coreplugins/ws/trunk/BioMartClient/target/surefire-reports> ------------------------------------------------------- T E S T S ------------------------------------------------------- Running edu.ucsd.bioeng.idekerlab.biomartclient.tests.QueryBuilderUtilTest Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.276 sec <<< FAILURE! Running edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 0.032 sec <<< FAILURE! Running edu.ucsd.bioeng.idekerlab.biomartclient.tests.XMLQueryBuilderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Results : Tests in error: testGetAllAliases(edu.ucsd.bioeng.idekerlab.biomartclient.tests.QueryBuilderUtilTest) testGetRegistry(edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest) testGetAvailableDatasets(edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest) testGetAvailableAttributes(edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest) testGetAllGOAnnotations(edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest) testSendQuery(edu.ucsd.bioeng.idekerlab.biomartclient.tests.BiomartStubTest) Tests run: 7, Failures: 0, Errors: 6, Skipped: 0 [ERROR] There are test failures. Please refer to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioMartClient/target/surefire-reports> for the individual test results. [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 17 classes. Report time: 582ms [INFO] Cobertura Report generation was successful. [INFO] BioMart Client Executing org.apache.maven.plugins:maven-surefire-plugin:[] [INFO] BioMart Client [class org.sonar.plugins.findbugs.FindbugsMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.cpd.CpdMavenCollector] executing [INFO] BioMart Client Collecting duplications... [INFO] BioMart Client File suffixes : java [INFO] BioMart Client Exclusions : {} [INFO] BioMart Client [class org.sonar.plugins.checkstyle.CheckstyleMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.pmd.PmdMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.core.SaveProfileMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.core.sources.ImportJavaSourcesMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.core.SaveProjectLinksFromPom] executing [INFO] BioMart Client [class org.sonar.plugins.javancss.JavaNcssMavenCollector] executing [INFO] BioMart Client [class org.sonar.plugins.cobertura.CoberturaMavenCollector] executing [INFO] BioMart Client parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioMartClient/target/site/cobertura/coverage.xml> [INFO] BioMart Client [class org.sonar.plugins.surefire.SurefireMavenCollector] executing [INFO] BioMart Client parsing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioMartClient/target/surefire-reports> [INFO] BioPAX Selected quality profile : Cytoscape, language=java [INFO] BioPAX Executing org.codehaus.mojo:findbugs-maven-plugin:[findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Building BioPAX [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:1.2:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 16 resources [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [findbugs:findbugs] [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using FindBugs Version: 1.3.2 [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Using the xdoc format [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Debugging is Off [INFO] Using bug include filter <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/BioPAX/target/sonar/findbugs-include.xml> [INFO] No bug exclude filter. # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f151da5defa, pid=4287, tid=139728654284560 # # JRE version: 6.0_20-b02 # Java VM: Java HotSpot(TM) 64-Bit Server VM (16.3-b01 mixed mode linux-amd64 ) # Problematic frame: # C [libc.so.6+0x86efa] memcpy+0x29a # # An error report file with more information is saved as: # <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/hs_err_pid4287.log> # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug. # -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
