See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/2185/changes>
Changes: [jm] References #1684: Updated license headers. Now we're using maven-license-plugin. Licenses of code we don't own haven't been updated. Changed Network Analyzer to use LGPL 2.1 instead of 3 since we have received permission from Mario Albrecht's group ------------------------------------------ [...truncated 10499 lines...] [INFO] META-INF/sun-jaxb.episode already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] images already added, skipping [INFO] images/Icons already added, skipping [INFO] images/logo.png already added, skipping [INFO] images/Icons/open_session.png already added, skipping [INFO] images/Icons/net_db_import_small.png already added, skipping [INFO] images/Icons/net_file_import_small.png already added, skipping [INFO] images/background.png already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org/cytoscape/internal already added, skipping [INFO] org/cytoscape/internal/CyActivator.java already added, skipping [INFO] org already added, skipping [INFO] org/cytoscape already added, skipping [INFO] org/cytoscape/cmdline already added, skipping [INFO] [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/pom.xml> to /opt/tomcat-home/.m2/repository/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-SNAPSHOT.pom [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ model-impl-parent --- [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/target/model-impl-parent-3.1.0-SNAPSHOT-sources.jar> to /opt/tomcat-home/.m2/repository/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-SNAPSHOT-sources.jar [INFO] Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml [INFO] --- maven-deploy-plugin:2.5:deploy (default-deploy) @ model-impl-parent --- Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml (824 B at 2.3 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-20130123.220604-91.pom Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-20130123.220604-91.pom (4 KB at 35.4 KB/sec) Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml (584 B at 12.7 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml (824 B at 7.5 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml (584 B at 10.6 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-20130123.220604-91-sources.jar Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-20130123.220604-91-sources.jar (42288 KB at 7513.8 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.1.0-SNAPSHOT/maven-metadata.xml (824 B at 9.1 KB/sec) [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$model-impl-parent/builds/2013-01-23_17-03-08/archive/org.cytoscape/model-impl-parent/3.1.0-SNAPSHOT/model-impl-parent-3.1.0-SNAPSHOT.pom [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/target/model-impl-parent-3.1.0-SNAPSHOT-sources.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$model-impl-parent/builds/2013-01-23_17-03-08/archive/org.cytoscape/model-impl-parent/3.1.0-20130123.220604-91/model-impl-parent-3.1.0-20130123.220604-91-sources.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Model Impl (model-impl) 3.1.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-api/3.1.0-SNAPSHOT/model-api-3.1.0-20130123.011152-52-tests.jar Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-api/3.1.0-SNAPSHOT/model-api-3.1.0-20130123.011152-52-tests.jar (75 KB at 470.0 KB/sec) [INFO] [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ model-impl --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ model-impl --- [INFO] Compiling 36 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/target/classes> [INFO] [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/resources> [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ model-impl --- [INFO] [INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ model-impl --- [INFO] Compiling 22 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/target/test-classes> [INFO] [INFO] Surefire report directory: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/target/surefire-reports> ------------------------------------------------------- T E S T S ------------------------------------------------------- [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ model-impl --- Running org.cytoscape.model.TestCyNetworkFactory Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.918 sec Running org.cytoscape.model.CyNetworkTableManagerTest Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.509 sec Running org.cytoscape.model.subnetwork.CyRootNetworkCyNetworkTest Tests run: 36, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.886 sec Running org.cytoscape.model.subnetwork.CySubNetworkCyTableManagerTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec Running org.cytoscape.model.subnetwork.CySubNetworkTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.375 sec Running org.cytoscape.model.subnetwork.CySubNetworkCyNetworkTest Tests run: 36, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.023 sec Running org.cytoscape.model.subnetwork.CyRootNetworkTest Tests run: 36, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.943 sec Running org.cytoscape.model.TableTestSupportTest # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0xb76a0dcf, pid=13413, tid=3066956656 # # JRE version: 6.0_32-b05 # Java VM: Java HotSpot(TM) Client VM (20.7-b02 mixed mode, sharing linux-x86 ) # Problematic frame: # C [libc.so.6+0x78dcf] unsigned long+0x2f # # An error report file with more information is saved as: # <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/hs_err_pid13413.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. # Aborted Results : Tests run: 161, Failures: 0, Errors: 0, Skipped: 0 [JENKINS] Recording test results [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$model-impl/builds/2013-01-23_17-03-08/archive/org.cytoscape/model-impl/3.1.0-SNAPSHOT/model-impl-3.1.0-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [1:25.607s] [INFO] Cytoscape BioPAX Impl (biopax-impl) ............... SUCCESS [12.863s] [INFO] Cytoscape Command Executor Impl (command-executor-impl) SUCCESS [5.847s] [INFO] Cytoscape Equations Impl (equations-impl) ......... SUCCESS [9.830s] [INFO] Cytoscape Model Impl Parent (model-impl-parent) ... SUCCESS [48.352s] [INFO] Cytoscape Model Impl (model-impl) ................. FAILURE [10.921s] [INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) SKIPPED [INFO] Cytoscape View Model Impl (viewmodel-impl) ........ SKIPPED [INFO] Cytoscape Ding Impl Parent (ding-impl) ............ SKIPPED [INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) SKIPPED [INFO] org.cytoscape.work-impl ........................... SKIPPED [INFO] Cytoscape Core Task Impl (core-task-impl) ......... SKIPPED [INFO] Cytoscape CPath2 Impl (cpath2-impl) ............... SKIPPED [INFO] Cytoscape Groups Impl (group-impl) ................ SKIPPED [INFO] Cytoscape IO Impl Parent (io-impl-parent) ......... SKIPPED [INFO] Cytoscape IO Impl (io-impl) ....................... SKIPPED [INFO] Cytoscape Event Impl Parent (event-impl-parent) ... SKIPPED [INFO] Cytoscape Event Impl (event-impl) ................. SKIPPED [INFO] Cytoscape Layout Impl (layout-impl) ............... SKIPPED [INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) SKIPPED [INFO] Cytoscape Editor Impl (editor-impl) ............... SKIPPED [INFO] Cytoscape Equation Functions Impl (equations-functions-impl) SKIPPED [INFO] Cytoscape Filters Impl (filter-impl) .............. SKIPPED [INFO] Cytoscape GraphML Impl (graphml-impl) ............. SKIPPED [INFO] Cytoscape Group Data Impl (group-data-impl) ....... SKIPPED [INFO] Cytoscape Group View Impl (group-view-impl) ....... SKIPPED [INFO] Cytoscape IO Impl Performance (io-impl-performance) SKIPPED [INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) SKIPPED [INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) . SKIPPED [INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl) SKIPPED [INFO] Cytoscape Linkout Impl (linkout-impl) ............. SKIPPED [INFO] Cytoscape Log Swing Impl (log-swing-impl) ......... SKIPPED [INFO] Cytoscape Manual Layout Impl (manual-layout-impl) . SKIPPED [INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) SKIPPED [INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) SKIPPED [INFO] Cytoscape NetworkAnalyzer Impl (network-analyzer-impl) SKIPPED [INFO] Cytoscape Merge Impl (network-merge-impl) ......... SKIPPED [INFO] Cytoscape App Impl (app-impl) ..................... SKIPPED [INFO] Cytoscape Presentation Impl (presentation-impl) ... SKIPPED [INFO] Cytoscape Property Impl (property-impl) ........... SKIPPED [INFO] Cytoscape PSI-MI Impl Parent (psi-mi-impl-parent) . SKIPPED [INFO] Cytoscape PSI-MI Impl (psi-mi-impl) ............... SKIPPED [INFO] Cytoscape PSI-MI Impl Performance (psi-mi-impl-performance) SKIPPED [INFO] Cytoscape SBML Impl (sbml-impl) ................... SKIPPED [INFO] Cytoscape Search Impl (search-impl) ............... SKIPPED [INFO] Cytoscape Session Impl Parent (session-impl-parent) SKIPPED [INFO] Cytoscape Session Impl (session-impl) ............. SKIPPED [INFO] Cytoscape Datasource Impl (datasource-impl) ....... SKIPPED [INFO] org.cytoscape.work-headless-impl .................. SKIPPED [INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) . SKIPPED [INFO] Cytoscape VizMap Impl (vizmap-impl) ............... SKIPPED [INFO] Cytoscape Application Impl (application-impl) ..... SKIPPED [INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) ....... SKIPPED [INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) SKIPPED [INFO] Cytoscape Work Swing Impl (work-swing-impl) ....... SKIPPED [INFO] Cytoscape Session Impl Integration Test (session-impl-integration-test) SKIPPED [INFO] Cytoscape Help Impl (help-impl) ................... SKIPPED [INFO] Cytoscape Swing Utility Impl (swing-util-impl) .... SKIPPED [INFO] Cytoscape Swing Application Impl (swing-application-impl) SKIPPED [INFO] Cytoscape Table Browser Impl (table-browser-impl) . SKIPPED [INFO] Cytoscape Table Import Impl (table-import-impl) ... SKIPPED [INFO] Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) SKIPPED [INFO] Cytoscape Biomart Webservice Impl (webservice-biomart-client-impl) SKIPPED [INFO] Cytoscape Webservice Impl (webservice-impl) ....... SKIPPED [INFO] Cytoscape PSIQUIC Web Service Impl (webservice-psicquic-client-impl) SKIPPED [INFO] Cytoscape BioGrid Datasource Impl (datasource-biogrid-impl) SKIPPED [INFO] Cytoscape Welcome Screen Impl (welcome-impl) ...... SKIPPED [INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) SKIPPED [INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) ... SKIPPED [INFO] Cytoscape Scripting Impl (scripting-impl) ......... SKIPPED [INFO] Cytoscape Headless Application Impl (headless-application-impl) SKIPPED [INFO] Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3:25.137s [INFO] Finished at: Wed Jan 23 17:06:37 GMT-05:00 2013 [INFO] Final Memory: 39M/220M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project model-impl: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test failed: The forked VM terminated without saying properly goodbye. VM crash or System.exit called ? cause : Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test failed: The forked VM terminated without saying properly goodbye. VM crash or System.exit called ? Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project model-impl: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test failed: The forked VM terminated without saying properly goodbye. VM crash or System.exit called ? at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:225) 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:319) 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:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) 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:112) at hudson.maven.Maven3Builder.call(Maven3Builder.java:70) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:287) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) Caused by: org.apache.maven.plugin.PluginExecutionException: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test failed: The forked VM terminated without saying properly goodbye. VM crash or System.exit called ? at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:110) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Caused by: java.lang.RuntimeException: The forked VM terminated without saying properly goodbye. VM crash or System.exit called ? at org.apache.maven.plugin.surefire.booterclient.output.ForkClient.close(ForkClient.java:257) at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:301) at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:116) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:740) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAllProviders(AbstractSurefireMojo.java:682) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:648) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:586) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) ... 28 more Sending e-mails to: [email protected] channel stopped Skipping sonar analysis due to bad build status FAILURE -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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