See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/472/changes>
Changes: [rozagh] fixes #637 Listener handlers for NetworkDestroy and NetworkViewDestroy events are implemented in the undoMonitor class which discard the edits when the last view or the last network is destroyed. The SetCurrentNetworkView listener handles the other situations where the undo stack needs to be cleaned out. [mes] added unit tests that validate network event firing ------------------------------------------ [...truncated 4097 lines...] [INFO] org.cytoscape.ding-customgraphics-manager-impl [INFO] io-impl-parent [INFO] org.cytoscape.io-impl [org.cytoscape.io.internal] [INFO] event-impl-parent [INFO] org.cytoscape.event-impl [INFO] org.cytoscape.layout-impl [INFO] org.cytoscape.ding-impl-performance-debug [INFO] org.cytoscape.editor-impl [INFO] org.cytoscape.equations-functions-impl [INFO] org.cytoscape.event-impl-it [INFO] org.cytoscape.filter-impl [org.cytoscape.filter.internal] [INFO] GraphML Reader and Writer for Cytoscape 3 [INFO] org.cytoscape.group-impl [org.cytoscape.group.internal] [INFO] org.cytoscape.group-view-impl [org.cytoscape.group.view.internal] [INFO] org.cytoscape.io-impl-performance [INFO] org.cytoscape.layout-cytoscape-impl [csapps.layout] [INFO] org.cytoscape.layout-jgraph-impl [csapps.layout] [INFO] org.cytoscape.layout-prefuse-impl [org.cytoscape.prefuse.layouts.internal] [INFO] org.cytoscape.linkout-impl [org.cytoscape.linkout.internal] [INFO] org.cytoscape.log-swing-impl [org.cytoscape.log.internal] [INFO] Manual Layout [INFO] NetworkAnalyzer [INFO] Advanced Network Merge [INFO] org.cytoscape.app-impl [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation.internal] [INFO] org.cytoscape.property.internal [INFO] psi-mi-impl-parent [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi.internal] [INFO] org.cytoscape.psi-mi-impl-performance [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml.internal] [INFO] org.cytoscape.search-impl [org.cytoscape.search.internal] [INFO] org.cytoscape.session-impl [INFO] Cytoscape Swing Application Impl [INFO] Cytoscape Table Browser Implementation [INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport.internal] [INFO] org.cytoscape.vizmap-gui-impl [INFO] vizmap-impl-parent [INFO] org.cytoscape.view.vizmap-impl [INFO] org.cytoscape.io.webservice-biomart-client-impl [org.cytoscape.io.webservice.biomart] [INFO] org.cytoscape.webservice-impl [org.cytoscape.webservice.internal] [INFO] org.cytoscape.webservice-ncbi-client-impl [org.cytoscape.webservice.ncbi] [INFO] work-swing-impl-parent [INFO] org.cytoscape.work-swing-impl [INFO] org.cytoscape.application-impl [INFO] org.cytoscape.webservice-psicquic-client-impl [org.cytoscape.webservice.psicquic] [INFO] datasource-impl [INFO] datasource-biogrid-impl [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Implementation Parent Project POM 3.0.0-alpha8-SNAPSHOT [INFO] ------------------------------------------------------------------------ ignoring exception during new ExecutedMojo null log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. [INFO] [INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ impl-parent --- [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ impl-parent --- [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> to /opt/tomcat-home/.m2/repository/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-SNAPSHOT.pom [INFO] [INFO] --- maven-deploy-plugin:2.5:deploy (default-deploy) @ impl-parent --- Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 6.0 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20120216.200446-613.pom Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20120216.200446-613.pom (11 KB at 90.2 KB/sec) Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (405 B at 14.1 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 6.2 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (405 B at 4.3 KB/sec) [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$impl-parent/builds/2012-02-16_15-04-35/archive/org.cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-SNAPSHOT.pom [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.biopax-impl [org.cytoscape.biopax] 3.0.0-alpha8-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/biopax-snapshot/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://maven.itextpdf.com/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-release/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-milestone/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (2 KB at 6.8 KB/sec) Downloading: http://www.ebi.ac.uk/~maven/m2repo_snapshots/org/cytoscape/swing-application-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/biopax-snapshot/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://maven.itextpdf.com/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-release/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-milestone/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://www.ebi.ac.uk/~maven/m2repo_snapshots/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/swing-util-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (2 KB at 9.8 KB/sec) Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/biopax-snapshot/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/spring-osgi-external/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://maven.itextpdf.com/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (1 KB at 12.2 KB/sec) Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-release/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://code.cytoscape.org/nexus/content/repositories/zodiac-milestone/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloading: http://www.ebi.ac.uk/~maven/m2repo_snapshots/org/cytoscape/service-api/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ biopax-impl --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 12 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ biopax-impl --- [INFO] Compiling 28 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/target/classes> [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java>:[15,-1] cannot access org.cytoscape.application.swing.CySwingApplication bad class file: org/cytoscape/application/swing/CySwingApplication.class(org/cytoscape/application/swing:CySwingApplication.class) unable to access file: corrupted zip file [INFO] 1 error [INFO] ------------------------------------------------------------- [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$biopax-impl/builds/2012-02-16_15-04-35/archive/org.cytoscape/biopax-impl/3.0.0-alpha8-SNAPSHOT/biopax-impl-3.0.0-alpha8-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [4.564s] [INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] .. FAILURE [4.871s] [INFO] Command Executor .................................. SKIPPED [INFO] org.cytoscape.equations-impl ...................... SKIPPED [INFO] model-impl-parent ................................. SKIPPED [INFO] org.cytoscape.model-impl .......................... SKIPPED [INFO] viewmodel-impl-parent ............................. SKIPPED [INFO] org.cytoscape.viewmodel-impl ...................... SKIPPED [INFO] Ding Implementation Parent Pom .................... SKIPPED [INFO] org.cytoscape.util-intr ........................... SKIPPED [INFO] org.cytoscape.spacial ............................. SKIPPED [INFO] org.cytoscape.graph-render ........................ SKIPPED [INFO] org.cytoscape.ding-presentation-impl .............. SKIPPED [INFO] org.cytoscape.core-task-impl ...................... SKIPPED [INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] .. SKIPPED [INFO] org.cytoscape.ding-customgraphics-manager-impl .... SKIPPED [INFO] io-impl-parent .................................... SKIPPED [INFO] org.cytoscape.io-impl [org.cytoscape.io.internal] . SKIPPED [INFO] event-impl-parent ................................. SKIPPED [INFO] org.cytoscape.event-impl .......................... SKIPPED [INFO] org.cytoscape.layout-impl ......................... SKIPPED [INFO] org.cytoscape.ding-impl-performance-debug ......... SKIPPED [INFO] org.cytoscape.editor-impl ......................... SKIPPED [INFO] org.cytoscape.equations-functions-impl ............ SKIPPED [INFO] org.cytoscape.event-impl-it ....................... SKIPPED [INFO] org.cytoscape.filter-impl [org.cytoscape.filter.internal] SKIPPED [INFO] GraphML Reader and Writer for Cytoscape 3 ......... SKIPPED [INFO] org.cytoscape.group-impl [org.cytoscape.group.internal] SKIPPED [INFO] org.cytoscape.group-view-impl [org.cytoscape.group.view.internal] SKIPPED [INFO] org.cytoscape.io-impl-performance ................. SKIPPED [INFO] org.cytoscape.layout-cytoscape-impl [csapps.layout] SKIPPED [INFO] org.cytoscape.layout-jgraph-impl [csapps.layout] .. SKIPPED [INFO] org.cytoscape.layout-prefuse-impl [org.cytoscape.prefuse.layouts.internal] SKIPPED [INFO] org.cytoscape.linkout-impl [org.cytoscape.linkout.internal] SKIPPED [INFO] org.cytoscape.log-swing-impl [org.cytoscape.log.internal] SKIPPED [INFO] Manual Layout ..................................... SKIPPED [INFO] NetworkAnalyzer ................................... SKIPPED [INFO] Advanced Network Merge ............................ SKIPPED [INFO] org.cytoscape.app-impl ............................ SKIPPED [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation.internal] SKIPPED [INFO] org.cytoscape.property.internal ................... SKIPPED [INFO] psi-mi-impl-parent ................................ SKIPPED [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi.internal] SKIPPED [INFO] org.cytoscape.psi-mi-impl-performance ............. SKIPPED [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml.internal] SKIPPED [INFO] org.cytoscape.search-impl [org.cytoscape.search.internal] SKIPPED [INFO] org.cytoscape.session-impl ........................ SKIPPED [INFO] Cytoscape Swing Application Impl .................. SKIPPED [INFO] Cytoscape Table Browser Implementation ............ SKIPPED [INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport.internal] SKIPPED [INFO] org.cytoscape.vizmap-gui-impl ..................... SKIPPED [INFO] vizmap-impl-parent ................................ SKIPPED [INFO] org.cytoscape.view.vizmap-impl .................... SKIPPED [INFO] org.cytoscape.io.webservice-biomart-client-impl [org.cytoscape.io.webservice.biomart] SKIPPED [INFO] org.cytoscape.webservice-impl [org.cytoscape.webservice.internal] SKIPPED [INFO] org.cytoscape.webservice-ncbi-client-impl [org.cytoscape.webservice.ncbi] SKIPPED [INFO] work-swing-impl-parent ............................ SKIPPED [INFO] org.cytoscape.work-swing-impl ..................... SKIPPED [INFO] org.cytoscape.application-impl .................... SKIPPED [INFO] org.cytoscape.webservice-psicquic-client-impl [org.cytoscape.webservice.psicquic] SKIPPED [INFO] datasource-impl ................................... SKIPPED [INFO] datasource-biogrid-impl ........................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12.497s [INFO] Finished at: Thu Feb 16 15:04:52 GMT-05:00 2012 [INFO] Final Memory: 20M/47M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project biopax-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java>:[15,-1] cannot access org.cytoscape.application.swing.CySwingApplication bad class file: org/cytoscape/application/swing/CySwingApplication.class(org/cytoscape/application/swing:CySwingApplication.class) unable to access file: corrupted zip file cause : Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java>:[15,-1] cannot access org.cytoscape.application.swing.CySwingApplication bad class file: org/cytoscape/application/swing/CySwingApplication.class(org/cytoscape/application/swing:CySwingApplication.class) unable to access file: corrupted zip file Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project biopax-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java>:[15,-1] cannot access org.cytoscape.application.swing.CySwingApplication bad class file: org/cytoscape/application/swing/CySwingApplication.class(org/cytoscape/application/swing:CySwingApplication.class) unable to access file: corrupted zip file 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: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:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) 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:471) 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:636) Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java>:[15,-1] cannot access org.cytoscape.application.swing.CySwingApplication bad class file: org/cytoscape/application/swing/CySwingApplication.class(org/cytoscape/application/swing:CySwingApplication.class) unable to access file: corrupted zip file at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:656) at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:128) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Sending e-mails to: [email protected] channel stopped -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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