See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/1622/changes>
Changes: [scooter] Landing first part of reorganization of customgraphics implementation in preparation for exposing a custom graphics api. ------------------------------------------ [...truncated 24441 lines...] [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyTable' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyColumn' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyColumn' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/work/util/ListSingleSelection' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/work/util/ListSingleSelection' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/layout/CyLayoutAlgorithm' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/CyNetworkView' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/CyNetworkView' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/View' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/View' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/ToolBarComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/ToolBarComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/ToolBarComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/ToolBarComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelName' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CytoPanelComponent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/events/CytoPanelStateChangedEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/events/CytoPanelComponentSelectedEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/AbstractCyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CySwingApplication' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/AbstractCyAction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/work/AbstractTask' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CyHelpBroker' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/CySwingApplication' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/work/TunableValidator' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/work/TaskFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowsSetEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowsSetEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowsSetEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowSetRecord' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowSetRecord' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowSetRecord' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CySubNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CyRootNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CyRootNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/CyNetworkViewManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CySubNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CyRootNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/subnetwork/CySubNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetworkManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/CyNetworkViewManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetwork' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyNetworkManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/view/model/CyNetworkViewManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/events/CytoPanelStateChangedEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/application/swing/events/CytoPanelStateChangedEvent' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/datasource/DataSource' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/datasource/DataSource' is not accessible through the ClassLoader. [INFO] Java bytecode scan done: 557 ms [INFO] Java Squid scan... [INFO] Java Squid scan done: 12 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 153 ms [INFO] Squid extraction done: 442 ms [INFO] Sensor SquidSensor done: 1743 ms [INFO] Sensor FindbugsSensor... [INFO] Execute Findbugs 1.3.9... [INFO] Found findbugs plugin: file:/tmp/sonar-batch62256160608677756933301918210527849/plugins/findbugs/META-INF/lib/findbugs-1.3.9.jar [INFO] Loaded plugin edu.umd.cs.findbugs.plugins.core [INFO] Findbugs output report: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/sonar/findbugs-result.xml> The following classes needed for analysis were missing: org.osgi.util.tracker.ServiceTracker [INFO] Execute Findbugs 1.3.9 done: 15488 ms [INFO] Sensor FindbugsSensor done: 15567 ms [INFO] Sensor SurefireSensor... [INFO] parsing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/surefire-reports> [INFO] Sensor SurefireSensor done: 0 ms [INFO] Sensor CpdSensor... [INFO] Sensor CpdSensor done: 163 ms [INFO] Sensor CheckstyleSensor... [INFO] Execute Checkstyle 5.1... [INFO] Checkstyle configuration: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/sonar/checkstyle.xml> [INFO] Execute Checkstyle 5.1 done: 2061 ms [INFO] Sensor CheckstyleSensor done: 2061 ms [INFO] Sensor PmdSensor... [INFO] Execute PMD 4.2.5... [INFO] Java version: 1.6 [INFO] PMD configuration: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/sonar/pmd.xml> [INFO] PMD output report: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/sonar/pmd-result.xml> [INFO] Execute PMD 4.2.5 done: 16483 ms [INFO] Sensor PmdSensor done: 16522 ms [INFO] Sensor ProfileSensor... [INFO] Sensor ProfileSensor done: 366 ms [INFO] Sensor ProfileEventsSensor... [INFO] Sensor ProfileEventsSensor done: 31 ms [INFO] Sensor ProjectLinksSensor... [INFO] Sensor ProjectLinksSensor done: 3 ms [INFO] Sensor VersionEventsSensor... [INFO] Sensor VersionEventsSensor done: 11 ms [INFO] Sensor CoberturaSensor... [INFO] parsing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/swing-application-impl/target/site/cobertura/coverage.xml> [INFO] Sensor CoberturaSensor done: 346 ms [INFO] Sensor Maven dependencies... [INFO] Sensor Maven dependencies done: 76 ms [INFO] Execute decorators... [INFO] ------------- Analyzing Cytoscape Table Browser Impl (table-browser-impl) [INFO] Selected quality profile : [name=Cytoscape,language=java] [INFO] Configure maven plugins... [INFO] Compare to previous analysis (2012-09-05) [INFO] Compare over 5 days (2012-09-01, analysis of 2012-09-01 20:23:38.0) [INFO] Compare over 30 days (2012-08-07, analysis of 2012-08-07 20:21:16.0) [INFO] Initializer FindbugsMavenInitializer... [INFO] Initializer FindbugsMavenInitializer done: 0 ms [INFO] Initializer MavenInitializer... [INFO] Java source version: 1.6 [INFO] Java target version: 1.6 [INFO] Source encoding: UTF-8 [INFO] Initializer MavenInitializer done: 0 ms [INFO] Execute maven plugin cobertura-maven-plugin... [INFO] Execute org.codehaus.mojo:cobertura-maven-plugin:2.5:cobertura... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Table Browser Impl (table-browser-impl) 3.0.0-alpha10-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] >>> cobertura-maven-plugin:2.5:cobertura (default-cli) @ table-browser-impl >>> [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ table-browser-impl --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 23 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ table-browser-impl --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- cobertura-maven-plugin:2.5:instrument (default-cli) @ table-browser-impl --- [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 87 files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/table-browser-impl/target/generated-classes/cobertura> [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class org.cytoscape.browser.internal.TableChooser$1. Perhaps you need to compile with debug=true? Cobertura: Saved information on 87 classes. Instrument time: 599ms [INFO] Instrumentation was successful. [INFO] NOT adding cobertura ser file to attached artifacts list. [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ table-browser-impl --- [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/table-browser-impl/src/test/resources> [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ table-browser-impl --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ table-browser-impl --- [INFO] Surefire report directory: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/table-browser-impl/target/surefire-reports> ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.cytoscape.browser.internal.BrowserTableTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 sec Flushing results... Flushing results done Cobertura: Loaded information on 87 classes. Cobertura: Saved information on 87 classes. Results : Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] <<< cobertura-maven-plugin:2.5:cobertura (default-cli) @ table-browser-impl <<< [INFO] [INFO] --- cobertura-maven-plugin:2.5:cobertura (default-cli) @ table-browser-impl --- [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 87 classes. Report time: 1462ms [INFO] Cobertura Report generation was successful. [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 22:12.451s [INFO] Finished at: Thu Sep 06 20:45:37 GMT-05:00 2012 [INFO] Final Memory: 76M/270M [INFO] ------------------------------------------------------------------------ [INFO] Execute org.codehaus.mojo:cobertura-maven-plugin:2.5:cobertura done: 7472 ms [INFO] Execute maven plugin cobertura-maven-plugin done: 7472 ms [INFO] Initializer CoberturaMavenInitializer... [INFO] Initializer CoberturaMavenInitializer done: 0 ms [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 237 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 246 ms [INFO] Java bytecode scan... [WARN] Class 'org/cytoscape/model/events/ColumnCreatedListener' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/ColumnDeletedListener' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/ColumnNameChangedListener' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowsSetListener' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/events/RowsCreatedListener' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyTable' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyColumn' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyColumn' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyTable' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyRow' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyTable' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/CyColumn' is not accessible through the ClassLoader. # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0xb761ee9f, pid=20250, tid=3066436464 # # 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+0x75e9f] unsigned long+0x2f # # An error report file with more information is saved as: # <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/hs_err_pid20250.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. # Sonar analysis completed: FAILURE Build step 'Sonar' changed build result to FAILURE Build step 'Sonar' marked build as failure -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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