See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/1469/changes>
Changes: [mes] added better support for groups/metanodes based on mini retreat discussion ------------------------------------------ [...truncated 3 lines...] A impl/osgi.bnd A impl/src A impl/src/test A impl/src/test/java A impl/src/test/java/org A impl/src/test/java/org/cytoscape A impl/src/test/java/org/cytoscape/model A impl/src/test/java/org/cytoscape/model/IdentifiableTest.java A impl/src/test/java/org/cytoscape/model/CyEdgeTest.java A impl/src/test/java/org/cytoscape/model/CyNodeTest.java A impl/src/test/java/org/cytoscape/model/CyTableTest.java A impl/src/test/java/org/cytoscape/model/subnetwork A impl/src/test/java/org/cytoscape/model/subnetwork/CyRootNetworkCyNetworkTest.java A impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkTest.java A impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyNetworkTest.java A impl/src/test/java/org/cytoscape/model/subnetwork/CyRootNetworkTest.java A impl/src/test/java/org/cytoscape/model/subnetwork/CySubNetworkCyTableManagerTest.java A impl/src/test/java/org/cytoscape/model/CyNetworkTest.java A impl/src/test/java/org/cytoscape/model/GraphObjectTest.java A impl/src/test/java/org/cytoscape/model/internal A impl/src/test/java/org/cytoscape/model/internal/tsort A impl/src/test/java/org/cytoscape/model/internal/tsort/TopologicalSortTest.java A impl/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java A impl/src/test/java/org/cytoscape/model/CyTableManagerTest.java A impl/src/main A impl/src/main/java A impl/src/main/java/org A impl/src/main/java/org/cytoscape A impl/src/main/java/org/cytoscape/model A impl/src/main/java/org/cytoscape/model/internal A impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java A impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java A impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java A impl/src/main/java/org/cytoscape/model/internal/CyNetworkManagerImpl.java A impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkFactoryImpl.java A impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java A impl/src/main/java/org/cytoscape/model/internal/VirtualColumn.java A impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java A impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java A impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java A impl/src/main/java/org/cytoscape/model/internal/CyColumnImpl.java A impl/src/main/java/org/cytoscape/model/internal/AttribTopoGraphNode.java A impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java A impl/src/main/java/org/cytoscape/model/internal/CyTableRowUpdateServiceImpl.java A impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java A impl/src/main/java/org/cytoscape/model/internal/NodePointer.java A impl/src/main/java/org/cytoscape/model/internal/CyTableEntryImpl.java A impl/src/main/java/org/cytoscape/model/internal/tsort A impl/src/main/java/org/cytoscape/model/internal/tsort/TopologicalSort.java A impl/src/main/java/org/cytoscape/model/internal/tsort/TopoGraphNode.java A impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java A impl/src/main/javadoc A impl/src/main/javadoc/org A impl/src/main/javadoc/org/cytoscape A impl/src/main/javadoc/org/cytoscape/model A impl/src/main/javadoc/org/cytoscape/model/subnetwork A impl/src/main/javadoc/org/cytoscape/model/subnetwork/package.html A impl/src/main/javadoc/org/cytoscape/model/events A impl/src/main/javadoc/org/cytoscape/model/events/package.html A impl/src/main/javadoc/org/cytoscape/model/package.html A impl/src/main/resources A impl/src/main/resources/META-INF A impl/src/main/resources/META-INF/spring A impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml A impl/src/main/resources/META-INF/spring/bundle-context.xml A impl/src/main/resources/readme.txt A impl/pom.xml A pom.xml A it A it/src A it/src/test A it/src/test/java A it/src/test/java/org A it/src/test/java/org/cytoscape A it/src/test/java/org/cytoscape/model A it/src/test/java/org/cytoscape/model/ServiceConfigurationTest.java A it/pom.xml U . At revision 24345 No emails were triggered. Parsing POMs [trunk] $ java -cp /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-agent-1.385.jar:/R1/tools/maven/apache-maven-2.1.0/boot/classworlds-1.1.jar hudson.maven.agent.Main /R1/tools/maven/apache-maven-2.1.0 /R1/resources/webservers/tomcat_2/webapps/hudson/WEB-INF/lib/remoting-1.385.jar /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-interceptor-1.385.jar 41856 /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven2.1-interceptor-1.2.jar <===[HUDSON REMOTING CAPACITY]===> channel started Executing Maven: -B -f <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] model-impl-parent [INFO] org.cytoscape.model-impl [INFO] org.cytoscape.model-impl-it WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building model-impl-parent [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [site:attach-descriptor] [INFO] [javadoc:jar {execution: attach-javadocs}] [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] Preparing source:jar [WARNING] Removing: jar from forked lifecycle, to prevent recursive invocation. [INFO] No goals needed for project - skipping [INFO] [source:jar {execution: attach-sources}] [INFO] [install:install] [INFO] Installing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/target/pom-transformed.xml> to /home/bturner/.m2/repository/org/cytoscape/model-impl-parent/3.0.0-alpha3-SNAPSHOT/model-impl-parent-3.0.0-alpha3-SNAPSHOT.pom [INFO] [deploy:deploy] [INFO] Retrieving previous build number from snapshots Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha3-SNAPSHOT/model-impl-parent-3.0.0-alpha3-20110309.000224-111.pom 3K uploaded (model-impl-parent-3.0.0-alpha3-20110309.000224-111.pom) [INFO] Retrieving previous metadata from snapshots [INFO] Uploading repository metadata for: 'snapshot org.cytoscape:model-impl-parent:3.0.0-alpha3-SNAPSHOT' [INFO] Retrieving previous metadata from snapshots [INFO] Uploading repository metadata for: 'artifact org.cytoscape:model-impl-parent' [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 Model impl/modules/org.cytoscape$model-impl-parent/builds/2011-03-08_19-02-11/archive/org.cytoscape/model-impl-parent/3.0.0-alpha3-SNAPSHOT/pom.xml [HUDSON] Archiving /home/bturner/.m2/repository/org/cytoscape/model-impl-parent/3.0.0-alpha3-SNAPSHOT/model-impl-parent-3.0.0-alpha3-SNAPSHOT.pom to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 Model impl/modules/org.cytoscape$model-impl-parent/builds/2011-03-08_19-02-11/archive/org.cytoscape/model-impl-parent/3.0.0-alpha3-20110309.000224-111/model-impl-parent-3.0.0-alpha3-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.model-impl [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [pax:compile] [INFO] Compiling 20 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/target/classes> [INFO] [recovering meta-data] [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 Model impl/modules/org.cytoscape$model-impl/builds/2011-03-08_19-02-12/archive/org.cytoscape/model-impl/3.0.0-alpha3-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java>:[44,0] org.cytoscape.model.internal.CyNodeImpl is not abstract and does not override abstract method setNestedNetwork(org.cytoscape.model.CyNetwork) in org.cytoscape.model.CyNode [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13 seconds [INFO] Finished at: Tue Mar 08 19:02:30 EST 2011 [INFO] Final Memory: 65M/715M [INFO] ------------------------------------------------------------------------ Sending e-mails to: [email protected] channel stopped [trunk] $ /R1/tools/maven/apache-maven-2.1.0/bin/mvn org.codehaus.sonar:sonar-maven-plugin:1.8:sonar -Dsonar.jdbc.driver=com.mysql.jdbc.Driver -Dsonar.jdbc.username=sonar -Dsonar.jdbc.password=deploysonar -Dsonar.jdbc.url=jdbc:mysql://localhost:3306/sonar -Dsonar.host.url=http://localhost:8021/sonar/ -Dsonar.skipInstall=true [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] model-impl-parent [INFO] org.cytoscape.model-impl [INFO] org.cytoscape.model-impl-it WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building model-impl-parent [INFO] task-segment: [org.codehaus.sonar:sonar-maven-plugin:1.8:sonar] (aggregator-style) [INFO] ------------------------------------------------------------------------ [INFO] [sonar:sonar] [INFO] Sonar host: http://localhost:8021/sonar [INFO] Sonar version: 2.4 [INFO] [sonar-core:internal] [INFO] Database dialect class org.sonar.jpa.dialect.MySql [INFO] ------------- Analyzing org.cytoscape.model-impl [INFO] Selected quality profile : [name=Cytoscape,language=java] [INFO] Configure maven plugins... [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 524 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 0 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 716 ms [INFO] Java bytecode scan... [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNodeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyEdgeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowCreatedMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyEdgeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyRootNetworkFactoryImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNetworkManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowSetMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNodeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/AttribTopoGraphNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/AttribTopoGraphNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableFactoryImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowCreatedMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyEdgeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyRootNetworkFactoryImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNetworkManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowSetMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNodeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/AttribTopoGraphNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableFactoryImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyColumnImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowCreatedMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyEdgeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyRootNetworkFactoryImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNetworkManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableRowUpdateServiceImpl$RowSetMicroListenerProxy' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyNodeImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/AttribTopoGraphNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/model/internal/CyTableFactoryImpl' is not accessible through the ClassLoader. [INFO] Java bytecode scan done: 270 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 24 ms [INFO] Squid extraction done: 401 ms [INFO] Sensor SquidSensor done: 1443 ms [INFO] Sensor FindbugsSensor... [INFO] Execute Findbugs 1.3.9... [INFO] Findbugs output report: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/target/sonar/findbugs-result.xml> The following classes needed for analysis were missing: org.cytoscape.model.internal.CyColumnImpl org.cytoscape.model.internal.CyEdgeImpl org.cytoscape.model.internal.AttribTopoGraphNode org.cytoscape.model.internal.CyNodeImpl [INFO] Execute Findbugs 1.3.9 done: 8981 ms [INFO] Sensor FindbugsSensor done: 9214 ms [INFO] Execute maven plugin cobertura-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.model-impl [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin::cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Preparing cobertura:cobertura [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [pax:compile] [INFO] Compiling 8 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/target/classes> [INFO] [recovering meta-data] [INFO] ------------------------------------------------------------------------ [ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Can not execute Sonar Embedded error: Unable to execute maven plugin Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Model%20impl/ws/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java>:[44,0] org.cytoscape.model.internal.CyNodeImpl is not abstract and does not override abstract method setNestedNetwork(org.cytoscape.model.CyNetwork) in org.cytoscape.model.CyNode [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 27 seconds [INFO] Finished at: Tue Mar 08 19:03:03 EST 2011 [INFO] Final Memory: 73M/739M [INFO] ------------------------------------------------------------------------ -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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