See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/1499/changes>
Changes: [ruschein] Layouts are now Tasks and CyLayoutAlgorithm is now a TaskFactory. ------------------------------------------ [...truncated 102 lines...] A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttributeDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttributeDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFType.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFTitle.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFFormat.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AbstractHandler.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFSource.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroup.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttributeDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroupDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroupNode.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDate.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDF.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleList.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNetworkAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFIdentifier.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDescription.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java A src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java A src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java A src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java A src/main/java/org/cytoscape/io/internal/read/AbstractTableReader.java A src/main/java/org/cytoscape/io/internal/util A src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java A src/main/java/org/cytoscape/io/internal/util/ReadUtils.java A src/main/resources A src/main/resources/META-INF A src/main/resources/META-INF/spring A src/main/resources/META-INF/spring/bundle-context-osgi.xml A src/main/resources/META-INF/spring/bundle-context.xml A pom.xml At revision 21801 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-1.369.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-1.369.jar /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-interceptor-1.369.jar 56361 /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%20IO%20impl/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 0 resource [INFO] [pax:compile] [INFO] Compiling 75 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/classes> [INFO] [recovering meta-data] [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 IO impl/modules/org.cytoscape$io-impl/builds/2010-09-10_18-07-09/archive/org.cytoscape/io-impl/1.0-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java>:[164,26] getDefaultLayout() in org.cytoscape.view.layout.CyLayouts cannot be applied to (org.cytoscape.view.model.CyNetworkView) [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7 seconds [INFO] Finished at: Fri Sep 10 18:07:19 EDT 2010 [INFO] Final Memory: 53M/600M [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... WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [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: 2.2 [INFO] [sonar-core:internal] [INFO] Database dialect class org.sonar.api.database.dialect.MySql [INFO] ------------- Analyzing org.cytoscape.io-impl [org.cytoscape.io] [INFO] Selected quality profile : Cytoscape, language=java [INFO] Configure maven plugins... [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 694 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 30 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 673 ms [INFO] Java bytecode scan... [WARN] Class 'org/cytoscape/io/internal/read/AbstractTableReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/datatable/TextDataTableReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraph' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/Interaction' is not accessible through the ClassLoader. [WARN] Class '[Lorg/cytoscape/io/internal/read/xgmml/RDFTags;' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/CyTableReaderManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraph' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNetworkAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGroupNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdge' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdge' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDescription' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFIdentifier' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFTitle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFSource' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleList' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/AbstractNetworkViewReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFType' is not accessible through the ClassLoader. [WARN] Class '[Lorg/cytoscape/io/internal/read/xgmml/ParseState;' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics' is not accessible through the ClassLoader. [WARN] Class '[Lorg/cytoscape/io/internal/read/xgmml/ObjectType;' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDescription' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/ViewWriterManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFTitle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNetworkAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleList' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/GenericReaderManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLFileFilter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdge' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFSource' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/util/StreamUtilImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGroupNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/graphics/BitmapWriter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/CyNetworkViewReaderManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFIdentifier' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/CyTableWriterManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/graphics/BitmapWriter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/graphics/PSExporter' is not accessible through the ClassLoader. [WARN] Class '[Lorg/cytoscape/io/internal/read/xgmml/MetadataEntries;' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/SIFNetworkViewReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/AbstractTableReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/datatable/TextDataTableReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraph' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/CyTableReaderManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/AbstractNetworkViewReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttributeDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDescription' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/ViewWriterManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFTitle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNetworkAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleList' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/GenericReaderManager' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLFileFilter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdge' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFSource' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/util/StreamUtilImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleGroupNode' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/CyNetworkViewReaderManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleRDFIdentifier' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleDone' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/CyTableWriterManagerImpl' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/graphics/BitmapWriter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/xgmml/handler/HandleMapAttribute' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/write/graphics/PSExporter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/io/internal/read/sif/SIFNetworkViewReader' is not accessible through the ClassLoader. [INFO] Java bytecode scan done: 153 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 42 ms [INFO] Squid extraction done: 1254 ms [INFO] Sensor SquidSensor done: 2143 ms [INFO] Sensor ProfileSensor... [INFO] Sensor ProfileSensor done: 25 ms [INFO] Sensor ProjectLinksSensor... [INFO] Sensor ProjectLinksSensor done: 5 ms [INFO] Sensor VersionEventsSensor... [INFO] Sensor VersionEventsSensor done: 37 ms [INFO] Sensor Maven dependencies... [INFO] Sensor Maven dependencies done: 332 ms [INFO] Execute maven plugin findbugs-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:2.3.1:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 0 resource [INFO] [pax:compile] [INFO] Compiling 37 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/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%20IO%20impl/ws/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java>:[164,26] getDefaultLayout() in org.cytoscape.view.layout.CyLayouts cannot be applied to (org.cytoscape.view.model.CyNetworkView) [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13 seconds [INFO] Finished at: Fri Sep 10 18:07:44 EDT 2010 [INFO] Final Memory: 75M/721M [INFO] ------------------------------------------------------------------------ -- 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.
