See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/1139/changes>
Changes: [mes] updated method names in CyRow to be a bit more sensible ------------------------------------------ Started by an SCM change Checking out http://chianti.ucsd.edu/svn/core3/layout-cytoscape-impl/trunk A osgi.bnd A src A src/main A src/main/java A src/main/java/csplugins A src/main/java/csplugins/layout A src/main/java/csplugins/layout/Profile.java A src/main/java/csplugins/layout/algorithms A src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken A src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java A src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java A src/main/java/csplugins/layout/algorithms/circularLayout A src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java A src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java A src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java A src/main/java/csplugins/layout/algorithms/StackedNodeLayoutTask.java A src/main/java/csplugins/layout/algorithms/bioLayout A src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java A src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java A src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask.java A src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java A src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java A src/main/java/csplugins/layout/algorithms/graphPartition A src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java A src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java A src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java A src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java A src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayoutTask.java A src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java A src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java A src/main/java/csplugins/layout/algorithms/hierarchicalLayout A src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java A src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java A src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Edge.java A src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.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 U . At revision 22359 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 43955 /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%20Layout%20impl/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.layout-cytoscape-impl [csplugins.layout] [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [pax:compile] [INFO] Compiling 23 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/classes> [INFO] [recovering meta-data] [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 Layout impl/modules/org.cytoscape$layout-cytoscape-impl/builds/2010-10-25_14-05-05/archive/org.cytoscape/layout-cytoscape-impl/1.0-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java>:[61,62] cannot find symbol symbol : method getType(java.lang.String) location: interface org.cytoscape.model.CyRow [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7 seconds [INFO] Finished at: Mon Oct 25 14:05:15 EDT 2010 [INFO] Final Memory: 44M/491M [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.layout-cytoscape-impl [csplugins.layout] [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.layout-cytoscape-impl [csplugins.layout] [INFO] Selected quality profile : Cytoscape, language=java [INFO] Configure maven plugins... [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 542 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 34 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 1165 ms [INFO] Java bytecode scan... [WARN] Class 'csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask$AttributeComparator' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask$PartialDerivatives' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask$AttributeComparator' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithmTask$PartialDerivatives' is not accessible through the ClassLoader. [WARN] Class 'csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask' is not accessible through the ClassLoader. [INFO] Java bytecode scan done: 458 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 23 ms [INFO] Squid extraction done: 838 ms [INFO] Sensor SquidSensor done: 2621 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: 53 ms [INFO] Sensor Maven dependencies... [INFO] Sensor Maven dependencies done: 133 ms [INFO] Execute maven plugin findbugs-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.layout-cytoscape-impl [csplugins.layout] [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] [pax:compile] [INFO] Compiling 2 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/classes> [INFO] [findbugs:findbugs] [INFO] Locale is en [java] Warnings generated: 82 [INFO] Execute maven plugin findbugs-maven-plugin done: 18944 ms [INFO] Sensor FindbugsSensor... [INFO] Sensor FindbugsSensor done: 289 ms [INFO] Sensor CheckstyleSensor... [INFO] Execute Checkstyle 5.1... [INFO] Checkstyle output report: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/sonar/checkstyle-result.xml> [INFO] Checkstyle configuration: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/sonar/checkstyle.xml> [INFO] Execute Checkstyle 5.1 done: 1103 ms [INFO] Sensor CheckstyleSensor done: 1785 ms [INFO] Sensor PmdSensor... [INFO] Execute PMD 4.2.5... [INFO] Java version: 1.6 [INFO] PMD configuration: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/sonar/pmd.xml> [INFO] PMD output report: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/sonar/pmd-result.xml> [INFO] Execute PMD 4.2.5 done: 5052 ms [INFO] Sensor PmdSensor done: 5180 ms [INFO] Execute maven plugin cobertura-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.layout-cytoscape-impl [csplugins.layout] [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 2 resources [INFO] [pax:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [cobertura:instrument] [INFO] Cobertura 1.9.2 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 34 files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/generated-classes/cobertura> [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class csplugins.layout.algorithms.graphPartition.AttributeCircleLayoutTask$1. Perhaps you need to compile with debug=true? Cobertura: Saved information on 34 classes. Instrument time: 1000ms [INFO] Instrumentation was successful. [INFO] [resources:testResources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/src/test/resources> [INFO] [pax:testCompile] [INFO] No sources to compile [INFO] [surefire:test] [INFO] No tests to run. [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9.2 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 34 classes. Report time: 1431ms [INFO] Cobertura Report generation was successful. [INFO] Execute maven plugin cobertura-maven-plugin done: 3885 ms [INFO] Sensor CoberturaSensor... [INFO] parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/site/cobertura/coverage.xml> [INFO] Sensor CoberturaSensor done: 440 ms [INFO] Sensor CpdSensor... [INFO] Sensor CpdSensor done: 290 ms [INFO] Execute maven plugin taglist-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.layout-cytoscape-impl [csplugins.layout] [INFO] task-segment: [org.codehaus.mojo:taglist-maven-plugin:2.4:taglist] [INFO] ------------------------------------------------------------------------ [WARNING] DEPRECATED [tags]: No reason given [INFO] [taglist:taglist] [WARNING] Using legacy tag format. This is not recommended. [INFO] Execute maven plugin taglist-maven-plugin done: 1121 ms [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@40591a4d... [INFO] Sensor org.sonar.plugins.taglist.taglistsen...@40591a4d done: 83 ms [INFO] Sensor SurefireSensor... [INFO] parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Layout%20impl/ws/trunk/target/surefire-reports> [INFO] Sensor SurefireSensor done: 25 ms [INFO] Execute decorators... [INFO] ANALYSIS SUCCESSFUL, you can browse http://localhost:8021/sonar/ [INFO] Database optimization... [INFO] Database optimization done: 1527 ms [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 48 seconds [INFO] Finished at: Mon Oct 25 14:06:14 EDT 2010 [INFO] Final Memory: 87M/775M [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.
