See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/177/changes>
Changes: [kono] fixes #386 Edge transparency had been implemented. ------------------------------------------ [...truncated 3659 lines...] A network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/RainbowCanvas.java A network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/SpringUtilities.java A network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/SettingsAction.java A network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java A network-analyzer-impl/src/main/javadoc A network-analyzer-impl/src/main/javadoc/de A network-analyzer-impl/src/main/javadoc/de/mpg A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/settings/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/filter/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/io A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/io/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/ui/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/data/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/dec A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/dec/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/sconnect/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/charts/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/filter/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/dec/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/ui/package.html A network-analyzer-impl/src/main/javadoc/de/mpg/mpi_inf/bioinf/netanalyzer/package.html A network-analyzer-impl/src/main/resources A network-analyzer-impl/src/main/resources/META-INF A network-analyzer-impl/src/main/resources/META-INF/spring A network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy A network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy A network-analyzer-impl/src/main/resources/de A network-analyzer-impl/src/main/resources/de/mpg A network-analyzer-impl/src/main/resources/de/mpg/mpi_inf A network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf A network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer A network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data A network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data/images AU network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data/images/arrow-right.png AU network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/data/images/00.png AU 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network-analyzer-impl/src/main/resources/de/mpg/mpi_inf/bioinf/netanalyzer/NetworkAnalyzer.xml A network-analyzer-impl/pom.xml U . At revision 27146 No emails were triggered. Parsing POMs Modules changed, recalculating dependency graph [trunk] $ /usr/lib/jvm/java-6-openjdk/bin/java -Djava.awt.headless=true -Xmx768M -XX:MaxPermSize=256M -cp /var/lib/jenkins/plugins/maven-plugin/WEB-INF/lib/maven3-agent-1.2.jar:/opt/apache-maven-3.0.3/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /opt/apache-maven-3.0.3 /var/lib/tomcat6/webapps/jenkins/WEB-INF/lib/remoting-2.9.jar /var/lib/jenkins/plugins/maven-plugin/WEB-INF/lib/maven3-interceptor-1.2.jar 39293 <===[JENKINS REMOTING CAPACITY]===> channel started Executing Maven: -B -f <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.cytoscape:model-impl:bundle:3.0.0-alpha8-SNAPSHOT [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.cytoscape:di-util-api:jar -> duplicate declaration of version (?) @ org.cytoscape:model-impl-parent:3.0.0-alpha8-SNAPSHOT, <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/pom.xml,> line 87, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.cytoscape:model-impl-parent:pom:3.0.0-alpha8-SNAPSHOT [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.cytoscape:di-util-api:jar -> duplicate declaration of version (?) @ line 87, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.cytoscape:swing-application-impl:bundle:3.0.0-alpha8-SNAPSHOT [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.cytoscape:service-api:jar -> duplicate declaration of version (?) @ line 114, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Cytoscape Implementation Parent Project POM [INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] [INFO] Command Executor [INFO] org.cytoscape.equations-impl [INFO] model-impl-parent [INFO] org.cytoscape.model-impl [INFO] viewmodel-impl-parent [INFO] org.cytoscape.viewmodel-impl [INFO] Ding Implementation Parent Pom [INFO] org.cytoscape.util-intr [INFO] org.cytoscape.spacial [INFO] org.cytoscape.graph-render [INFO] org.cytoscape.ding-presentation-impl [INFO] org.cytoscape.core-task-impl [INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] [INFO] org.cytoscape.ding-customgraphics-manager-impl [INFO] io-impl-parent [INFO] org.cytoscape.io-impl [org.cytoscape.io] [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] [INFO] org.cytoscape.io-impl-performance [INFO] org.cytoscape.layout-cytoscape-impl [csplugins.layout] [INFO] org.cytoscape.layout-jgraph-impl [csplugins.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] [INFO] Manual Layout [INFO] NetworkAnalyzer [INFO] Advanced Network Merge [INFO] org.cytoscape.plugin-impl [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation] [INFO] org.cytoscape.property.internal [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi] [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml] [INFO] org.cytoscape.search-impl [org.cytoscape.search] [INFO] org.cytoscape.session-impl [INFO] Cytoscape Swing Application Impl [INFO] Cytoscape Table Browser Implementation [INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport] [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] [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Implementation Parent Project POM 3.0.0-alpha8-SNAPSHOT [INFO] ------------------------------------------------------------------------ ignoring exception during new ExecutedMojo null [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 /var/lib/tomcat6/.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://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 0.4 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20111012.220335-203.pom Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20111012.220335-203.pom (11 KB at 28.8 KB/sec) Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Downloaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (291 B at 8.4 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 5.6 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (291 B at 1.8 KB/sec) [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> to /var/lib/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$impl-parent/builds/2011-10-12_17-03-22/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] ------------------------------------------------------------------------ [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 14 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ biopax-impl --- [INFO] Compiling 34 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/target/classes> [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/util/BioPaxUtil.java>:[403,37] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/util/BioPaxUtil.java>:[438,21] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java>:[857,37] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ExternalLinkUtil.java>:[36,36] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java>:[903,7] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java>:[903,40] [deprecation] <T>xrefToExternalLinks(org.biopax.paxtools.model.BioPAXElement,java.lang.Class<T>) in org.cytoscape.biopax.util.BioPaxUtil has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ExternalLinkUtil.java>:[189,4] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ExternalLinkUtil.java>:[189,25] [deprecation] org.cytoscape.biopax.internal.ExternalLink in org.cytoscape.biopax.internal has been deprecated [INFO] [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/biopax-impl/src/test/resources> [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ biopax-impl --- [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ biopax-impl --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.10:test (default-test) @ biopax-impl --- [INFO] No tests to run. [INFO] Surefire report directory: <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/target/surefire-reports> ------------------------------------------------------- T E S T S ------------------------------------------------------- Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [JENKINS] Recording test results [INFO] [INFO] --- maven-bundle-plugin:2.3.4:bundle (default-bundle) @ biopax-impl --- # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0xb771029f, pid=14243, tid=3022715760 # # JRE version: 6.0_20-b20 # Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 ) # Derivative: IcedTea6 1.9.9 # Distribution: Ubuntu 10.04.1 LTS, package 6b20-1.9.9-0ubuntu1~10.04.2 # Problematic frame: # C [libc.so.6+0x7629f] memcpy+0x2f # # An error report file with more information is saved as: # <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/hs_err_pid14243.log> # # If you would like to submit a bug report, please include # instructions how to reproduce the bug and visit: # https://bugs.launchpad.net/ubuntu/+source/openjdk-6/ # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug. # ERROR: Maven JVM terminated unexpectedly with exit code 134 Skipping sonar analysis due to SCM build trigger -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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