See <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/11/changes>
Changes: [scooter] We want to treat plugin versions as "." separated integers, not as floats. ------------------------------------------ [...truncated 66 lines...] [INFO] schemaDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd> [INFO] schemaIncludes:[Ljava.lang.String;@110b888 [INFO] schemaExcludes:null [INFO] bindingDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd> [INFO] bindingIncludes:[Ljava.lang.String;@c323bc [INFO] bindingExcludes:null [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:com.sun.org.apache.xml.internal.resolver.tools.CatalogResolver [INFO] generatePackage:cytoscape.generated [INFO] generateDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc> [INFO] readOnly:false [INFO] extension:false [INFO] strict:true [INFO] writeCode:true [INFO] verbose:true [INFO] debug:false [INFO] args:[] [INFO] forceRegenerate:true [INFO] removeOldOutput:false [INFO] produces:[**/*.*, **/*.java, **/bgm.ser, **/jaxb.properties] [INFO] otherDepends:null [INFO] episodeFile:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc/META-INF/sun-jaxb.episode> [INFO] episode:true [INFO] classpathElements:[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/classes]> [INFO] plugins:null [INFO] episodes:null [INFO] xjcPlugins:null [INFO] episodes:null [INFO] specVersion:2.1 [INFO] schemaFiles (calculated):[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd/cysession.xsd]> [INFO] bindingFiles (calculated):[] [INFO] xjcPluginArtifacts (resolved):[] [INFO] xjcPluginFiles (resolved):[] [INFO] xjcPluginURLs (resolved):[] [INFO] episodeArtifacts (resolved):[] [INFO] episodeFiles (resolved):[] [INFO] The schemaLanguage setting was not defined, assuming 'AUTODETECT'. Cannot find CatalogManager.properties Using java.util.ServiceLoader [INFO] Parsing input schema(s)... [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc].> [INFO] XJC writing: cytoscape/generated/Child.java [INFO] XJC writing: cytoscape/generated/Cysession.java [INFO] XJC writing: cytoscape/generated/Cytopanel.java [INFO] XJC writing: cytoscape/generated/Cytopanels.java [INFO] XJC writing: cytoscape/generated/Desktop.java [INFO] XJC writing: cytoscape/generated/DesktopSize.java [INFO] XJC writing: cytoscape/generated/Edge.java [INFO] XJC writing: cytoscape/generated/HiddenEdges.java [INFO] XJC writing: cytoscape/generated/HiddenNodes.java [INFO] XJC writing: cytoscape/generated/Network.java [INFO] XJC writing: cytoscape/generated/NetworkFrame.java [INFO] XJC writing: cytoscape/generated/NetworkFrames.java [INFO] XJC writing: cytoscape/generated/NetworkTree.java [INFO] XJC writing: cytoscape/generated/Node.java [INFO] XJC writing: cytoscape/generated/ObjectFactory.java [INFO] XJC writing: cytoscape/generated/Ontology.java [INFO] XJC writing: cytoscape/generated/OntologyServer.java [INFO] XJC writing: cytoscape/generated/Panel.java [INFO] XJC writing: cytoscape/generated/Panels.java [INFO] XJC writing: cytoscape/generated/Parent.java [INFO] XJC writing: cytoscape/generated/Plugin.java [INFO] XJC writing: cytoscape/generated/Plugins.java [INFO] XJC writing: cytoscape/generated/SelectedEdges.java [INFO] XJC writing: cytoscape/generated/SelectedNodes.java [INFO] XJC writing: cytoscape/generated/Server.java [INFO] XJC writing: cytoscape/generated/SessionState.java [INFO] XJC writing: cytoscape/generated/ViewableNodes.java [INFO] Finished execution. [INFO] [INFO] Started execution. [INFO] JAXB API is loaded from the [jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!]. [INFO] Detected JAXB API version [2.1]. [INFO] pluginArtifacts:[org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.4:, org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.4:compile, org.codehaus.plexus:plexus-utils:jar:1.1:compile, junit:junit:jar:4.8.1:compile, org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1:compile, org.sonatype.plexus:plexus-build-api:jar:0.0.6:compile, com.sun.xml.bind:jaxb-impl:jar:2.1.13:compile, javax.xml.bind:jaxb-api:jar:2.1:compile, javax.xml.stream:stax-api:jar:1.0-2:compile, javax.activation:activation:jar:1.1:compile, org.jvnet.jaxb2_commons:jaxb2-basics-jaxb-xjc:jar:2.1.13.MR2:compile, com.sun.codemodel:codemodel:jar:2.3:compile, com.sun.xml.dtd-parser:dtd-parser:jar:1.1:compile, com.sun.istack:istack-commons-tools:jar:2.2.MR1:compile, org.apache.ant:ant:jar:1.7.0:compile, org.apache.ant:ant-launcher:jar:1.7.0:compile, relaxngDatatype:relaxngDatatype:jar:20020414:compile, com.sun.org.apache.xml.internal:resolver:jar:20050927:compile, org.kohsuke.rngom:rngom:jar:20100718:compile, com.sun.xsom:xsom:jar:20100725:compile, sun.jdk:tools:jar:1.5.0:system] [INFO] schemaLanguage:null [INFO] schemaDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd> [INFO] schemaIncludes:[Ljava.lang.String;@cd9b4f [INFO] schemaExcludes:null [INFO] bindingDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd> [INFO] bindingIncludes:[Ljava.lang.String;@8f9236 [INFO] bindingExcludes:null [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:com.sun.org.apache.xml.internal.resolver.tools.CatalogResolver [INFO] generatePackage:cytoscape.bookmarks [INFO] generateDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc> [INFO] readOnly:false [INFO] extension:false [INFO] strict:true [INFO] writeCode:true [INFO] verbose:true [INFO] debug:false [INFO] args:[] [INFO] forceRegenerate:true [INFO] removeOldOutput:false [INFO] produces:[**/*.*, **/*.java, **/bgm.ser, **/jaxb.properties] [INFO] otherDepends:null [INFO] episodeFile:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc/META-INF/sun-jaxb.episode> [INFO] episode:true [INFO] classpathElements:[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/classes]> [INFO] plugins:null [INFO] episodes:null [INFO] xjcPlugins:null [INFO] episodes:null [INFO] specVersion:2.1 [INFO] schemaFiles (calculated):[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/resources/xsd/bookmarks.xsd]> [INFO] bindingFiles (calculated):[] [INFO] xjcPluginArtifacts (resolved):[] [INFO] xjcPluginFiles (resolved):[] [INFO] xjcPluginURLs (resolved):[] [INFO] episodeArtifacts (resolved):[] [INFO] episodeFiles (resolved):[] [INFO] The schemaLanguage setting was not defined, assuming 'AUTODETECT'. Using java.util.ServiceLoader [INFO] Parsing input schema(s)... [INFO] --- maven-jaxb2-plugin:0.7.4:generate (bookmarks) @ application --- [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/generated-sources/xjc].> [INFO] XJC writing: cytoscape/bookmarks/Attribute.java [INFO] XJC writing: cytoscape/bookmarks/Bookmarks.java [INFO] XJC writing: cytoscape/bookmarks/Category.java [INFO] XJC writing: cytoscape/bookmarks/DataSource.java [INFO] XJC writing: cytoscape/bookmarks/ObjectFactory.java [INFO] Finished execution. [INFO] [INFO] --- maven-resources-plugin:2.4.3:resources (default-resources) @ application --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 155 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ application --- [INFO] Compiling 757 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/target/classes> [INFO] ------------------------------------------------------------- [WARNING] COMPILATION WARNING : [INFO] ------------------------------------------------------------- [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/OntologyTerm.java>:[222,29] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Ontology.java>:[100,17] [deprecation] cytoscape.data.annotation.OntologyTerm in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Ontology.java>:[140,8] [deprecation] cytoscape.data.annotation.OntologyTerm in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Ontology.java>:[280,8] [deprecation] cytoscape.data.annotation.OntologyDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/parsers/ObjectToString.java>:[47,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/mappings/discrete/DiscreteMappingWriter.java>:[48,31] [deprecation] cytoscape.visual.parsers.ObjectToString in cytoscape.visual.parsers has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[41,32] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[42,32] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[47,32] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[48,32] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[96,27] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[142,8] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[160,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[175,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[175,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[207,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[223,37] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[69,27] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[87,8] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[100,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[112,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[112,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[139,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerInterface.java>:[152,37] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Annotation.java>:[92,48] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Annotation.java>:[128,25] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/Annotation.java>:[137,8] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/editors/discrete/ObjectPositionCellRenderer.java>:[41,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java>:[59,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java>:[152,27] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/LabelPlacerGraphic.java>:[162,27] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[56,32] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[57,32] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[58,32] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[362,8] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[394,8] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[447,33] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[447,56] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[447,11] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[679,27] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[709,8] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[727,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[743,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[743,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[779,33] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[796,37] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java>:[41,32] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java>:[42,32] [deprecation] cytoscape.data.annotation.OntologyTerm in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java>:[59,1] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyFlatFileReader.java>:[239,8] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java>:[41,32] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java>:[42,32] [deprecation] cytoscape.data.annotation.OntologyTerm in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java>:[63,1] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/OntologyXmlReader.java>:[140,8] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/LabelPlacerControl.java>:[54,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/ui/LabelPlacerControl.java>:[76,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/properties/NodeLabelPositionProp.java>:[50,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/properties/NodeLabelPositionProp.java>:[144,32] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java>:[39,23] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java>:[56,11] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/parsers/LabelPositionParser.java>:[67,11] [deprecation] cytoscape.visual.LabelPosition in cytoscape.visual has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java>:[41,32] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java>:[60,1] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/AnnotationFlatFileReader.java>:[267,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/AnnotationXmlReader.java>:[62,1] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/annotation/readers/AnnotationXmlReader.java>:[139,8] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/actions/GinyUtils.java>:[107,30] [deprecation] getEdgeIndicesArray(int,int,boolean,boolean) in giny.model.GraphPerspective has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/actions/GinyUtils.java>:[158,22] [deprecation] getEdgeIndicesArray(int,int,boolean) in giny.model.GraphPerspective has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/calculators/BasicCalculator.java>:[84,27] [deprecation] NODE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/calculators/BasicCalculator.java>:[85,24] [deprecation] EDGE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/NodeAppearanceCalculator.java>:[97,30] [deprecation] NodeAppearance(cytoscape.visual.VisualPropertyDependency) in cytoscape.visual.NodeAppearance has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/SelectFilter.java>:[375,29] [deprecation] getHiddenNodes() in giny.model.GraphPerspectiveChangeEvent has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/CyNode.java>:[90,16] [deprecation] setGraphPerspective(giny.model.GraphPerspective) in giny.model.Node has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/CyNode.java>:[77,25] [deprecation] getGraphPerspective() in giny.model.Node has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/properties/AbstractVisualProperty.java>:[136,13] [deprecation] applyToEdgeView(giny.view.EdgeView,java.lang.Object) in cytoscape.visual.VisualProperty has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/visual/properties/AbstractVisualProperty.java>:[122,13] [deprecation] applyToNodeView(giny.view.NodeView,java.lang.Object) in cytoscape.visual.VisualProperty has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/writers/InteractionWriter.java>:[122,23] [deprecation] getAdjacentEdgesList(giny.model.Node,boolean,boolean,boolean) in giny.model.GraphPerspective has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[99,2] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[99,34] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[104,3] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[104,31] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[145,2] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[145,36] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[146,85] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[163,2] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[163,42] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[178,10] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[194,2] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[194,42] [deprecation] cytoscape.data.annotation.AnnotationDescription in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[210,2] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[210,27] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[226,2] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[226,27] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[238,2] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[238,22] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[238,69] [deprecation] cytoscape.data.annotation.Annotation in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/dialogs/preferences/BookmarkDialog.java>:[401,60] [deprecation] toURL() in java.io.File has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[381,10] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[381,39] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/data/servers/BioDataServer.java>:[443,10] [deprecation] cytoscape.data.annotation.Ontology in cytoscape.data.annotation has been deprecated [INFO] 100 warnings [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/src/main/java/cytoscape/plugin/PluginManager.java>:[371,13] setObjectVersion(java.lang.String) in cytoscape.plugin.DownloadableInfo cannot be applied to (double) [INFO] 1 error [INFO] ------------------------------------------------------------- [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/cytoscape$application/ws/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape$application/builds/2011-11-18_18-02-49/archive/cytoscape/application/2.8.3-SNAPSHOT/application-2.8.3-SNAPSHOT.pom -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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