See <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/15/changes>
Changes: [scooter] Fix tests to correspond to changes in the way we store version ------------------------------------------ [...truncated 6936 lines...] [INFO] xjcPlugins:null [INFO] episodes:null [INFO] specVersion:2.1 [INFO] schemaFiles (calculated):[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/target/classes> [INFO] ------------------------------------------------------------- [WARNING] COMPILATION WARNING : [INFO] ------------------------------------------------------------- [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/src/main/java/cytoscape/data/servers/BioDataServerRmi.java>:[207,33] [deprecation] 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<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/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/ws/trunk/application/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape$application/builds/2011-11-21_18-02-38/archive/cytoscape/application/2.8.3-SNAPSHOT/application-2.8.3-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Parent POM .............................. SUCCESS [6.132s] [INFO] Cytoscape Core Libraries Parent POM ............... SUCCESS [0.605s] [INFO] commons-cli-1-x-cytocape-custom ................... SUCCESS [17.889s] [INFO] equations ......................................... SUCCESS [14.551s] [INFO] util-intr ......................................... SUCCESS [10.079s] [INFO] geom-spacial ...................................... SUCCESS [7.238s] [INFO] geom-rtree ........................................ SUCCESS [8.063s] [INFO] GINY API .......................................... SUCCESS [8.574s] [INFO] graph-fixed ....................................... SUCCESS [7.442s] [INFO] graph-dynamic ..................................... SUCCESS [17.326s] [INFO] nerius-math-xform ................................. SUCCESS [6.853s] [INFO] obo ............................................... SUCCESS [8.321s] [INFO] phoebe-dnd ........................................ SUCCESS [6.975s] [INFO] render-immed ...................................... SUCCESS [6:53.272s] [INFO] render-export ..................................... SUCCESS [7.906s] [INFO] render-stateful ................................... SUCCESS [10.935s] [INFO] task .............................................. SUCCESS [10.733s] [INFO] undo-support ...................................... SUCCESS [7.236s] [INFO] fing .............................................. SUCCESS [9.734s] [INFO] ding .............................................. SUCCESS [14.273s] [INFO] Cytoscape Documentation ........................... SUCCESS [43.572s] [INFO] Cytoscape Application ............................. FAILURE [18.379s] [INFO] Cytoscape Core Plugins Parent POM ................. SKIPPED [INFO] Advanced Network Merge ............................ SKIPPED [INFO] Automatic Layout .................................. SKIPPED [INFO] BioMart Client .................................... SKIPPED [INFO] BioPAX ............................................ SKIPPED [INFO] Editor ............................................ SKIPPED [INFO] Equation Functions ................................ SKIPPED [INFO] Manual Layout ..................................... SKIPPED [INFO] NCBI Client ....................................... SKIPPED [INFO] PSI-MI ............................................ SKIPPED [INFO] QuickFind ......................................... SKIPPED [INFO] RFilters .......................................... SKIPPED [INFO] SBML Reader ....................................... SKIPPED [INFO] Table Import ...................................... SKIPPED [INFO] Attribute Browser ................................. SKIPPED [INFO] cPath ............................................. SKIPPED [INFO] cPath2 ............................................ SKIPPED [INFO] Filters ........................................... SKIPPED [INFO] Linkout ........................................... SKIPPED [INFO] Core Commands Plugin .............................. SKIPPED [INFO] NetworkAnalyzer ................................... SKIPPED [INFO] Cytoscape Distribution ............................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11:17.216s [INFO] Finished at: Mon Nov 21 18:14:00 GMT-05:00 2011 [INFO] Final Memory: 34M/111M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project application: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/src/main/java/cytoscape/plugin/PluginManager.java>:[371,13] setObjectVersion(java.lang.String) in cytoscape.plugin.DownloadableInfo cannot be applied to (double) cause : Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/src/main/java/cytoscape/plugin/PluginManager.java>:[371,13] setObjectVersion(java.lang.String) in cytoscape.plugin.DownloadableInfo cannot be applied to (double) Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project application: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/src/main/java/cytoscape/plugin/PluginManager.java>:[371,13] setObjectVersion(java.lang.String) in cytoscape.plugin.DownloadableInfo cannot be applied to (double) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59) at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:319) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156) at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239) at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158) at hudson.maven.Maven3Builder.call(Maven3Builder.java:112) at hudson.maven.Maven3Builder.call(Maven3Builder.java:70) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:287) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:636) Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/application/src/main/java/cytoscape/plugin/PluginManager.java>:[371,13] setObjectVersion(java.lang.String) in cytoscape.plugin.DownloadableInfo cannot be applied to (double) at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:656) at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:128) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Sending e-mails to: [email protected] channel stopped -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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