See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/1384/>
------------------------------------------ [...truncated 743 lines...] [INFO] Velocimacro : VM library template macro registration complete. [INFO] Velocimacro : allowInline = true : VMs can be defined inline in templates [INFO] Velocimacro : allowInlineToOverride = false : VMs defined inline may NOT replace previous VM definitions [INFO] Velocimacro : allowInlineLocal = false : VMs defined inline will be global in scope if allowed. [INFO] Velocimacro : initialization complete. [INFO] Velocity successfully started. [INFO] [checkstyle:checkstyle] [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent! [INFO] There are 113 checkstyle errors. [INFO] org.cytoscape.io-impl [org.cytoscape.io] Executing org.apache.maven.plugins:maven-pmd-plugin:[pmd] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [INFO] task-segment: [org.apache.maven.plugins:maven-pmd-plugin:2.4:pmd] [INFO] ------------------------------------------------------------------------ [INFO] [pmd:pmd] [INFO] org.cytoscape.io-impl [org.cytoscape.io] Executing org.codehaus.mojo:javancss-maven-plugin:[report] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [INFO] task-segment: [org.codehaus.mojo:javancss-maven-plugin:2.0-beta-2:report] [INFO] ------------------------------------------------------------------------ [INFO] [javancss:report] [INFO] org.cytoscape.io-impl [org.cytoscape.io] Executing org.codehaus.mojo:cobertura-maven-plugin:[cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin:2.2:cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Preparing cobertura:cobertura [INFO] [resources:resources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 2 resources [INFO] Copying 0 resource [INFO] [pax:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [cobertura:instrument] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 79 files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/generated-classes/cobertura> Cobertura: Saved information on 79 classes. Instrument time: 3143ms [INFO] Instrumentation was successful. [INFO] [resources:testResources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 6 resources [INFO] [pax:testCompile] [INFO] Nothing to compile - all classes are up to date [INFO] [surefire:test] [INFO] Surefire report directory: <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/surefire-reports> [org.springframework.test.context.junit4.SpringJUnit4ClassRunner] : SpringJUnit4ClassRunner constructor called with [class org.cytoscape.io.internal.BeanIntegrationTest]. ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.cytoscape.io.internal.read.ssf.test.SSFReaderTest Current Line: M1 A Length = 2 Got Module: Node suid: 10 index: 0 network suid: 1 Current Line: M2 B pp C Length = 4 Got Module: Node suid: 13 index: 2 network suid: 1 Current Line: - A pp B Length = 4 Got Module: null Node Count = 5 Edge Count = 2 ========================== Current Line: M1 A Length = 2 Got Module: Node suid: 27 index: 0 network suid: 18 Current Line: M2 M1 pp B Length = 4 Got Module: Node suid: 30 index: 2 network suid: 18 Current Line: M3 M2 pp C Length = 4 Got Module: Node suid: 34 index: 4 network suid: 18 Current Line: M4 M3 pp D Length = 4 Got Module: Node suid: 38 index: 6 network suid: 18 Node Count = 8 Edge Count = 3 ========================== Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.17 sec Running org.cytoscape.io.internal.BeanIntegrationTest [org.springframework.test.context.junit4.SpringJUnit4ClassRunner] : Invoking test method [public void org.cytoscape.io.internal.BeanIntegrationTest.readerManagerTest() throws java.lang.Exception] [org.springframework.test.context.support.DependencyInjectionTestExecutionListener] : Performing dependency injection for test context [[testcont...@5a5e179a testClass = BeanIntegrationTest, locations = array<String>['classpath:META-INF/spring/bundle-context.xml'], testInstance = org.cytoscape.io.internal.beanintegrationt...@575fadcf, testMethod = [null], testException = [null]]]. [org.springframework.test.context.support.AbstractGenericContextLoader] : Loading ApplicationContext for locations [classpath:META-INF/spring/bundle-context.xml]. [org.springframework.beans.factory.xml.XmlBeanDefinitionReader] : Loading XML bean definitions from class path resource [META-INF/spring/bundle-context.xml] [org.springframework.beans.factory.xml.DefaultDocumentLoader] : Using JAXP provider [com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl] [org.springframework.beans.factory.xml.PluggableSchemaResolver] : Loading schema mappings from [META-INF/spring.schemas] [org.springframework.beans.factory.xml.PluggableSchemaResolver] : Loaded schema mappings: {http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.5.xsd, http://www.springframework.org/schema/lang/spring-lang-2.5.xsd=org/springframework/scripting/config/spring-lang-2.5.xsd, http://www.springframework.org/schema/context/spring-context-2.5.xsd=org/springframework/context/config/spring-context-2.5.xsd, http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd=org/springframework/osgi/config/spring-osgi-1.0.xsd, http://www.springframework.org/schema/osgi-compendium/spring-osgi-compendium-1.0.xsd=org/springframework/osgi/compendium/config/spring-osgi-compendium-1.0.xsd, http://www.springframework.org/schema/context/spring-context.xsd=org/springframework/context/config/spring-context-2.5.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.5.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.5.xsd=org/springframework/beans/factory/xml/spring-util-2.5.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/osgi/spring-osgi-1.2.xsd=org/springframework/osgi/config/spring-osgi-1.2.xsd, http://www.springframework.org/schema/osgi-compendium/spring-osgi-compendium-1.2.xsd=org/springframework/osgi/compendium/config/spring-osgi-compendium-1.2.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/osgi/spring-osgi.xsd=org/springframework/osgi/config/spring-osgi-1.2.xsd, http://www.springframework.org/schema/tool/spring-tool-2.5.xsd=org/springframework/beans/factory/xml/spring-tool-2.5.xsd, http://www.springframework.org/schema/osgi-compendium/spring-osgi-compendium.xsd=org/springframework/osgi/compendium/config/spring-osgi-compendium-1.2.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.5.xsd, http://www.springframework.org/schema/beans/spring-beans-2.5.xsd=org/springframework/beans/factory/xml/spring-beans-2.5.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.5.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.5.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/osgi/spring-osgi-1.1.xsd=org/springframework/osgi/config/spring-osgi-1.1.xsd, http://www.springframework.org/schema/osgi-compendium/spring-osgi-compendium-1.1.xsd=org/springframework/osgi/compendium/config/spring-osgi-compendium-1.1.xsd, http://www.springframework.org/schema/jee/spring-jee-2.5.xsd=org/springframework/ejb/config/spring-jee-2.5.xsd, http://www.springframework.org/schema/aop/spring-aop-2.5.xsd=org/springframework/aop/config/spring-aop-2.5.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.5.xsd} [org.springframework.beans.factory.xml.PluggableSchemaResolver] : Found XML schema [http://www.springframework.org/schema/beans/spring-beans-2.5.xsd] in classpath: org/springframework/beans/factory/xml/spring-beans-2.5.xsd [org.springframework.beans.factory.xml.PluggableSchemaResolver] : Found XML schema [http://www.springframework.org/schema/context/spring-context-2.5.xsd] in classpath: org/springframework/context/config/spring-context-2.5.xsd [org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader] : Loading bean definitions [org.springframework.beans.factory.xml.DefaultNamespaceHandlerResolver] : Loaded mappings [{http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/osgi-compendium=org.springframework.osgi.compendium.config.CompendiumNamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/osgi=org.springframework.osgi.config.OsgiNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://www.springframework.org/schema/context=org.springframework.context.config.ContextNamespaceHandler}] [org.springframework.beans.factory.xml.XmlBeanDefinitionReader] : Loaded 17 bean definitions from location pattern [classpath:META-INF/spring/bundle-context.xml] [org.springframework.context.support.GenericApplicationContext] : Refreshing org.springframework.context.support.genericapplicationcont...@7f09fd93: display name [org.springframework.context.support.genericapplicationcont...@7f09fd93]; startup date [Sat Aug 14 20:16:51 EDT 2010]; root of context hierarchy [org.springframework.context.support.GenericApplicationContext] : Bean factory for application context [org.springframework.context.support.genericapplicationcont...@7f09fd93]: org.springframework.beans.factory.support.defaultlistablebeanfact...@3f9f3736 [org.springframework.context.support.GenericApplicationContext] : 17 beans defined in org.springframework.context.support.genericapplicationcont...@7f09fd93: display name [org.springframework.context.support.genericapplicationcont...@7f09fd93]; startup date [Sat Aug 14 20:16:51 EDT 2010]; root of context hierarchy [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'org.springframework.context.annotation.internalCommonAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'org.springframework.context.annotation.internalCommonAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'org.springframework.context.annotation.internalCommonAnnotationProcessor' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'org.springframework.context.annotation.internalCommonAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'org.springframework.context.annotation.internalAutowiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'org.springframework.context.annotation.internalAutowiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'org.springframework.context.annotation.internalAutowiredAnnotationProcessor' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'org.springframework.context.annotation.internalAutowiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'org.springframework.context.annotation.internalRequiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'org.springframework.context.annotation.internalRequiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'org.springframework.context.annotation.internalRequiredAnnotationProcessor' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'org.springframework.context.annotation.internalRequiredAnnotationProcessor' [org.springframework.context.support.GenericApplicationContext] : Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.delegatingmessagesou...@45b34126] [org.springframework.context.support.GenericApplicationContext] : Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.simpleapplicationeventmulticas...@3e018c74] [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Pre-instantiating singletons in org.springframework.beans.factory.support.defaultlistablebeanfact...@3f9f3736: defining beans [org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,sifReaderFactory,xgmmlReaderFactory,sifFilter,xgmmlFilter,sifReader,objectTypeMap,attributeValueUtil,handlerFactory,readDataManager,xgmmlParser,xgmmlReader,cyReaderManager,readUtil,streamUtil]; root of factory hierarchy [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'org.springframework.context.annotation.internalCommonAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'org.springframework.context.annotation.internalAutowiredAnnotationProcessor' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'org.springframework.context.annotation.internalRequiredAnnotationProcessor' [org.springframework.beans.factory.annotation.InjectionMetadata] : Found injected field on class [org.cytoscape.io.internal.BeanIntegrationTest]: AutowiredFieldElement for private org.cytoscape.io.read.CyReaderManager org.cytoscape.io.internal.BeanIntegrationTest.manager [org.springframework.beans.factory.annotation.InjectionMetadata] : Processing injected field of bean 'org.cytoscape.io.internal.BeanIntegrationTest': AutowiredFieldElement for private org.cytoscape.io.read.CyReaderManager org.cytoscape.io.internal.BeanIntegrationTest.manager [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'cyReaderManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'cyReaderManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'cyReaderManager' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'cyReaderManager' [org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor] : Autowiring by type from bean name 'org.cytoscape.io.internal.BeanIntegrationTest' to bean named 'cyReaderManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'sifReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'sifReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'readUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'readUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'streamUtil' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'readUtil' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'readUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'sifReader' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'sifReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'xgmmlReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'xgmmlReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'xgmmlReader' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'xgmmlParser' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'xgmmlParser' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'xgmmlParser' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'handlerFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'handlerFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'readDataManager' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'attributeValueUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'attributeValueUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'attributeValueUtil' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'objectTypeMap' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'objectTypeMap' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'objectTypeMap' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'objectTypeMap' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'attributeValueUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'handlerFactory' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'handlerFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'xgmmlParser' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'readDataManager' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'attributeValueUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'xgmmlReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'sifFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'sifFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'streamUtil' [org.springframework.beans.BeanUtils] : No property editor [org.cytoscape.io.DataCategoryEditor] found for type org.cytoscape.io.DataCategory according to 'Editor' suffix convention [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'sifFilter' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'sifFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'sifReaderFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'sifReaderFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'sifFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'sifReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'sifReaderFactory' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'sifReaderFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'xgmmlReaderFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'xgmmlReaderFactory' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating shared instance of singleton bean 'xgmmlFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Creating instance of bean 'xgmmlFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'xgmmlFilter' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'xgmmlFilter' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'xgmmlReader' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Returning cached instance of singleton bean 'streamUtil' [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Eagerly caching bean 'xgmmlReaderFactory' to allow for resolving potential circular references [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Finished creating instance of bean 'xgmmlReaderFactory' --------------------------------------- SIF Description = SIF files (*.sif) --------------------------------------- Reader Manager Test Begins --------------------------------------- End of reader manager test [org.springframework.test.context.junit4.SpringMethodRoadie] : Test method [public void org.cytoscape.io.internal.BeanIntegrationTest.readerManagerTest() throws java.lang.Exception] threw exception: null [org.springframework.test.context.support.DirtiesContextTestExecutionListener] : After test method: context [[testcont...@5a5e179a testClass = BeanIntegrationTest, locations = array<String>['classpath:META-INF/spring/bundle-context.xml'], testInstance = org.cytoscape.io.internal.beanintegrationt...@575fadcf, testMethod = readermanagert...@beanintegrationtest, testException = [null]]], dirtiesContext [false]. Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 sec Results : Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 [org.springframework.context.support.GenericApplicationContext] : Closing org.springframework.context.support.genericapplicationcont...@7f09fd93: display name [org.springframework.context.support.genericapplicationcont...@7f09fd93]; startup date [Sat Aug 14 20:16:51 EDT 2010]; root of context hierarchy [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Destroying singletons in org.springframework.beans.factory.support.defaultlistablebeanfact...@3f9f3736: defining beans [org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,sifReaderFactory,xgmmlReaderFactory,sifFilter,xgmmlFilter,sifReader,objectTypeMap,attributeValueUtil,handlerFactory,readDataManager,xgmmlParser,xgmmlReader,cyReaderManager,readUtil,streamUtil]; root of factory hierarchy [org.springframework.beans.factory.support.DefaultListableBeanFactory] : Retrieved dependent beans for bean 'cyReaderManager': [org.cytoscape.io.internal.BeanIntegrationTest] Exception in thread "Thread-0" java.lang.ExceptionInInitializerError at java.io.File.deleteOnExit(File.java:939) at net.sourceforge.cobertura.util.FileLocker.<init>(FileLocker.java:80) at net.sourceforge.cobertura.coveragedata.ProjectData.saveGlobalProjectData(ProjectData.java:230) at net.sourceforge.cobertura.coveragedata.SaveTimer.run(SaveTimer.java:31) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.IllegalStateException: Shutdown in progress at java.lang.Shutdown.add(Shutdown.java:62) at java.lang.System$2.registerShutdownHook(System.java:1146) at java.io.DeleteOnExitHook.<clinit>(DeleteOnExitHook.java:20) ... 5 more [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 79 classes. Report time: 928ms [INFO] Cobertura Report generation was successful. [INFO] org.cytoscape.io-impl [org.cytoscape.io] Executing org.apache.maven.plugins:maven-surefire-plugin:[] [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.findbugs.FindbugsMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.cpd.CpdMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] Collecting duplications... [INFO] org.cytoscape.io-impl [org.cytoscape.io] File suffixes : java [INFO] org.cytoscape.io-impl [org.cytoscape.io] Exclusions : {} [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.checkstyle.CheckstyleMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.pmd.PmdMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.core.SaveProfileMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.core.sources.ImportJavaSourcesMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.core.SaveProjectLinksFromPom] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.javancss.JavaNcssMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.cobertura.CoberturaMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/site/cobertura/coverage.xml> [INFO] org.cytoscape.io-impl [org.cytoscape.io] [class org.sonar.plugins.surefire.SurefireMavenCollector] executing [INFO] org.cytoscape.io-impl [org.cytoscape.io] parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/surefire-reports> [INFO] Trigger server [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1 minute 4 seconds [INFO] Finished at: Sat Aug 14 20:17:00 EDT 2010 [INFO] Final Memory: 92M/842M [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.
