From: Vladimir G. <vla...@du...> - 2010-09-09 22:18:56
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Shouldn't trouble like this be fixable by a complete rebuild? I do 'mvn clean' all the time. My only next guess along this line of thought is that Maven update magic went wrong in my account and I should try nixing the Maven repository and rebuilding treebase from a fresh SVN checkout. In either case, this does not enlighten me what goes wrong between SVN versions 730 and 731 -- the startup error seems to come from deep inside Spring, so I have no clue how updates in #731 could have affected that behavior. A feeble guess is that something is fishy with pom.xml changes that did occur in #731. I'll try to get hold of the WAR built by Hudson for treebase-dev and see if it runs on my tomcat... --VG On Sep 9, 2010, at 4:45 PM, Hilmar Lapp wrote: > This sounds like a class with an abstract method is being > instantiated. > > This can happen in Java for example if a different version of an > external library changes the definition (signature) of an abstract > method in a (therefore abstract) class so that the inheriting class > in your own code that previously implemented the abstract method now > no longer does so, or if it adds a new abstract method to the class > that your implementing class wasn't aware of at the time it was > implemented. > > In other words, this smells like a version incompatibility with an > external library, likely the Xerces parser given the error message. > > Does this ring a bell or give you a target for trying to fix the > issue? > > -hilmar > > On Sep 9, 2010, at 4:31 PM, Vladimir Gapeyev wrote: > >> >> Hi, Youjun, >> >> I cannot start a local TB instance in Tomcat, for any of the recent >> versions: the application breaks on startup. The catalina.out error >> log for the tomcat startup sequence is appended below. >> >> I tracked the problem down to SVN#731 that you committed on 7/13: >> versions up to 730 start up and run just fine, while 731 and the >> later >> ones, up to the head (#748) break at startup with the same error. >> Inexplicably, rebuild on treebase-dev works just fine. >> >> Looking at the error log below and the SVN log for 731 that I am >> resending separately, do you have any idea what has changed in #731 >> that made things go wrong? >> >> Thanks, >> >> --Vladimir >> >> >> ----------------------------------------------------------------------------------------------- >> Thursday, September 9, 2010 4:20:30 PM US/Eastern >> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener >> lifecycleEvent >> INFO: The Apache Tomcat Native library which allows optimal >> performance in production environments was not found on the >> java.library.path: .:/Library/Java/Extensions:/System/Library/Java/ >> Extensions:/usr/lib/java >> Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol >> init >> INFO: Initializing Coyote HTTP/1.1 on http-8080 >> Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load >> INFO: Initialization processed in 479 ms >> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start >> INFO: Starting service Catalina >> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start >> INFO: Starting Servlet Engine: Apache Tomcat/5.5.28 >> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start >> INFO: XML validation disabled >> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader >> validateJarFile >> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- >> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo- >> servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3, >> section 9.7.2. Offending class: javax/servlet/Servlet.class >> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader >> validateJarFile >> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- >> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) - >> jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: >> javax/servlet/Servlet.class >> [main] DEBUG org.cipres.treebase.web.listeners.StartupListener - >> contextInitialized(ServletContextEvent) - >> FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart >> [main] WARN org.hibernate.cache.CacheFactory - read-only cache >> configured for mutable class: staticCache >> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find >> configuration [org.hibernate.cache.UpdateTimestampsCache]; using >> defaults. >> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find >> configuration [org.hibernate.cache.StandardQueryCache]; using >> defaults. >> [main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite - >> Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/ >> TreeBase/mytomcat/mesquite-2.01.tb >> Sep 9, 2010 4:20:40 PM >> org.apache.cxf.service.factory.ReflectionServiceFactoryBean >> buildServiceFromClass >> INFO: Creating Service {http:// >> webservices.web.treebase.cipres.org/}StudiesContainingKeyword from >> class org.cipres.treebase.web.webservices.StudyServiceByKeyword >> [main] ERROR org.springframework.web.context.ContextLoader - Context >> initialization failed >> org.springframework.beans.factory.BeanCreationException: Error >> creating bean with name 'searchStudiesByKeyword': Invocation of init >> method failed; nested exception is java.lang.AbstractMethodError: >> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ >> String; >> Caused by: >> java.lang.AbstractMethodError: >> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ >> String; >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at >> org >> .apache >> .ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: >> 602) >> at >> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: >> 84) >> at >> org >> .apache >> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: >> 424) >> at >> org >> .apache >> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: >> 418) >> at >> org >> .apache >> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java: >> 142) >> at >> org >> .apache >> .cxf >> .databinding >> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93) >> at >> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: >> 345) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345) >> at >> org >> .apache >> .cxf >> .jaxws >> .support >> .JaxWsServiceFactoryBean >> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .initializeServiceModel(ReflectionServiceFactoryBean.java:396) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .create(ReflectionServiceFactoryBean.java: >> 181) >> at >> org >> .apache >> .cxf >> .jaxws >> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: >> 163) >> at >> org >> .apache >> .cxf >> .frontend >> .AbstractWSDLBasedEndpointFactory >> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79) >> at >> org >> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: >> 114) >> at >> org >> .apache >> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: >> 164) >> at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java: >> 334) >> at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java: >> 251) >> at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201) >> at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .createBean(AbstractAutowireCapableBeanFactory.java:427) >> at org.springframework.beans.factory.support.AbstractBeanFactory >> $1.getObject(AbstractBeanFactory.java:249) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .DefaultSingletonBeanRegistry >> .getSingleton(DefaultSingletonBeanRegistry.java:155) >> at >> org >> .springframework >> .beans >> .factory >> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: >> 246) >> at >> org >> .springframework >> .beans >> .factory >> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: >> 160) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .DefaultListableBeanFactory >> .preInstantiateSingletons(DefaultListableBeanFactory.java:291) >> at >> org >> .springframework >> .context >> .support >> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: >> 352) >> at org.springframework.web.context.ContextLoader.createWebApplicationContext >> (ContextLoader.java:245) >> at org.springframework.web.context.ContextLoader.initWebApplicationContext >> (ContextLoader.java:188) >> at org.springframework.web.context.ContextLoaderListener.contextInitialized >> (ContextLoaderListener.java:49) >> at >> org >> .cipres >> .treebase >> .web >> .listeners.StartupListener.contextInitialized(StartupListener.java: >> 45) >> at >> org >> .apache >> .catalina.core.StandardContext.listenerStart(StandardContext.java: >> 3795) >> at >> org.apache.catalina.core.StandardContext.start(StandardContext.java: >> 4252) >> at >> org >> .apache >> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) >> at >> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: >> 740) >> at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: >> 544) >> at >> org >> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: >> 626) >> at >> org >> .apache >> .catalina.startup.HostConfig.deployDescriptors(HostConfig.java: >> 553) >> at >> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: >> 488) >> at org.apache.catalina.startup.HostConfig.start(HostConfig.java: >> 1150) >> at >> org >> .apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: >> 311) >> at >> org >> .apache >> .catalina >> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) >> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: >> 1022) >> at org.apache.catalina.core.StandardHost.start(StandardHost.java: >> 736) >> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: >> 1014) >> at >> org.apache.catalina.core.StandardEngine.start(StandardEngine.java: >> 443) >> at >> org.apache.catalina.core.StandardService.start(StandardService.java: >> 448) >> at >> org.apache.catalina.core.StandardServer.start(StandardServer.java: >> 700) >> at org.apache.catalina.startup.Catalina.start(Catalina.java:552) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) >> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) >> [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. >> [localhost].[/treebase-web] - Exception sending context initialized >> event to listener instance of class org.cipres.treebase.web.listeners.StartupListener >> org.springframework.beans.factory.BeanCreationException: Error >> creating bean with name 'searchStudiesByKeyword': Invocation of init >> method failed; nested exception is java.lang.AbstractMethodError: >> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ >> String; >> Caused by: >> java.lang.AbstractMethodError: >> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ >> String; >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at >> org >> .apache >> .ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: >> 602) >> at >> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: >> 84) >> at >> org >> .apache >> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: >> 424) >> at >> org >> .apache >> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: >> 418) >> at >> org >> .apache >> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java: >> 142) >> at >> org >> .apache >> .cxf >> .databinding >> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93) >> at >> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: >> 345) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345) >> at >> org >> .apache >> .cxf >> .jaxws >> .support >> .JaxWsServiceFactoryBean >> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .initializeServiceModel(ReflectionServiceFactoryBean.java:396) >> at >> org >> .apache >> .cxf >> .service >> .factory >> .ReflectionServiceFactoryBean >> .create(ReflectionServiceFactoryBean.java: >> 181) >> at >> org >> .apache >> .cxf >> .jaxws >> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: >> 163) >> at >> org >> .apache >> .cxf >> .frontend >> .AbstractWSDLBasedEndpointFactory >> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79) >> at >> org >> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: >> 114) >> at >> org >> .apache >> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: >> 164) >> at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java: >> 334) >> at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java: >> 251) >> at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201) >> at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .AbstractAutowireCapableBeanFactory >> .createBean(AbstractAutowireCapableBeanFactory.java:427) >> at org.springframework.beans.factory.support.AbstractBeanFactory >> $1.getObject(AbstractBeanFactory.java:249) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .DefaultSingletonBeanRegistry >> .getSingleton(DefaultSingletonBeanRegistry.java:155) >> at >> org >> .springframework >> .beans >> .factory >> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: >> 246) >> at >> org >> .springframework >> .beans >> .factory >> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: >> 160) >> at >> org >> .springframework >> .beans >> .factory >> .support >> .DefaultListableBeanFactory >> .preInstantiateSingletons(DefaultListableBeanFactory.java:291) >> at >> org >> .springframework >> .context >> .support >> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: >> 352) >> at org.springframework.web.context.ContextLoader.createWebApplicationContext >> (ContextLoader.java:245) >> at org.springframework.web.context.ContextLoader.initWebApplicationContext >> (ContextLoader.java:188) >> at org.springframework.web.context.ContextLoaderListener.contextInitialized >> (ContextLoaderListener.java:49) >> at >> org >> .cipres >> .treebase >> .web >> .listeners.StartupListener.contextInitialized(StartupListener.java: >> 45) >> at >> org >> .apache >> .catalina.core.StandardContext.listenerStart(StandardContext.java: >> 3795) >> at >> org.apache.catalina.core.StandardContext.start(StandardContext.java: >> 4252) >> at >> org >> .apache >> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) >> at >> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: >> 740) >> at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: >> 544) >> at >> org >> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: >> 626) >> at >> org >> .apache >> .catalina.startup.HostConfig.deployDescriptors(HostConfig.java: >> 553) >> at >> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: >> 488) >> at org.apache.catalina.startup.HostConfig.start(HostConfig.java: >> 1150) >> at >> org >> .apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: >> 311) >> at >> org >> .apache >> .catalina >> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) >> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: >> 1022) >> at org.apache.catalina.core.StandardHost.start(StandardHost.java: >> 736) >> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: >> 1014) >> at >> org.apache.catalina.core.StandardEngine.start(StandardEngine.java: >> 443) >> at >> org.apache.catalina.core.StandardService.start(StandardService.java: >> 448) >> at >> org.apache.catalina.core.StandardServer.start(StandardServer.java: >> 700) >> at org.apache.catalina.startup.Catalina.start(Catalina.java:552) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun >> .reflect >> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: >> 39) >> at >> sun >> .reflect >> .DelegatingMethodAccessorImpl >> .invoke(DelegatingMethodAccessorImpl.java: >> 25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) >> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) >> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start >> SEVERE: Error listenerStart >> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start >> SEVERE: Context [/treebase-web] startup failed due to previous errors >> WARN: The method class >> org.apache.commons.logging.impl.SLF4JLogFactory#release() was >> invoked. >> WARN: Please see http://www.slf4j.org/codes.html for an explanation. >> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start >> SEVERE: Error filterStart >> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start >> SEVERE: Context [/balancer] startup failed due to previous errors >> Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol >> start >> INFO: Starting Coyote HTTP/1.1 on http-8080 >> Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init >> INFO: JK: ajp13 listening on /0.0.0.0:8009 >> Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start >> INFO: Jk running ID=0 time=0/16 config=null >> Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader >> load >> INFO: Find registry server-registry.xml at classpath resource >> Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start >> INFO: Server startup in 8433 ms >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net Dev2Dev email is sponsored by: >> >> Show off your parallel programming skills. >> Enter the Intel(R) Threading Challenge 2010. >> http://p.sf.net/sfu/intel-thread-sfd >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > |