Can not upgrade confluence

when trying to Confluence 3.4.9 upgrading to version 3.5.x (eg 3.5.13) there is an error:

2012-02-07 07:27:18,202 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 3.5.13 (build #2171)
2012-02-07 07:27:21,119 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system
2012-02-07 07:27:21,382 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Plugin system started in 0:00:00.260
2012-02-07 07:27:22,848 INFO [main] [springframework.web.context.ContextLoader] initWebApplicationContext Root WebApplicationContext: initialization started
2012-02-07 07:27:24,675 INFO [main] [com.atlassian.confluence.lifecycle] <init> Loading EhCache cache manager
2012-02-07 07:27:33,701 ERROR [main] [springframework.web.context.ContextLoader] initWebApplicationContext Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginResourceLocator' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'webResourceIntegration' while setting constructor argument with index 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webResourceIntegration' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'settingsManager' while setting constructor argument with index 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webResourceIntegration' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'settingsManager' while setting constructor argument with index 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: java.lang.NegativeArraySizeException
    at org.apache.lucene.store.IndexInput.readString(IndexInput.java:122)
    at org.apache.lucene.index.FieldInfos.read(FieldInfos.java:356)
    at org.apache.lucene.index.FieldInfos.<init>(FieldInfos.java:71)
    at org.apache.lucene.index.SegmentReader$CoreReaders.<init>(SegmentReader.java:120)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:667)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:628)
    at org.apache.lucene.index.DirectoryReader.<init>(DirectoryReader.java:108)
    at org.apache.lucene.index.DirectoryReader$1.doBody(DirectoryReader.java:80)
    at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:683)
    at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:73)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:476)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:300)
    at org.apache.lucene.search.IndexSearcher.<init>(IndexSearcher.java:87)
    at org.apache.lucene.search.DelayCloseIndexSearcher.<init>(DelayCloseIndexSearcher.java:87)
    at com.atlassian.bonnie.LuceneConnection.createSearcher(LuceneConnection.java:483)
    at com.atlassian.bonnie.LuceneConnection.<init>(LuceneConnection.java:93)
    at com.atlassian.bonnie.LuceneConnection.<init>(LuceneConnection.java:108)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
    at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:85)
    at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:187)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1100)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:862)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.AbstractAutowireCapableBeanFactory.autowireByName(AbstractAutowireCapableBeanFactory.java:881)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:829)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1100)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:862)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:385)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:121)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:385)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:121)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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:246)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:189)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49)
    at com.atlassian.spring.container.ContainerContextLoaderListener.contextInitialized(ContainerContextLoaderListener.java:32)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4205)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4704)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    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.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
2012-02-07 07:27:33,709 ERROR [main] [ContainerBase.[Standalone].[localhost].[/]] log Exception sending context initialized event to listener instance of class com.atlassian.config.bootstrap.BootstrappedContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginResourceLocator' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'webResourceIntegration' while setting constructor argument with index 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webResourceIntegration' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'settingsManager' while setting constructor argument with index 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webResourceIntegration' defined in class path resource [services/pluginServiceContext.xml]: Cannot resolve reference to bean 'settingsManager' while setting constructor argument with index 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' while setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'systemInformationService' defined in class path resource [services/statusServiceContext.xml]: Cannot resolve reference to bean 'luceneConnection' while setting bean property 'luceneConnection'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'luceneConnection' defined in class path resource [indexingSubsystemContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.atlassian.bonnie.LuceneConnection]: Constructor threw exception; nested exception is java.lang.NegativeArraySizeException
Caused by: java.lang.NegativeArraySizeException
    at org.apache.lucene.store.IndexInput.readString(IndexInput.java:122)
    at org.apache.lucene.index.FieldInfos.read(FieldInfos.java:356)
    at org.apache.lucene.index.FieldInfos.<init>(FieldInfos.java:71)
    at org.apache.lucene.index.SegmentReader$CoreReaders.<init>(SegmentReader.java:120)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:667)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:628)
    at org.apache.lucene.index.DirectoryReader.<init>(DirectoryReader.java:108)
    at org.apache.lucene.index.DirectoryReader$1.doBody(DirectoryReader.java:80)
    at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:683)
    at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:73)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:476)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:300)
    at org.apache.lucene.search.IndexSearcher.<init>(IndexSearcher.java:87)
    at org.apache.lucene.search.DelayCloseIndexSearcher.<init>(DelayCloseIndexSearcher.java:87)
    at com.atlassian.bonnie.LuceneConnection.createSearcher(LuceneConnection.java:483)
    at com.atlassian.bonnie.LuceneConnection.<init>(LuceneConnection.java:93)
    at com.atlassian.bonnie.LuceneConnection.<init>(LuceneConnection.java:108)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
    at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:85)
    at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:187)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1100)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:862)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.AbstractAutowireCapableBeanFactory.autowireByName(AbstractAutowireCapableBeanFactory.java:881)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:829)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1100)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:862)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:385)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:121)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:267)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
    at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:385)
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:121)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:800)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:718)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:386)
    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:246)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:189)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49)
    at com.atlassian.spring.container.ContainerContextLoaderListener.contextInitialized(ContainerContextLoaderListener.java:32)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4205)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4704)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    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.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
2012-02-07 07:27:33,713 ERROR [main] [ContainerBase.[Standalone].[localhost].[/]] log Exception sending context initialized event to listener instance of class com.atlassian.confluence.upgrade.UpgradeLauncherServletContextListener
java.lang.NullPointerException
    at com.atlassian.spring.container.ContainerManager.getComponent(ContainerManager.java:33)
    at com.atlassian.confluence.upgrade.UpgradeLauncherServletContextListener.contextInitialized(UpgradeLauncherServletContextListener.java:23)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4205)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4704)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    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.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
2012-02-07 07:27:34,018 INFO [main] [com.atlassian.confluence.lifecycle] contextDestroyed Stopping Confluence


2 answers

Andrey, this is caused by a corruption in Confluence index directory. This can be solved by removing the Confluence index directory, then restart Confluence to re-trigger the upgrade. More details of this issue is covered in this KB.

Hi Andrey,

I think you may be hitting this known issue - https://jira.atlassian.com/browse/CONF-22487 - a patch file for resolving this is attached to the bug report.

Andrew.

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