Develop Reference

Guice Creation Errors Magnolia

I am working on a project for the company I'm employed by. They are using Magnolia CMS. I am getting this error in the console in Eclipse when I try to start the Tomcat server.
I have searched for a solution but am finding it difficult. I've tried reinstalling eclipse, tomcat, deleting the .m2 repository and rebuilding, cleaning the project, cleaning tomcat working directory, commenting out the config for log4j in magnolia.properties.
I've googled the errors but not found anything helpful. I have tried on a completely different machine and I get the same error so it might be something to do with the code rather than the environment. However, I have colleagues who are on windows who dont get this error. Any help would be appreciated.
Tomcat 8.5, mac osx 10.13.6 high sierra, java 8 update 191 (build 1.8.0_191-b12), magnolia version is not the latest version (I will find out and update).
Initializing Log4J
Initializing Log4J from [WEB-INF/config/default/log4j.xml]
18-11-02 17:38:49 ERROR PUBLIC[main]info.magnolia.objectfactory.guice.GuiceComponentProviderBuilder: Magnolia failed to load module configuration with types {} and components {Key[type=info.magnolia.cms.pddescriptor.ProductDescriptorExtractor, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#4e251e4d, Key[type=info.magnolia.cms.util.UnicodeNormalizer$Normalizer, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#622f47c4, Key[type=info.magnolia.content2bean.Content2BeanProcessor, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#56c25298, Key[type=info.magnolia.cms.filters.FilterManager, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#210b1e0a, Key[type=info.magnolia.cms.beans.config.ConfigLoader, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#3b12c7f8, Key[type=info.magnolia.cms.core.FileSystemHelper, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#63167b60, Key[type=info.magnolia.cms.i18n.MessagesManager, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#9ac51e8b, Key[type=info.magnolia.cms.license.LicenseFileExtractor, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#e660a786, Key[type=info.magnolia.content2bean.TypeMapping, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#a0a859f1, Key[type=info.magnolia.context.SystemContext, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#f98910d0, Key[type=info.magnolia.cms.beans.config.VersionConfig, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#b2d693be, Key[type=info.magnolia.init.MagnoliaConfigurationProperties, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#69e0fc4f, Key[type=info.magnolia.jcr.registry.SessionProviderRegistry, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#1fa6adc2, Key[type=info.magnolia.transformer.BeanTypeResolver, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#be83187a, Key[type=info.magnolia.content2bean.TransformationState, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#a57e83b8, Key[type=info.magnolia.content2bean.Content2BeanTransformer, annotation=[none]]=info.magnolia.objectfactory.configuration.ImplementationConfiguration#753582eb}. Please ensure you don't have any legacy modules present in your web application.
com.google.inject.CreationException: Guice creation errors:
1) A binding to org.slf4j.Logger was already configured at [unknown source].
at info.magnolia.objectfactory.guice.GuiceParentBindingsModule.configure(GuiceParentBindingsModule.java:85)
1 error
at com.google.inject.internal.Errors.throwCreationExceptionIfErrorsExist(Errors.java:411)
at com.google.inject.internal.InternalInjectorCreator.initializeStatically(InternalInjectorCreator.java:167)
at com.google.inject.internal.InternalInjectorCreator.build(InternalInjectorCreator.java:119)
at com.google.inject.InjectorBuilder.build(InjectorBuilder.java:100)
at com.google.inject.Guice.createInjector(Guice.java:95)
at com.google.inject.Guice.createInjector(Guice.java:83)
at info.magnolia.objectfactory.guice.GuiceComponentProviderBuilder.build(GuiceComponentProviderBuilder.java:149)
at info.magnolia.objectfactory.guice.GuiceComponentProviderBuilder.build(GuiceComponentProviderBuilder.java:196)
at info.magnolia.init.MagnoliaServletContextListener.contextInitialized(MagnoliaServletContextListener.java:168)
at info.magnolia.init.MagnoliaServletContextListener.contextInitialized(MagnoliaServletContextListener.java:128)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4643)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5109)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1429)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1419)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:944)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:839)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1429)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1419)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:944)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:261)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:422)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:770)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Catalina.start(Catalina.java:682)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)
18-11-02 17:38:49 ERROR PUBLIC[main]info.magnolia.init.MagnoliaServletContextListener: Oops, Magnolia could not be started
com.google.inject.CreationException: Guice creation errors:

What the error is telling you is that various type mappings are missing. Based on the mappings mentioned in the error, I'd guess that those are mappings normally described in magnolia-core-x.y.z.jar:/META-INF/magnolia/core.xml. Jar itself or at least the classes it contains must be on the classpath otherwise Magnolia would not get even as far in the startup as it did. How you can be missing the mapping file from the jar is a mystery to me.
Are you trying to compile Magnolia from the sources or using existing precompiled version? Or perhaps you have file with same name somewhere on the classpath that is loaded by classloader prior the correct one from magnolia-core.jar?

Manage TomEE libs loading order

I have an EJB application that is currently deployed on TomEE 1.7.4 with OpenJDK 7 inside a docker container (openjdk 7, TomEE, and my war).
Note: The Jar files that I added within TomEE lib folder are reconized by the application, because I had some errors that has been solved after adding those Jar files.
The error log
INFO: PersistenceUnit(name=manager1, provider=org.hibernate.jpa.HibernatePersistenceProvider) - provider time 2214ms
Apr 25, 2018 5:35:21 PM org.apache.openejb.assembler.classic.Assembler destroyApplication
INFO: Undeploying app: /usr/local/tomee/webapps/myapp
Apr 25, 2018 5:35:21 PM org.apache.catalina.core.ContainerBase removeChild
SEVERE: ContainerBase.removeChild: destroy:
org.apache.catalina.LifecycleException: An invalid Lifecycle transition was attempted ([before_destroy]) for component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/myapp]] in state [STARTING_PREP]
at org.apache.catalina.util.LifecycleBase.invalidTransition(LifecycleBase.java:401)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:291)
at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:1038)
at org.apache.tomee.catalina.TomcatWebAppBuilder.undeploy(TomcatWebAppBuilder.java:1537)
at org.apache.tomee.catalina.TomcatWebAppBuilder.undeploy(TomcatWebAppBuilder.java:1518)
at org.apache.tomee.catalina.TomcatWebAppBuilder.undeployWebApps(TomcatWebAppBuilder.java:762)
at org.apache.openejb.assembler.classic.Assembler.destroyApplication(Assembler.java:1982)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:839)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:677)
at org.apache.tomee.catalina.TomcatWebAppBuilder.startInternal(TomcatWebAppBuilder.java:1261)
at org.apache.tomee.catalina.TomcatWebAppBuilder.configureStart(TomcatWebAppBuilder.java:1100)
at org.apache.tomee.catalina.GlobalListenerSupport.lifecycleEvent(GlobalListenerSupport.java:130)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5472)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:473)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1152)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:622)
at java.lang.Thread.run(Thread.java:748)
Apr 25, 2018 5:35:21 PM org.apache.tomee.catalina.TomcatWebAppBuilder startInternal
SEVERE: Unable to deploy collapsed ear in war StandardEngine[Catalina].StandardHost[localhost].StandardContext[/myapp]
org.apache.openejb.OpenEJBException: Creating application failed: /usr/local/tomee/webapps/myapp: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:843)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:677)
at org.apache.tomee.catalina.TomcatWebAppBuilder.startInternal(TomcatWebAppBuilder.java:1261)
at org.apache.tomee.catalina.TomcatWebAppBuilder.configureStart(TomcatWebAppBuilder.java:1100)
at org.apache.tomee.catalina.GlobalListenerSupport.lifecycleEvent(GlobalListenerSupport.java:130)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5472)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:473)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1152)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:622)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
at org.hibernate.cfg.annotations.EntityBinder.processComplementaryTableDefinitions(EntityBinder.java:973)
at org.hibernate.cfg.AnnotationBinder.bindClass(AnnotationBinder.java:824)
at org.hibernate.cfg.Configuration$MetadataSourceQueue.processAnnotatedClassesQueue(Configuration.java:3845)
at org.hibernate.cfg.Configuration$MetadataSourceQueue.processMetadata(Configuration.java:3799)
at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1412)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1846)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:857)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:850)
at org.hibernate.boot.registry.classloading.internal.ClassLoaderServiceImpl.withTccl(ClassLoaderServiceImpl.java:425)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:849)
at org.hibernate.jpa.HibernatePersistenceProvider.createContainerEntityManagerFactory(HibernatePersistenceProvider.java:152)
at org.apache.openejb.assembler.classic.EntityManagerFactoryCallable.call(EntityManagerFactoryCallable.java:64)
at org.apache.openejb.assembler.classic.ReloadableEntityManagerFactory.createDelegate(ReloadableEntityManagerFactory.java:116)
at org.apache.openejb.assembler.classic.ReloadableEntityManagerFactory.<init>(ReloadableEntityManagerFactory.java:102)
at org.apache.openejb.assembler.classic.PersistenceBuilder.createEntityManagerFactory(PersistenceBuilder.java:154)
at org.apache.openejb.assembler.classic.Assembler.loadPersistenceUnits(Assembler.java:982)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:741)
List of Jar added to TomEE lib folder:
mysql:mysql-connector-java:5.1.22
org.hibernate.javax.persistence:hibernate-jpa-2.1-api:1.0.0.Final
org.hibernate:hibernate-entitymanager:4.3.9.Final
org.hibernate:hibernate-core:4.3.9.Final
org.hibernate.common:hibernate-commons-annotations:4.0.5.Final
org.jboss:jandex:1.1.0.Final
org.jboss.logging:jboss-logging:3.1.3.GA
org.javassist:javassist:3.18.1-GA
antlr:antlr:2.7.7
dom4j:dom4j:1.6.1
Although, I tried to deploy other apps within this docker image and every think works as expected.

TLDR; your TomEE version does not support the apis you seem to be using.
I would go with upgrading TomEE, so you would get proper support for the apis you want to use. Other solutions are just workarounds that might break in numerous ways as they are not supported.
A bit longer answer:
This looks java app dependency problem/version conflict for me: see this thread for similar error message and its cause. The dependencies you've added depend on javax.persistence spec 2.1, but based on the stack trace your app seems to be using older apis.
You seem to want to use Java Persistence API 2.1, that comes with Java EE 7. Java EE 6 contains Java Persistence API 2.0.
Version of TomEE you're using, Apache TomEE 1.7.4, supports only Java EE 6 and thus Persistence API 2.0, and it was last version not supporting Java EE 7:
From this point on the TomEE community will be focusing most of it's efforts on TomEE 7.0.0, which will be the first TomEE Java EE 7 driven version running on Apache Tomcat 8.x.
So an upgrade of TomEE would be in order.

TomEE comes with OpenJPA as persistence engine.
You can change to Hibernate but you have to follow this guide
Extending the ClassPath is a bad solution although it does the job.

I fugured it out, the solution is to create a "setenv.sh" file in TomEE bin directory with the CLASSPATH of the "jpa 2.1" jar file.
setenv.sh
#!/bin/sh
CLASSPATH=/usr/local/tomee/lib/hibernate-jpa-2.1-api-1.0.0.Final.jar

java.lang.NoSuchMethodError: org.jboss.logging.Logger.getMessageLogger in Tomcat

I using Tomcat 8.0.26 and during the deploy (after executing ./startup) I am getting the following exception:
28-Mar-2018 15:07:58.926 SEVERE [localhost-startStop-2]
org.apache.catalina.core.StandardContext.listenerStart Exception
sending context initialized event to listener instance of class
ie.company.web.AppContextListener java.lang.NoSuchMethodError:
org.jboss.logging.Logger.getMessageLogger(Ljava/lang/Class;Ljava/lang/String;)Ljava/lang/Object;
at org.hibernate.ejb.Ejb3Configuration.(Ejb3Configuration.java:142)
at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:55)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:63)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:47)
at ie.company.persistence.PersistenceUtil.resetFactory(PersistenceUtil.java:44)
at ie.company.persistence.PersistenceUtil.createEntityManager(PersistenceUtil.java:37)
at ie.company.persistence.repository.impl.MerchantCategoryRepositoryImpl.findAllMerchantCategories(MerchantCategoryRepositoryImpl.java:38)
at ie.company.persistence.repository.impl.RepositoryImpl.findAllMerchantCategories(RepositoryImpl.java:1204)
at ie.company.web.AppContextListener.initStrutsApplicationContext(AppContextListener.java:113)
at ie.company.web.AppContextListener.contextInitialized(AppContextListener.java:86)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4729)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5167)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:945)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1768)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
I've seen dozens of posts about this exception:
java.lang.NoSuchMethodError:
org.jboss.logging.Logger.getMessageLogger(Ljava/lang/Class;Ljava/lang/String;)Ljava/lang/Objec
But no one does make sense to me, since I have the same “.war” file running on different servers (I don't have any problems running the application on my local system in Eclipse as well). Currently the application is running on Linux Opensuse and I am migrating it to Linux Ubuntu 16.04. I don't think that I am missing any library because I copied and pasted the exactly Tomcat installation from the old server on which the applications is currently running. Any clue? Please help me.

Trying to run the RSA SDK under Tomcat 8

Java newbie here.
Working on a some java App that uses the RSA SDK 8.2. All applications work fine when run as a console application. We're need to put a Web front end on it but we error out as shows below.
We've tried running it on both Wildfly 10 and Tomcat 8.0. Using Java 1.8
Below is error received when running on Tomcat. The error of NoSuchMethodException below from org.glassfish.tyrus.server.TyrusServerConfiguration.()
This exists in one of the Jars provided in the SDK. If we remove the jar Tomcat will serve up the page but will fail when a call to the SDK is made. If we include the jar, we get the error below.
SEVERE: Error during ServletContainerInitializer processing<br>
javax.servlet.ServletException: java.lang.InstantiationException: org.glassfish.tyrus.server.TyrusServerConfiguration<br>
at org.apache.tomcat.websocket.server.WsSci.onStartup(WsSci.java:88)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5303)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1408)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1398)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.InstantiationException: org.glassfish.tyrus.server.TyrusServerConfiguration
at java.lang.Class.newInstance(Class.java:427)
at org.apache.tomcat.websocket.server.WsSci.onStartup(WsSci.java:74)
... 8 more
Caused by: java.lang.NoSuchMethodException: org.glassfish.tyrus.server.TyrusServerConfiguration.<init>()
at java.lang.Class.getConstructor0(Class.java:3082)
at java.lang.Class.newInstance(Class.java:412)
... 9 more
Sep 26, 2017 3:00:39 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/tomcattest3] startup failed due to previous errors

I was able to duplicate this problem using Tomcat 9. I added websocket-ri-bundle-1.1.jar to Tomcat's lib without realizing that it already contained websocket-api-jar. When I removed the ri bundle I no longer got the error.

Possible root causes include a too low setting for -Xss and illegal cyclic inheritance dependencies

My app is quit big and using many jars and tools.
Platform - windows 2008 server, Spring , hibernate, Quarts, mysql, tomcat-7.35
When I deploy and start the server first time working perfectly,
but If I restart I am getting the below err
SEVERE: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/TestProject]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1114)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1673)
at java.util.concurrent.Executors$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:722)
Caused by: java.lang.IllegalStateException: Unable to complete the scan for annotations for web application [/TestProject]. Possible root causes include a too low setting for -Xss and illegal cyclic inheritance dependencies
at org.apache.catalina.startup.ContextConfig.processAnnotationsStream(ContextConfig.java:2109)
at org.apache.catalina.startup.ContextConfig.processAnnotationsJar(ContextConfig.java:1981)
at org.apache.catalina.startup.ContextConfig.processAnnotationsUrl(ContextConfig.java:1947)
at org.apache.catalina.startup.ContextConfig.processAnnotations(ContextConfig.java:1932)
at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1326)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:878)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:369)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5179)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 11 more
Caused by: java.lang.StackOverflowError
at java.util.HashSet.<init>(HashSet.java:103)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2252)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
at org.apache.catalina.startup.ContextConfig.populateSCIsForCacheEntry(ContextConfig.java:2269)
Feb 16, 2013 12:16:10 PM org.apache.catalina.startup.HostConfig deployDirectory
SEVERE: Error deploying web application directory C:\apache-tomcat-7.0.35\webapps\TestProject
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[TestProject]]
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:904)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1114)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1673)
at java.util.concurrent.Executors$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:722)

The stack trace says that tomcat is running out of stack space on the thread that is scanning your application looking for java based servlet configurations. There are three ways you can solve this problem.
Increase the stack size -Xss4m
Tell Tomcat not to scan your application if you are not using any java based Servlet configuration add metadata-complete="true" to your web-app in web.xml
Restrict what jar files tomcat scans. see http://tomcat.apache.org/tomcat-7.0-doc/config/jar-scanner.html
Update 1
you need to pass -Xss4m to your jvm to set the stack size, -Xss10m would set it to 10mb.
I am using Hibernate and Spring in my application too with annotations, the scanning that tomcat does is to look for Servlet 3.0 annotations so you can still restrict things while using hibernate and spring annotations, since hibernate and spring annoations are scanned for by spring and hibernate.
If you are running tomcat as a windows service you will need, to pass the arguments via procrun since that is the executable that is launching the jvm. The docs for procrun are at http://commons.apache.org/daemon/procrun.html. tomcat7.exe is really procrun.exe renamed, which means that all your jvm options are written to the registery under
The basic Service definitions are maintained under the registry key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\
Additional parameters are stored in the registry at:
HKEY_LOCAL_MACHINE\SOFTWARE\Apache Software Foundation\ProcRun
2.0\\Parameters
On 64-bit Windows procrun always uses 32-bit registry view for storing
the configuration. This means that parameters will be stored inside:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Apache Software
Foundation\ProcRun 2.0\
Update 2
Tomcat has been tweaking how the scanner works between point releases. try rolling forward through the versions 7.25,7.26 ... etc to find the version at which it breaks, the go through the release notes for that version to see if they changed how the scanner works.
Another thing you can try doing, is to create another war file which has all the third party jars in your WEB-INF\lib but not your code. See if you get that error if you start up, and if you do then should file a bug report with tomcat and make available to them your sample project that replicates the problem, on github or some other free code hosting system. I am sure if there is a bug they will fix it.

To fix this for TC Server 2.9, running Tomcat 7.0.39 I restricted the jars to skip during startup for the context config using:
org.apache.catalina.startup.ContextConfig.jarsToSkip=*.jar
in catalina.properties.

In My case iTextpdf JAR(5.06 version) causing problem as it had dependancy on org.bouncyCastle.*.jar and it was creating cyclic dependancy.
After updating it to 5.5.6 version, worked perfectly.
If you are adding maven dependancy , clean and update maven project.
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>itextpdf</artifactId>
<version>5.5.6</version>
</dependency>

I'm not running Tomcat as a Windows service, so to pass -Xss10m through, I edited catalina.bat, towards the bottom:
:doJpda
if not "%SECURITY_POLICY_FILE%" == "" goto doSecurityJpda
%_EXECJAVA% %JAVA_OPTS% %CATALINA_OPTS% %JPDA_OPTS% %DEBUG_OPTS% -Djava.endorsed.dirs="%JAVA_ENDORSED_DIRS%" -Xss10m -classpath "%CLASSPATH%" -
Dcatalina.base="%CATALINA_BASE%" -Dcatalina.home="%CATALINA_HOME%" -Djava.io.tmpdir="%CATALINA_TMPDIR%" %MAINCLASS% %CMD_LINE_ARGS% %ACTION%
goto end