I am using glassfish 3.1.2.2 server and idea ultimate edition 11 (on Ubuntu 12.04). While I am deploying my ear project there is an exception, first nullpointer then nosuchmethod. On 3.0.1 of glassfish it works, but in 3.1.2 doesnot.
Server log:
[#|2012-09-25T15:54:14.356+0300|WARNING|glassfish3.1.2|javax.enterprise.system.tools.deployment.org.glassfish.deployment.common|_ThreadID=45;_ThreadName=Thread-2;|DPL8027: Ignore WEB-INF/sun-web.xml in archive /home/kelevra/glassfish3/glassfish/domains/domain1/applications/MO-1.0.1-alpha1-SNAPSHOT/ViewController-1.0.1-alpha1-SNAPSHOT_war/, as GlassFish counterpart runtime xml WEB-INF/glassfish-web.xml is present in the same archive.|#]
[#|2012-09-25T15:54:14.565+0300|WARNING|glassfish3.1.2|javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors.util|_ThreadID=45;_ThreadName=Thread-2;|RAR8068: Using default datasource : __ds_jdbc_ra for pool : eFarmer-Pool|#]
[#|2012-09-25T15:54:14.591+0300|SEVERE|glassfish3.1.2|javax.enterprise.system.tools.deployment.org.glassfish.deployment.common|_ThreadID=78;_ThreadName=Thread-2;|Exception while visiting com/sun/gjc/util/SQLTraceTimerTask.class of size 570
java.lang.NullPointerException
at org.glassfish.hk2.classmodel.reflect.impl.TypesImpl.getType(TypesImpl.java:78)
at org.glassfish.hk2.classmodel.reflect.impl.ModelClassVisitor.visit(ModelClassVisitor.java:119)
at org.objectweb.asm.ClassReader.accept(Unknown Source)
at org.objectweb.asm.ClassReader.accept(Unknown Source)
at org.glassfish.hk2.classmodel.reflect.Parser$5.on(Parser.java:363)
at org.glassfish.hk2.classmodel.reflect.util.JarArchive.onSelectedEntries(JarArchive.java:125)
at org.glassfish.hk2.classmodel.reflect.Parser.doJob(Parser.java:348)
at org.glassfish.hk2.classmodel.reflect.Parser.access$300(Parser.java:70)
at org.glassfish.hk2.classmodel.reflect.Parser$3.call(Parser.java:307)
at org.glassfish.hk2.classmodel.reflect.Parser$3.call(Parser.java:296)
at java.util.concurrent.FutureTask$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)
|#]
[#|2012-09-25T15:54:14.965+0300|WARNING|glassfish3.1.2|javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors.util|_ThreadID=45;_ThreadName=Thread-2;|RAR8068: Using default datasource : __ds_jdbc_ra for pool : eFarmer-Pool|#]
[#|2012-09-25T15:54:17.224+0300|WARNING|glassfish3.1.2|org.eclipse.persistence.session.file:/home/kelevra/glassfish3/glassfish/domains/domain1/applications/MO-1.0.1-alpha1-SNAPSHOT/DataModel-1.0.1-alpha1-SNAPSHOT_jar/_eFarmer.weaver|_ThreadID=45;_ThreadName=Thread-2;|Weaver encountered an exception while trying to weave class com/km/orgfrm/datamodel/entity/AbstractEntity. The exception was: java.lang.RuntimeException: java.lang.ClassNotFoundException: com.km.orgfrm.datamodel.entity.AbstractEntity not found by org.eclipse.persistence.asm [232]|#]
java.lang.NoSuchMethodError: com.km.orgfrm.datamodel.entity.AbstractEntity.<init>(Lorg/eclipse/persistence/internal/descriptors/PersistenceObject;)V
at com.km.efarmer.datamodel.entity.order.operation.OperationTrackGeometryEntity.<init>(OperationTrackGeometryEntity.java)
at com.km.efarmer.datamodel.entity.order.operation.OperationTrackGeometryEntity._persistence_new(OperationTrackGeometryEntity.java)
at org.eclipse.persistence.internal.descriptors.PersistenceObjectInstantiationPolicy.buildNewInstance(PersistenceObjectInstantiationPolicy.java:30)
at org.eclipse.persistence.descriptors.ClassDescriptor.selfValidationAfterInitialization(ClassDescriptor.java:3870)
at org.eclipse.persistence.descriptors.ClassDescriptor.validateAfterInitialization(ClassDescriptor.java:5688)
at org.eclipse.persistence.descriptors.ClassDescriptor.postInitialize(ClassDescriptor.java:3547)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.initializeDescriptors(DatabaseSessionImpl.java:526)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.initializeDescriptors(DatabaseSessionImpl.java:476)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.initializeDescriptors(DatabaseSessionImpl.java:435)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.postConnectDatasource(DatabaseSessionImpl.java:676)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.login(DatabaseSessionImpl.java:634)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryProvider.login(EntityManagerFactoryProvider.java:208)
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl.deploy(EntityManagerSetupImpl.java:488)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.getDatabaseSession(EntityManagerFactoryDelegate.java:188)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.createEntityManagerImpl(EntityManagerFactoryDelegate.java:277)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManagerImpl(EntityManagerFactoryImpl.java:294)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:272)
at org.glassfish.persistence.jpa.PersistenceUnitLoader.loadPU(PersistenceUnitLoader.java:211)
at org.glassfish.persistence.jpa.PersistenceUnitLoader.<init>(PersistenceUnitLoader.java:120)
at org.glassfish.persistence.jpa.JPADeployer$1.visitPUD(JPADeployer.java:224)
at org.glassfish.persistence.jpa.JPADeployer$PersistenceUnitDescriptorIterator.iteratePUDs(JPADeployer.java:495)
at org.glassfish.persistence.jpa.JPADeployer.createEMFs(JPADeployer.java:233)
at org.glassfish.persistence.jpa.JPADeployer.prepare(JPADeployer.java:168)
at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:871)
at org.glassfish.javaee.full.deployment.EarDeployer.prepareBundle(EarDeployer.java:290)
at org.glassfish.javaee.full.deployment.EarDeployer.access$200(EarDeployer.java:86)
at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:141)
at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:138)
at org.glassfish.javaee.full.deployment.EarDeployer.doOnBundles(EarDeployer.java:215)
at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllTypedBundles(EarDeployer.java:224)
at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllBundles(EarDeployer.java:250)
at org.glassfish.javaee.full.deployment.EarDeployer.prepare(EarDeployer.java:138)
at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:871)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:410)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:240)
at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:389)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$1.execute(CommandRunnerImpl.java:348)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:363)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1085)
at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1200(CommandRunnerImpl.java:95)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1291)
at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1259)
at com.sun.enterprise.v3.admin.AdminAdapter.doCommand(AdminAdapter.java:461)
at com.sun.enterprise.v3.admin.AdminAdapter.service(AdminAdapter.java:212)
at com.sun.grizzly.tcp.http11.GrizzlyAdapter.service(GrizzlyAdapter.java:179)
at com.sun.enterprise.v3.server.HK2Dispatcher.dispath(HK2Dispatcher.java:117)
at com.sun.enterprise.v3.services.impl.ContainerMapper$Hk2DispatcherCallable.call(ContainerMapper.java:354)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
at java.lang.Thread.run(Thread.java:722)
|#]
[#|2012-09-25T15:54:18.366+0300|SEVERE|glassfish3.1.2|javax.enterprise.system.tools.admin.org.glassfish.deployment.admin|_ThreadID=45;_ThreadName=Thread-2;|Exception while preparing the app : com.km.orgfrm.datamodel.entity.AbstractEntity.<init>(Lorg/eclipse/persistence/internal/descriptors/PersistenceObject;)V|#]
This type of errors are usually due to having two different versions of the same library in your classpath.
Please check to see if the new version of glassfish doesn't come with a standard, included, version of one of the libraries your application is using and deploying. Being first on the scene of the crime :), the application server will load the first class (the standard one), which is different from the one your application wants to use.
Forcing use of different class loaders could solve this type of problem. However, I don't have experience with Glassfish, but have encountered similar problems on Weblogic.