java.lang.NoClassDefFoundError on glassfish 4.1.2

Question

I'm trying to port my application from glassfish 4.0 to 4.1.2.

On version 4.0 it works but on 4.1.2 i'm getting java.lang.NoClassDefFoundError exception on org/apache/commons/logging/LogFactory, but i checked and everything should be ok all jars are in war's WEB-INF/lib.

[2017-07-04T08:14:02.152+0200] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=49 _ThreadName=admin-listener(2)] [timeMillis: 1499148842152] [levelValue: 900] [[
  java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cdsGasCallbackMessageDispatcher' defined in ServletContext resource [/WEB-INF/config/cdsgas-config.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.ws.server.endpoint.mapping.PayloadRootAnnotationMethodEndpointMapping#0' defined in ServletContext resource [/WEB-INF/config/spring-config.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.ws.soap.server.endpoint.interceptor.DelegatingSmartSoapEndpointInterceptor#1': Cannot resolve reference to bean 'mySec' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mySec' defined in ServletContext resource [/WEB-INF/config/spring-config.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cdsGasCallbackMessageDispatcher' defined in ServletContext resource [/WEB-INF/config/cdsgas-config.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.ws.server.endpoint.mapping.PayloadRootAnnotationMethodEndpointMapping#0' defined in ServletContext resource [/WEB-INF/config/spring-config.xml]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.ws.soap.server.endpoint.interceptor.DelegatingSmartSoapEndpointInterceptor#1': Cannot resolve reference to bean 'mySec' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mySec' defined in ServletContext resource [/WEB-INF/config/spring-config.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1044)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:1024)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:747)
    at com.sun.enterprise.web.WebContainer.loadWebModule(WebContainer.java:2286)
    at com.sun.enterprise.web.WebContainer.loadWebModule(WebContainer.java:1932)
    at com.sun.enterprise.web.WebApplication.start(WebApplication.java:139)
    at org.glassfish.internal.data.EngineRef.start(EngineRef.java:122)
    at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:291)
    at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:352)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:500)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:219)
    at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:491)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:539)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:535)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:360)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:534)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:565)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:557)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:360)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:556)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1464)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1300(CommandRunnerImpl.java:109)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1846)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1722)
    at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:253)
    at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:231)
    at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:275)
    at org.glassfish.admin.rest.resources.TemplateListOfResource.createResource(TemplateListOfResource.java:133)
    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:497)
    at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
    at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:309)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:292)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1139)
    at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:375)
    at org.glassfish.admin.rest.adapter.RestAdapter$2.service(RestAdapter.java:316)
    at org.glassfish.admin.rest.adapter.RestAdapter.service(RestAdapter.java:179)
    at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
    at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
    at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
    at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
    at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:283)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:200)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:132)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:111)
    at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
    at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:536)
    at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:591)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:571)
    at java.lang.Thread.run(Thread.java:745)
]]

Is it some weird bug in gf 4.1.2 or am i doing something wrong?

EDIT: It actually seems like it's some kind of spring issue, because when i take another project using commons logging and xmlsec but doesn't use spring it deploys and works.

Answer 1

OK, I think I got you guys covered, let's try a few things.

First, which most likely won't work for you, try the things here from stackoverflow. Specifically, the first three answers. I'm guessing, however, that you've already been there and done that. You're probably even pissed for me suggesting it. I only included it for anyone else who makes it here and needs the info.

So, since that most likely didn't work, there is probably, like Akshay mentioned, a dependency problem. I think your problem is Glassfish, not Spring. First, check your dependencies for problems.

If you're using maven, use dependency tree to see what conflicts and which library brings in what.

mvn dependency:tree -Dverbose

The verbose gives you more info. Since you're looking for conflicts, go with:

mvn dependency:tree -Dverbose | grep 'omitted for conflict'

Does you see omitted for conflicts on any loggers?

I've had a similar problem where a logger was clashing with the older logger from Glassfish. Glassfish had a much older version stored separately from the other dependencies that was screwing things up. I had a problem with a jboss logger but it was the exact same error otherwise . It was such a pain in the ass I wrote down how I fixed it and where the answer came from.

The final solution that helped me out was this top answer from this question. (You would have never found this so don't feel bad.)

In glass fish This problem is caused by collision with dependencies of glassfish modules. If you check lib list in glassfishdir/modules you would see boss-logging.jar. You can delete it and replace with latest such as org.jboss.logging:jboss-logging:jar:3.3.0.Final. It worked for me.

Inside of my glassfish module (mine is located @ ->) C:\\glassfish4\\glassfish\\modules ,there was an outdated version of the jboss-logger. I deleted that and replaced it with the jboss-logging 3.3.0 final jar and it WORKED!