I still have problem running Jira 4.0.1 standalone on AIX 6.1 with IBM JDK, but because the exception is IMHO more related to JRA-19401 I've posted the issue there - can someone give me a feedback, which IBM JVM version is supposed to work?

This problem has also be experienced with old Sun JVMs. I believe this is the bug report for that problem: http://bugs.sun.com/view_bug.do?bug_id=6322301

Verified the issue with latest build provided by chris((v4.0.1#471). The issue is fixed and JIRA is working as desired.

OK, we've added these jars to WEB-INF/lib

This is an IBM JRE bug, RetentionPolicy.RUNTIME for one of its attributes should NOT cause the class to fail to load. I have not however been able to find a public bug report from them, only references such as this

assigning to you Jed as discussed

Bug reported in Gadget plugin as AG-1136

@Duane: Yes this bug affects Jira 4.0 running under WebSphere AppServer

The problem seems to be because the Gadget plugin uses the @ParametersAreNonnullByDefault annotation from net.sourceforge.findbugs but it does not provide this annotation class file.
I worked around it by adding jsr305-1.3.2.jar to JIRA's WEB-INF/lib/

Thanks for the link to the other issues Justus. As an FYI, I noticed your release of IBM's JDK was kinda old (SR5, current is SR10). I tried starting up a test instance here with SR10 and it failed similarly to your errors above. Below is a snippet of the java environment information, and the JIRA log. I can provide more if you think it'll help.

java version "1.5.0"
Java(TM) 2 Runtime Environment, Standard Edition (build pxi32dev-20090707 (SR10 ))
IBM J9 VM (build 2.3, J2RE 1.5.0 IBM J9 2.3 Linux x86-32 j9vmxi3223-20090707 (JIT enabled)
J9VM - 20090706_38445_lHdSMr
JIT - 20090623_1334_r8
GC - 200906_09)
JCL - 20090705

2009-10-18 20:37:40,396 http-8080-Processor25 ERROR anonymous 74255x1x1 yjfj4e http://localhost:8080/secure/Dashboard.jspa [webwork.util.ValueStack] query="/dashboardHtml"

java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
(...)
Caused by: java.lang.TypeNotPresentException: Type javax.annotation.ParametersAreNonnullByDefault not present
at com.ibm.oti.reflect.AnnotationHelper.getAnnotation(AnnotationHelper.java:38)
at com.ibm.oti.reflect.AnnotationHelper.getDeclaredAnnotations(AnnotationHelper.java:50)

Duane,

This particular issue is the result of using the IBM JVM to run tomcat. However, there are issues with Websphere (JRA-19401, JRA-19402). They may be the same or different from this one, which is why they are separately listed for the time being.

I have linked the issues about Websphere on JIRA 4.