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It failed in the M-3.0.4-20090207053440 build. The only thing that had changed from previous build was fix for bug 263890. The test passed, though, on a local build, which is why I say 'intermittent'. This test is also mentioned in bug 234409.
I'm likely to delete this specific build, since appears the fix for 263890 didn't apply quite right .... so will paste whole stack output here. estWebEJBModuleDependency Failure DependencyGraphManager does not report dependency between P/TestEAR and P/TestWeb junit.framework.AssertionFailedError: DependencyGraphManager does not report dependency between P/TestEAR and P/TestWeb at org.eclipse.jst.j2ee.dependency.tests.util.DependencyVerificationUtil.verifyDependency(DependencyVerificationUtil.java:65) at org.eclipse.jst.j2ee.dependency.tests.util.DependencyVerificationUtil.verifyEARDependency(DependencyVerificationUtil.java:239) at org.eclipse.jst.j2ee.dependency.tests.ProjectDependencyTests.testEARDependency(ProjectDependencyTests.java:68) at org.eclipse.jst.j2ee.dependency.tests.ProjectDependencyTests.testWebEJBModuleDependency(ProjectDependencyTests.java:92) at org.eclipse.wst.common.tests.BaseTestCase.run(BaseTestCase.java:146) at org.eclipse.test.EclipseTestRunner.run(EclipseTestRunner.java:354) at org.eclipse.test.EclipseTestRunner.run(EclipseTestRunner.java:206) at org.eclipse.test.CoreTestApplication.runTests(CoreTestApplication.java:35) at org.eclipse.test.CoreTestApplication.run(CoreTestApplication.java:31) at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:574) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:195) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:386) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179) at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:549) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:504) at org.eclipse.equinox.launcher.Main.run(Main.java:1236) at org.eclipse.equinox.launcher.Main.main(Main.java:1212) DependencyGraphManager does not report dependency between P/TestEAR and P/TestWeb
Please note that at this time, the entire Java EE Tools JUnit bucket has been removed from the automated build.