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Caleydo / caleydo

Caleydo - Visualization for Molecular Biology
http://caleydo.org
BSD 3-Clause "New" or "Revised" License
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problem with views when running Caleydo on fresh Mac OS X 10.10 install #1871

Closed ngehlenborg closed 9 years ago

ngehlenborg commented 9 years ago

I tried to launch Caleydo on a fresh Mac OS X 10.10 install with Java 1.7 SDK installed. Caleydo launched, but the views fail to load. Log below.

screen shot 2014-11-20 at 10 45 30 am

org.eclipse.core.runtime.CoreException: Plug-in org.caleydo.view.stratomex was unable to load class org.caleydo.view.stratomex.RcpGLStratomexView.
    at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194)
    at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:176)
    at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
    at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
    at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
    at org.eclipse.ui.internal.registry.ViewDescriptor.createView(ViewDescriptor.java:62)
    at org.eclipse.ui.internal.ViewReference.createPart(ViewReference.java:111)
    at org.eclipse.ui.internal.e4.compatibility.CompatibilityPart.createPart(CompatibilityPart.java:266)
    at org.eclipse.ui.internal.e4.compatibility.CompatibilityPart.create(CompatibilityPart.java:304)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:56)
    at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:877)
    at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:857)
    at org.eclipse.e4.core.internal.di.InjectorImpl.inject(InjectorImpl.java:119)
    at org.eclipse.e4.core.internal.di.InjectorImpl.internalMake(InjectorImpl.java:333)
    at org.eclipse.e4.core.internal.di.InjectorImpl.make(InjectorImpl.java:254)
    at org.eclipse.e4.core.contexts.ContextInjectionFactory.make(ContextInjectionFactory.java:162)
    at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.createFromBundle(ReflectionContributionFactory.java:102)
    at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.doCreate(ReflectionContributionFactory.java:71)
    at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.create(ReflectionContributionFactory.java:53)
    at org.eclipse.e4.ui.workbench.renderers.swt.ContributedPartRenderer.createWidget(ContributedPartRenderer.java:129)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createWidget(PartRenderingEngine.java:949)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.safeCreateGui(PartRenderingEngine.java:633)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$6.run(PartRenderingEngine.java:526)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createGui(PartRenderingEngine.java:511)
    at org.eclipse.e4.ui.workbench.renderers.swt.ElementReferenceRenderer.createWidget(ElementReferenceRenderer.java:61)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createWidget(PartRenderingEngine.java:949)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.safeCreateGui(PartRenderingEngine.java:633)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.safeCreateGui(PartRenderingEngine.java:735)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.access$2(PartRenderingEngine.java:706)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$7.run(PartRenderingEngine.java:700)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.createGui(PartRenderingEngine.java:685)
    at org.eclipse.e4.ui.internal.workbench.PartServiceImpl$1.handleEvent(PartServiceImpl.java:95)
    at org.eclipse.e4.ui.services.internal.events.UIEventHandler$1.run(UIEventHandler.java:41)
    at org.eclipse.swt.widgets.Synchronizer.syncExec(Synchronizer.java:180)
    at org.eclipse.ui.internal.UISynchronizer.syncExec(UISynchronizer.java:150)
    at org.eclipse.swt.widgets.Display.syncExec(Display.java:4650)
    at org.eclipse.e4.ui.internal.workbench.swt.E4Application$1.syncExec(E4Application.java:205)
    at org.eclipse.e4.ui.services.internal.events.UIEventHandler.handleEvent(UIEventHandler.java:38)
    at org.eclipse.equinox.internal.event.EventHandlerWrapper.handleEvent(EventHandlerWrapper.java:197)
    at org.eclipse.equinox.internal.event.EventHandlerTracker.dispatchEvent(EventHandlerTracker.java:197)
    at org.eclipse.equinox.internal.event.EventHandlerTracker.dispatchEvent(EventHandlerTracker.java:1)
    at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
    at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
    at org.eclipse.equinox.internal.event.EventAdminImpl.dispatchEvent(EventAdminImpl.java:135)
    at org.eclipse.equinox.internal.event.EventAdminImpl.sendEvent(EventAdminImpl.java:78)
    at org.eclipse.equinox.internal.event.EventComponent.sendEvent(EventComponent.java:39)
    at org.eclipse.e4.ui.services.internal.events.EventBroker.send(EventBroker.java:80)
    at org.eclipse.e4.ui.internal.workbench.UIEventPublisher.notifyChanged(UIEventPublisher.java:58)
    at org.eclipse.emf.common.notify.impl.BasicNotifierImpl.eNotify(BasicNotifierImpl.java:374)
    at org.eclipse.e4.ui.model.application.ui.impl.ElementContainerImpl.setSelectedElement(ElementContainerImpl.java:171)
    at org.eclipse.e4.ui.workbench.renderers.swt.StackRenderer$10.widgetSelected(StackRenderer.java:936)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:248)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4166)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1466)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1489)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1474)
    at org.eclipse.swt.widgets.Widget.notifyListeners(Widget.java:1279)
    at org.eclipse.swt.custom.CTabFolder.setSelection(CTabFolder.java:3080)
    at org.eclipse.swt.custom.CTabFolder.onMouse(CTabFolder.java:1772)
    at org.eclipse.swt.custom.CTabFolder$1.handleEvent(CTabFolder.java:279)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4166)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1466)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1489)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1474)
    at org.eclipse.swt.widgets.Widget.notifyListeners(Widget.java:1279)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4012)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3651)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1113)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:997)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:140)
    at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:611)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:567)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
    at org.caleydo.core.internal.Application.start(Application.java:97)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
Caused by: org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter$TerminatingClassNotFoundException: An error occurred while automatically activating bundle org.caleydo.view.stratomex (45).
    at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:124)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:469)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
    at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:395)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:464)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at org.eclipse.osgi.internal.loader.BundleLoader.loadClass(BundleLoader.java:340)
    at org.eclipse.osgi.framework.internal.core.BundleHost.loadClass(BundleHost.java:229)
    at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadClass(AbstractBundle.java:1212)
    at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:174)
    ... 94 more
Caused by: org.osgi.framework.BundleException: Exception in org.caleydo.view.stratomex.Activator.start() of bundle org.caleydo.view.stratomex.
    at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:734)
    at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:683)
    at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:381)
    at org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:300)
    at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:478)
    at org.eclipse.osgi.internal.loader.BundleLoader.setLazyTrigger(BundleLoader.java:263)
    at org.eclipse.core.runtime.internal.adaptor.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:109)
    ... 106 more
Caused by: java.lang.NoClassDefFoundError: javax/media/opengl/GLEventListener
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.defineClass(DefaultClassLoader.java:188)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClassHoldingLock(ClasspathManager.java:638)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClass(ClasspathManager.java:613)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findClassImpl(ClasspathManager.java:574)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClassImpl(ClasspathManager.java:492)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:465)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
    at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:395)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:464)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.defineClass(DefaultClassLoader.java:188)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClassHoldingLock(ClasspathManager.java:638)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClass(ClasspathManager.java:613)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findClassImpl(ClasspathManager.java:574)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClassImpl(ClasspathManager.java:492)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:465)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
    at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:395)
    at org.eclipse.osgi.internal.loader.SingleSourcePackage.loadClass(SingleSourcePackage.java:35)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:461)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.defineClass(DefaultClassLoader.java:188)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClassHoldingLock(ClasspathManager.java:638)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClass(ClasspathManager.java:613)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findClassImpl(ClasspathManager.java:574)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClassImpl(ClasspathManager.java:492)
    at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass(ClasspathManager.java:465)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass(DefaultClassLoader.java:216)
    at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:395)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:464)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at org.caleydo.view.stratomex.Activator.registerDataDomains(Activator.java:75)
    at org.caleydo.view.stratomex.Activator.start(Activator.java:35)
    at org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(BundleContextImpl.java:711)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:702)
    ... 112 more
Caused by: java.lang.ClassNotFoundException: javax.media.opengl.GLEventListener cannot be found by org.caleydo.core_3.1.4
    at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:501)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
    at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    ... 163 more
sgratzl commented 9 years ago

which version of Caleydo did you use? latest daily build, latest release,...? -> please paste the link to it

the interesting part is:

Caused by: java.lang.ClassNotFoundException: javax.media.opengl.GLEventListener cannot be found by org.caleydo.core_3.1.4

If you used the release, can you please test the latest daily build, too:

http://dev.caleydo.org/jenkins/job/caleydo.super/lastSuccessfulBuild/artifact/org.caleydo.rcp/target/products/caleydo-macosx.cocoa.x86_64.zip

mstreit commented 9 years ago

On my Mac both the release and the latest build work without problems

ngehlenborg commented 9 years ago

I am having the problem with the 3.1.4 release. Will try the latest build now.

ngehlenborg commented 9 years ago

Latest build works. What has changed?

sgratzl commented 9 years ago

the latest build uses a different jogl version.

ngehlenborg commented 9 years ago

Ok, thanks for the clarification.