Trouble with GSEA desktop app after updating to macOS High Sierra?

[jhoj]

Hello,

I recently updated to High Sierra (macOS 10.13) on my mac, and ever since then have had trouble running the GSEA desktop app. The app loads and opens just fine to the home page, and there are no warning/error messages that pop up. However, none of the buttons within the app are functional (ie, clicking on "Load Data", "Run GSEA", etc. does not take me anywhere). As such, I can't upload any files to the program, nor can I run any analysis. Anyone else run into this issue? Based off of the error message in the log below, looks like it might be something wrong with Java? Any suggestions for how to fix?

Java Version:

java version "1.8.0_152"

Java(TM) SE Runtime Environment (build 1.8.0_152-b16)

Java HotSpot(TM) 64-Bit Server VM (build 25.152-b16, mixed mode)

Here is my log from the GSEA session (after the app opens and I try to click on "Load Data" button):

< Process output will appear below >

Done initing things while splashing

Exception in thread "AWT-EventQueue-2" java.lang.Error: java.lang.reflect.InaccessibleObjectException: Unable to make void java.awt.EventDispatchThread.pumpEvents(java.awt.Conditional) accessible: module java.desktop does not "opens java.awt" to unnamed module @88d3933

at foxtrot.pumps.SunJDK14ConditionalEventPump.<clinit>(SunJDK14ConditionalEventPump.java:75)

at foxtrot.Worker.initializeEventPump(Worker.java:268)

at foxtrot.Worker.post(Worker.java:86)

at foxtrot.Worker.post(Worker.java:131)

at edu.mit.broad.xbench.actions.WidgetAction.actionPerformed(WidgetAction.java:92)

at xapps.api.frameworks.WorkspaceToolBar$1.actionPerformed(WorkspaceToolBar.java:77)

at java.desktop/javax.swing.AbstractButton.fireActionPerformed(Unknown Source)

at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)

at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)

at java.desktop/javax.swing.DefaultButtonModel.setPressed(Unknown Source)

at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)

at com.jidesoft.plaf.basic.BasicJideButtonListener.mouseReleased(Unknown Source)

at java.desktop/java.awt.Component.processMouseEvent(Unknown Source)

at java.desktop/javax.swing.JComponent.processMouseEvent(Unknown Source)

at java.desktop/java.awt.Component.processEvent(Unknown Source)

at java.desktop/java.awt.Container.processEvent(Unknown Source)

at java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source)

at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)

at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)

at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)

at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)

at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)

at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)

at java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source)

at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)

at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)

at java.desktop/java.awt.EventQueue.access$500(Unknown Source)

at java.desktop/java.awt.EventQueue$3.run(Unknown Source)

at java.desktop/java.awt.EventQueue$3.run(Unknown Source)

at java.base/java.security.AccessController.doPrivileged(Native Method)

at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)

at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)

at java.desktop/java.awt.EventQueue$4.run(Unknown Source)

at java.desktop/java.awt.EventQueue$4.run(Unknown Source)

at java.base/java.security.AccessController.doPrivileged(Native Method)

at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)

at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)

at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)

[David Eby]

Hi,

Thanks for letting us know.  I suspect it might be due to a recent Java update rather than High Sierra.  Actually, those look like Java 9 error messages.

Are you launching this through the JNLPs on our website?  If so, try enabling the Java console and double-check the version on Java reported when that launches.

We're in the process of evaluating Java 9, though it's difficult since we're operating with reduced resources while we wait to hear about renewed funding.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

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[jhoj]

Thanks for the reply! Yep, the problem was due to the Java 9 installation on my computer. I reverted back to Java 8 and everything is working great.

Thanks for your help and best of luck with the funding renewal!

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