MAC M2 can not open GSEA

[Xinyi Deng]

I have try the version for all computer and I installed the JAVA11 and using the command to open GSEA:  $ java --module-path=modules -Xmx4g @gsea.args --patch-module=jide.common=lib/jide-components-3.7.4.jar:lib/jide-dock-3.7.4.jar:lib/jide-grids-3.7.4.jar --module=org.gsea_msigdb.gsea/xapps.gsea.GSEA

But I can not open it also. My computer show: 

 ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: java [33331] Path: /opt/homebrew/*/java Identifier: java Version: ??? Code Type: ARM-64 (Native) Parent Process: zsh [29087] Responsible: Terminal [10117] User ID: 501 Date/Time: 2024-07-02 14:47:22.4592 -0400 OS Version: macOS 14.0 (23A344) Report Version: 12 Anonymous UUID: EA2A8101-8C51-EF08-B280-B6D298FD023F Sleep/Wake UUID: 2B67E92D-6A47-4145-87FA-3A49A1CD02A5 Time Awake Since Boot: 87000 seconds Time Since Wake: 1362 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0000000000000001, 0x000000018fbc961c Termination Reason: Namespace SIGNAL, Code 5 Trace/BPT trap: 5 Terminating Process: exc handler [33331] Application Specific Information: References to Carbon menus are disallowed with AppKit menu system (see rdar://101002625). Use instances of NSMenu and NSMenuItem directly instead.

Is that the possible of the Compatibility issues? Did anyone fix that before？

Thank you so much for your help.

Best,

Xinyi

[David Eby]

Hi Xinyi,

Sorry for the delayed reply, I'm full-time on another project these days and only check messages here occasionally.  This one slipped through the cracks earlier and I didn't see it until today.

Are you still having issues with this?  It looks like you are running Java installed via Homebrew, which is a configuration we haven't ever tested, so it's possible that is the cause of the issue.

Which GSEA bundle are you using?  Is there a reason you aren't using the Mac bundle with the built-in OpenJDK?  That should run fine on an Apple M2, though it might prompt you about installing Rosetta the first time it launches.

If you need to run this at the command line, could you try with Eclipse Temurin OpenJDK 11 instead?  We're a small team with limited resources, and unfortunately I'm not going to be in a position to look at this using Homebrew any time soon.

Thanks,

David

David Eby
www.gsea-msigdb.org

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[Xinyi Deng]

Hi David,

Thank you so much for getting back to me. I am using GSEA v4.5.5 MAC, but when I try to open it, it doesn't show installing Rosetta,  but shows the error I posted before. so I just can not open GSEA. And I installed rosetta manually, but it still doesn't work. 

Best,

Xinyi

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[Anthony Castanza]

Hi Xinyi,

At this point my suggestion would be to uninstall GSEA, uninstall the JAVA11 distirbution you installed, uninstall Rosetta, then reinstall GSEA with a fresh download of the GSEA v4.3.3 Mac App that includes a bundled Java VM.

Please be sure to follow all the steps I outlined. Let me know how this works for you.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Xinyi Deng]

Hi Anthony,

Thank you for your reply. But I still can not open GSEA in my MacM2.

I deleted the java and v4.3.3 again. When I try to download v4.3.3 Mac App  and click it to open GSEA, it will show this error. 

[Anthony Castanza]

Hi  Xinyi,

At this point, it would appear to be a technical issue with mac platform app, likely as a result of some change that Apple has made. At the moment we don't really have the technical bandwidth to fully diagnose and patch the issue. My recommendation in the interim would be to perform your GSEA through the web-hosted tool available through cloud.genepattern.org/

Direct link to the tool once you're registered/signed in:
GSEA: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20.4.0

GSEAPreranked: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7.4.0

The GenePattern hosted tools offers all the same features as the desktop application and will allow you to perform your analysis while the Mac Application isn't functioning.

Sorry I couldn't be of more help here

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego