cant open GSEA

[Lior Roitman]

I just downloaded the app and every time I try to open the software I get the following error:

Translated Report (Full Report Below)
-------------------------------------

Process:               java [9433]
Path:                  /private/var/folders/*/GSEA_4.3.3.app/Contents/MacOS/../jdk-11/bin/java
Identifier:            java
Version:               ???
Code Type:             X86-64 (Native)
Parent Process:        launchd [1]
User ID:               502

Date/Time:             2024-02-12 13:52:43.5910 -0500
OS Version:            macOS 14.0 (23A344)
Report Version:        12
Bridge OS Version:     8.0 (21P365)
Anonymous UUID:        7C076893-19B6-7812-8DB3-EE7926964A15


Time Awake Since Boot: 5700 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGABRT)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000020
Exception Codes:       0x0000000000000001, 0x0000000000000020

Termination Reason:    Namespace SIGNAL, Code 6 Abort trap: 6
Terminating Process:   java [9433]

VM Region Info: 0x20 is not in any region.  Bytes before following region: 140737487527904
      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      shared memory            7ffffff36000-7ffffff37000 [    4K] r-x/r-x SM=SHM  

Application Specific Information:
References to Carbon menus are disallowed with AppKit menu system (see rdar://101002625). Use instances of NSMenu and NSMenuItem directly instead.


Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib             0x7ff8197737a6 __pthread_kill + 10
1   libsystem_pthread.dylib           0x7ff8197abf30 pthread_kill + 262
2   libsystem_c.dylib                 0x7ff8196caa4d abort + 126
3   libjvm.dylib                          0x102fcb304 os::abort(bool, void*, void const*) + 22
4   libjvm.dylib                          0x10315cd78 VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long) + 2814
5   libjvm.dylib                          0x10315c256 VMError::report_and_die(Thread*, unsigned int, unsigned char*, void*, void*, char const*, ...) + 148
6   libjvm.dylib                          0x10315cebd VMError::report_and_die(Thread*, unsigned int, unsigned char*, void*, void*) + 33
7   libjvm.dylib                          0x102fcf4de JVM_handle_bsd_signal + 1428
8   libjvm.dylib                          0x102fccdc4 signalHandler(int, __siginfo*, void*) + 47
9   libsystem_platform.dylib           0x7ff8197d937d _sigtramp + 29
10  UIFoundation                       0x7ff81e25ceb5 -[NSAttributeDictionary isEqualToDictionary:] + 54
11  AppKit                             0x7ff81dadd898 _NSGetCarbonMenu + 15
12  JavaRuntimeSupport                 0x7ffb1c03207b -[JRSMenu installCarbonEventHandlers:] + 204
13  CoreFoundation                     0x7ff81987c7b0 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 137
14  CoreFoundation                     0x7ff81990d436 ___CFXRegistrationPost_block_invoke + 88
15  CoreFoundation                     0x7ff81990d380 _CFXRegistrationPost + 532
16  CoreFoundation                     0x7ff81984c6bb _CFXNotificationPost + 682
17  Foundation                         0x7ff81a7c97a7 -[NSNotificationCenter postNotificationName:object:userInfo:] + 82
18  AppKit                             0x7ff81ce8161c -[NSMenu insertItem:atIndex:] + 736
19  Foundation                         0x7ff81a83d2d5 __NSThreadPerformPerform + 178
20  CoreFoundation                     0x7ff819887337 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
21  CoreFoundation                     0x7ff8198872d9 __CFRunLoopDoSource0 + 157
22  CoreFoundation                     0x7ff8198870a4 __CFRunLoopDoSources0 + 215
23  CoreFoundation                     0x7ff819885d21 __CFRunLoopRun + 919
24  CoreFoundation                     0x7ff819885372 CFRunLoopRunSpecific + 557
25  HIToolbox                         0x7ff8240f19d9 RunCurrentEventLoopInMode + 292
26  HIToolbox                         0x7ff8240f17e6 ReceiveNextEventCommon + 665
27  HIToolbox                         0x7ff8240f1531 _BlockUntilNextEventMatchingListInModeWithFilter + 66
28  AppKit                             0x7ff81ce8d0c5 _DPSNextEvent + 880
29  AppKit                             0x7ff81d77e150 -[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1304
30  libosxapp.dylib                      0x101b3c678 -[NSApplicationAWT nextEventMatchingMask:untilDate:inMode:dequeue:] + 121
31  AppKit                             0x7ff81ce7e63a -[NSApplication run] + 603
32  libosxapp.dylib                      0x101b3c45f +[NSApplicationAWT runAWTLoopWithApp:] + 165
33  libawt_lwawt.dylib                    0x1026227f6 +[AWTStarter starter:headless:] + 508
34  libosxapp.dylib                      0x101b3df6f +[ThreadUtilities invokeBlockCopy:] + 15
35  Foundation                         0x7ff81a83d2d5 __NSThreadPerformPerform + 178
36  CoreFoundation                     0x7ff819887337 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
37  CoreFoundation                     0x7ff8198872d9 __CFRunLoopDoSource0 + 157
38  CoreFoundation                     0x7ff8198870a4 __CFRunLoopDoSources0 + 215
39  CoreFoundation                     0x7ff819885d21 __CFRunLoopRun + 919
40  CoreFoundation                     0x7ff819885372 CFRunLoopRunSpecific + 557
41  libjli.dylib                          0x101687f49 CreateExecutionEnvironment + 381
42  libjli.dylib                          0x1016841fb JLI_Launch + 1342
43  java                                  0x10164ec15 main + 360
44  dyld                               0x7ff8194233a6 start + 1942

Thread 1:
0   libsystem_kernel.dylib             0x7ff81976e1e2 __ulock_wait + 10
1   libsystem_pthread.dylib           0x7ff8197ada01 _pthread_join + 348
2   libjli.dylib                          0x101688637 CallJavaMainInNewThread + 143
3   libjli.dylib                          0x10168722a ContinueInNewThread + 153
4   libjli.dylib                          0x10168544e JLI_Launch + 6033
5   java                                  0x10164ec15 main + 360
6   libjli.dylib                          0x101688c70 apple_main + 84
7   libsystem_pthread.dylib           0x7ff8197ac202 _pthread_start + 99
8   libsystem_pthread.dylib           0x7ff8197a7bab thread_start + 15

[David Eby]

Hi,

Thanks for letting us know.  We've had similar reports and are working on diagnosing the issue; we suspect OS-level changes as it seems to be fine on Ventura. Unfortunately, it may take some time to put together a fix.

In the meanwhile, you might be able to use our 'GSEA for the Command Line' bundle instead. The code and functionality is the same, just the packaging is different. It requires that you separately install OpenJDK 11 and launch from the command line, but there is a launcher for the full GSEA GUI and it will work the same way as the Mac-specific GSEA bundle.

Sorry for the delayed response; I'm full-time on a different project at the moment and only checking messages occasionally.

- David

David Eby
www.gsea-msigdb.org

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[David Eby]

Just to follow up, does this Mac have the newer M1/M2 "Apple silicon" CPU, and do you have Rosetta installed?

David Eby
www.gsea-msigdb.org