Brain Explorer 2 crashing when visualizing human gene data

Technical
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1

Hi Community,

I have been trying to visualize human brain gene expression data in the Brain Explorer 2 desktop software (Mac). I launch the explorer from the human microarray page for a particular gene (e.g. GRB14, see link below). However, the app crashes as soon as it opens without visualizing the gene expression, with the following error message (see below).

I’ve tried 1) redownloading the app, 2) tried to visualise other genes and 3) using different machines (with OSX El Capitan and Mojave) to the same effect.

Does anyone have any fix for this? Thanks!

–PK

1. Link:
http://human.brain-map.org/microarray/search/show?exact_match=false&search_term=grb14&search_type=gene

2. Error message:

Brain Explorer 2 quit unexpectedly.
Process: Brain Explorer 2 [27159]
Path: /Users/USER/Desktop/*/Brain Explorer 2.app/Contents/MacOS/Brain Explorer 2
Identifier: org.alleninstitute.BrainExplorer2
Version: 2.3.5 (2393)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: Brain Explorer 2 [27159]
User ID: 507

Date/Time: 2019-07-01 13:28:43.939 +0800
OS Version: Mac OS X 10.11.6 (15G31)
Report Version: 11
Anonymous UUID: E272B2C8-4013-C537-8310-1073D2F98D69

Time Awake Since Boot: 1000000 seconds

System Integrity Protection: enabled

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

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
terminating with uncaught exception of type std::runtime_error: Error while reading data: parse error: premature EOF

abort() called

Global Trace Buffer (reverse chronological seconds):
2.421397 CFNetwork 0x00007fff9ab6bdd8 NSURLConnection finished with error - code -1004
2.421565 CFNetwork 0x00007fff9ab7aeb5 HTTP load failed (error code: -1004 [1:61])
2.422252 CFNetwork 0x00007fff9aaab9c6 TCP Conn 0x101c29020 Failed : error 0:61 [61]
2.422252 CFNetwork 0x00007fff9aaab659 TCP Conn 0x101c29020 complete. fd: -1, err: 61
2.422904 CFNetwork 0x00007fff9ab39f33 TCP Conn 0x101c29020 event 3. err: 61
2.426315 CFNetwork 0x00007fff9aaaa92b TCP Conn 0x101c29020 started
2.429069 CFNetwork 0x00007fff9aa6e56e Creating default cookie storage with process/bundle identifier
2.429069 CFNetwork 0x00007fff9aa6e506 Faulting in CFHTTPCookieStorage singleton
2.429069 CFNetwork 0x00007fff9aa6e395 Faulting in NSHTTPCookieStorage singleton

2

Hi PK, thanks for the note; we’re able to reproduce the problem and are looking into a solution. Note that this is affecting Windows users as well as Mac users.

Tim

3

PK,
Thanks for reporting this. We believe the problem should be fixed for all users now. Please let us know if you’re still experiencing an issue.

4

It works now, thanks!

1 Like
5

I have the same issue right now on Mac OSX 10.15.2.

App doesn’t visualize either brain or mouse data. Upon opening the app, the screen is completely black. Same black screen upon launching from the human microarray page of a particular gene. App crashes if you click one of the Nissl-stained planes.

Redownloading/reinstalling on the computer didn’t work.

Error message is somewhat similar, but not identical:

Process: Brain Explorer 2 [1072]
Path: /Applications/Brain Explorer 2.app/Contents/MacOS/Brain Explorer 2
Identifier: org.alleninstitute.BrainExplorer2
Version: 2.3.5 (2393)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: Brain Explorer 2 [1072]
User ID: 501

Date/Time: 2020-01-16 18:39:51.692 -0500
OS Version: Mac OS X 10.15.2 (19C57)
Report Version: 12
Bridge OS Version: 4.2 (17P2551)
Anonymous UUID: 9EBD6135-E2C3-8F85-EB58-3764417FFDE2

Time Awake Since Boot: 2900 seconds

System Integrity Protection: enabled

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

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11
Termination Reason: Namespace SIGNAL, Code 0xb
Terminating Process: exc handler [1072]

VM Regions Near 0:
→
__TEXT 0000000100000000-00000001001e1000 [ 1924K] r-x/rwx SM=COW /Applications/Brain Explorer 2.app/Contents/MacOS/Brain Explorer 2

Application Specific Information:
Performing @selector(changeAtlasPlaneVisibility:) from sender NSSegmentedControl 0x10046c3c0
∫4àˇ

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 org.alleninstitute.BrainExplorer2 0x000000010001b5a5 -[BrainExplorerDoc(Toolbar) setMPRPlaneVisibility:visible:] + 37
1 com.apple.AppKit 0x00007fff2c9c6018 -[NSApplication(NSResponder) sendAction:to:from:] + 299
2 com.apple.AppKit 0x00007fff2c9c5eb4 -[NSControl sendAction:to:] + 86
3 com.apple.AppKit 0x00007fff2c9c5de6 __26-[NSCell _sendActionFrom:]_block_invoke + 136
4 com.apple.AppKit 0x00007fff2c9c5ce8 -[NSCell _sendActionFrom:] + 171
5 com.apple.AppKit 0x00007fff2cadb90f -[NSSegmentedCell _sendActionFrom:] + 161
6 com.apple.AppKit 0x00007fff2c9c1ecd NSControlTrackMouse + 1745
7 com.apple.AppKit 0x00007fff2c9c17d4 -[NSCell trackMouse:inRect:ofView:untilMouseUp:] + 130
8 com.apple.AppKit 0x00007fff2cadb015 -[NSSegmentedCell trackMouse:inRect:ofView:untilMouseUp:] + 781
9 com.apple.AppKit 0x00007fff2c9c0a13 -[NSControl mouseDown:] + 748
10 com.apple.AppKit 0x00007fff2c9beded -[NSWindow(NSEventRouting) _handleMouseDownEvent:isDelayedEvent:] + 4907
11 com.apple.AppKit 0x00007fff2c928f3c -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 2612
12 com.apple.AppKit 0x00007fff2c9282e5 -[NSWindow(NSEventRouting) sendEvent:] + 349
13 com.apple.AppKit 0x00007fff2c92665c -[NSApplication(NSEvent) sendEvent:] + 352
14 com.apple.AppKit 0x00007fff2c7723df -[NSApplication run] + 707
15 com.apple.AppKit 0x00007fff2c744775 NSApplicationMain + 777
16 org.alleninstitute.BrainExplorer2 0x00000001000013f4 start + 52

…

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x00000001001f0f68 rbx: 0x0000600002138190 rcx: 0x0000000000000001 rdx: 0x0000000000000002
rdi: 0x0000000000000000 rsi: 0x0000000100166742 rbp: 0x00007ffeefbfecd0 rsp: 0x00007ffeefbfeca0
r8: 0x0000000000000003 r9: 0x0000000000000000 r10: 0x00000001001e9628 r11: 0x000000010001b580
r12: 0x00000001007310d0 r13: 0x00007fff6589c000 r14: 0x0000000000000160 r15: 0x0000000000000001
rip: 0x000000010001b5a5 rfl: 0x0000000000010202 cr2: 0x0000000000000000

Logical CPU: 0
Error Code: 0x00000004 (no mapping for user data write)
Trap Number: 14

…

The error message is actually longer; I have only included threads that seemed to lead to crash. I can share full text if you want.

I am using a standard MacBook Pro (13-inch, 2018, Four Thunderbolt 3 Ports), but could share more hardware details if necessary. I tried it on a collegue’s MacBook air running OSX 10.15 and that seemed to be no problem.

Any help/suggestions much appreciated!

–Oliver

6

I’m experiencing the same problem as Oliver. My computer is the 2016 version of his. My colleague also has a MacBook Air and runs Brain Explorer 2 with no issues.

Any help is welcome!

-Trish

7

Hi @TrishSinc,

This issue is addressed on another thread: