![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#4946 closed defect (can't reproduce)
Crash with trashed stack
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x0000000111c03e00 (most recent call first):
File "/private/var/folders/_3/b55nykd52mn85qhsd_x6qzfc0000gr/T/AppTranslocation/78E1A0F2-6365-41E0-BE2E-2DE2C951F103/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Ve
Process: ChimeraX [1273]
Path: /private/var/folders/*/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.2.5 (1.2.5.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [1273]
User ID: 504
Date/Time: 2021-07-23 13:31:53.318 +0200
OS Version: macOS 11.4 (20F71)
Report Version: 12
Bridge OS Version: 3.0 (14Y908)
Anonymous UUID: CF1461FF-F149-4C8C-BFE2-89261E33B9DF
Sleep/Wake UUID: EE783F69-6810-40B9-8512-47275CB367A7
Time Awake Since Boot: 1500 seconds
Time Since Wake: 28 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_MEMORY_ERROR at 0x000000010ecdf449
Exception Note: EXC_CORPSE_NOTIFY
Termination Signal: Bus error: 10
Termination Reason: Namespace SIGNAL, Code 0xa
Terminating Process: exc handler [1273]
VM Regions Near 0x10ecdf449:
shared memory 10eb90000-10eb91000 [ 4K] r--/r-- SM=SHM
--> mapped file 10eb91000-10edc8000 [ 2268K] r-x/rwx SM=COW Object_id=7bcc44f
mapped file 10edc8000-10ee02000 [ 232K] rw-/rwx SM=COW Object_id=718404f
Thread 0 Crashed:: CrBrowserMain
0 ??? 0x000000010ecdf449 0 + 4543345737
1 ??? 0x000000010ecd53a3 0 + 4543304611
2 ??? 0x000000010ecd54f7 0 + 4543304951
3 ??? 0x000000010ecd57e3 0 + 4543305699
4 ??? 0x000000010ed366b8 0 + 4543702712
5 ??? 0x00007fff2037ad7d 0 + 140733733907837
6 ChimeraX 000000000000000000 0 + 0
7 ??? 0x00007fff2042dbc5 0 + 140733734640581
8 ??? 0x00007fff2042d386 0 + 140733734638470
9 ??? 0x00007fff2042c64c 0 + 140733734635084
10 ??? 0x00007fff2866aab3 0 + 140733871205043
11 ??? 0x00007fff2866a815 0 + 140733871204373
12 ??? 0x00007fff2866a5b3 0 + 140733871203763
13 ??? 0x00007fff22c2d6f2 0 + 140733776582386
14 ??? 0x00007fff22c2bec5 0 + 140733776576197
15 ??? 0x00007fff22c1e239 0 + 140733776519737
16 ??? 0x000000012905b62f 0 + 4983207471
17 ??? 0x00000001104f7acf 0 + 4568611535
18 ??? 0x00000001104fc042 0 + 4568629314
19 ??? 0x0000000110c80702 0 + 4576511746
20 ??? 0x000000010ebb20c2 0 + 4542111938
21 ??? 0x000000010ebb1a85 0 + 4542110341
22 ??? 0x000000010ec80665 0 + 4542957157
23 ??? 0x000000010ec7d46e 0 + 4542944366
24 ??? 0x000000010ebb23d0 0 + 4542112720
25 ??? 0x000000010ebb4a9a 0 + 4542122650
26 ??? 0x000000010ec8060c 0 + 4542957068
27 ??? 0x000000010ec7d46e 0 + 4542944366
28 ??? 0x000000010ec81454 0 + 4542960724
29 ??? 0x000000010ebb256e 0 + 4542113134
30 ??? 0x000000010ec8060c 0 + 4542957068
31 ??? 0x000000010ec7d505 0 + 4542944517
32 ??? 0x000000010ec81454 0 + 4542960724
33 ??? 0x000000010ec76f44 0 + 4542918468
34 ??? 0x000000010ec74332 0 + 4542907186
35 ??? 0x000000010ebee5ff 0 + 4542359039
36 ??? 0x000000010ec8060c 0 + 4542957068
37 ??? 0x000000010ec7d505 0 + 4542944517
38 ??? 0x000000010ec81454 0 + 4542960724
39 ??? 0x000000010ebb256e 0 + 4542113134
40 ??? 0x000000010ec8060c 0 + 4542957068
41 ??? 0x000000010ec7d505 0 + 4542944517
42 ??? 0x000000010ec81454 0 + 4542960724
43 ??? 0x000000010ebb256e 0 + 4542113134
44 ??? 0x000000010ebb1dad 0 + 4542111149
45 ??? 0x000000010ece3eb3 0 + 4543364787
46 ??? 0x000000010ece3585 0 + 4543362437
47 ??? 0x000000010ece3bdf 0 + 4543364063
48 ??? 0x000000010ece3aeb 0 + 4543363819
49 ??? 0x000000010eb85dc8 0 + 4541930952
50 ??? 0x00007fff20350f5d 0 + 140733733736285
Thread 1:
0 ??? 0x00007fff20302cde 0 + 140733733416158
1 ??? 0x0000000111f7d27b 0 + 4596421243
2 ??? 0x00007fff203358fc 0 + 140733733624060
3 ??? 0x00007fff20331443 0 + 140733733606467
Thread 2:: ThreadPoolServiceThread
0 ??? 0x00007fff203091d2 0 + 140733733442002
1 ??? 0x000000011e9a8cc7 0 + 4808412359
2 ??? 0x000000011e93162b 0 + 4807923243
3 ??? 0x000000011e8f57cb 0 + 4807677899
4 ??? 0x000000011e93ca94 0 + 4807969428
5 ??? 0x000000011e950a7d 0 + 4808051325
6 ??? 0x000000011e999e07 0 + 4808351239
7 ??? 0x00007fff203358fc 0 + 140733733624060
8 ??? 0x00007fff20331443 0 + 140733733606467
Thread 3:: ThreadPoolBackgroundWorker
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e946778 0 + 4808009592
4 ??? 0x000000011e947150 0 + 4808012112
5 ??? 0x000000011e946c44 0 + 4808010820
6 ??? 0x000000011e999e07 0 + 4808351239
7 ??? 0x00007fff203358fc 0 + 140733733624060
8 ??? 0x00007fff20331443 0 + 140733733606467
Thread 4:: Chrome_IOThread
0 ??? 0x00007fff203091d2 0 + 140733733442002
1 ??? 0x000000011e9a8cc7 0 + 4808412359
2 ??? 0x000000011e93162b 0 + 4807923243
3 ??? 0x000000011e8f57cb 0 + 4807677899
4 ??? 0x0000000122875f06 0 + 4874264326
5 ??? 0x000000011e950a7d 0 + 4808051325
6 ??? 0x000000011e999e07 0 + 4808351239
7 ??? 0x00007fff203358fc 0 + 140733733624060
8 ??? 0x00007fff20331443 0 + 140733733606467
Thread 5:: NetworkConfigWatcher
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 6:: ThreadPoolForegroundWorker
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e946778 0 + 4808009592
4 ??? 0x000000011e947150 0 + 4808012112
5 ??? 0x000000011e946cd4 0 + 4808010964
6 ??? 0x000000011e999e07 0 + 4808351239
7 ??? 0x00007fff203358fc 0 + 140733733624060
8 ??? 0x00007fff20331443 0 + 140733733606467
Thread 7:: CompositorTileWorker1
0 ??? 0x00007fff20302cde 0 + 140733733416158
1 ??? 0x000000011e995e18 0 + 4808334872
2 ??? 0x000000011fc4d5f8 0 + 4827960824
3 ??? 0x000000011e999e07 0 + 4808351239
4 ??? 0x00007fff203358fc 0 + 140733733624060
5 ??? 0x00007fff20331443 0 + 140733733606467
Thread 8:: Chrome_InProcGpuThread
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e8c620f 0 + 4807483919
4 ??? 0x000000011e93162b 0 + 4807923243
5 ??? 0x000000011e8f57cb 0 + 4807677899
6 ??? 0x000000011e950a7d 0 + 4808051325
7 ??? 0x000000011e999e07 0 + 4808351239
8 ??? 0x00007fff203358fc 0 + 140733733624060
9 ??? 0x00007fff20331443 0 + 140733733606467
Thread 9:: Chrome_ChildIOThread
0 ??? 0x00007fff203091d2 0 + 140733733442002
1 ??? 0x000000011e9a8cc7 0 + 4808412359
2 ??? 0x000000011e93162b 0 + 4807923243
3 ??? 0x000000011e8f57cb 0 + 4807677899
4 ??? 0x000000011e950a7d 0 + 4808051325
5 ??? 0x000000011e999e07 0 + 4808351239
6 ??? 0x00007fff203358fc 0 + 140733733624060
7 ??? 0x00007fff20331443 0 + 140733733606467
Thread 10:: VizCompositorThread
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 11:: NetworkConfigWatcher
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 12:: NetworkConfigWatcher
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 13:: ThreadPoolSingleThreadForegroundBlocking0
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e94676a 0 + 4808009578
5 ??? 0x000000011e947150 0 + 4808012112
6 ??? 0x000000011e946d34 0 + 4808011060
7 ??? 0x000000011e999e07 0 + 4808351239
8 ??? 0x00007fff203358fc 0 + 140733733624060
9 ??? 0x00007fff20331443 0 + 140733733606467
Thread 14:: MemoryInfra
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 15:: NetworkConfigWatcher
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e8c61db 0 + 4807483867
5 ??? 0x000000011e93162b 0 + 4807923243
6 ??? 0x000000011e8f57cb 0 + 4807677899
7 ??? 0x000000011e950a7d 0 + 4808051325
8 ??? 0x000000011e999e07 0 + 4808351239
9 ??? 0x00007fff203358fc 0 + 140733733624060
10 ??? 0x00007fff20331443 0 + 140733733606467
Thread 16:: com.apple.NSEventThread
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x00007fff2042eb5f 0 + 140733734644575
3 ??? 0x00007fff2042d23f 0 + 140733734638143
4 ??? 0x00007fff2042c64c 0 + 140733734635084
5 ??? 0x00007fff22db368a 0 + 140733778179722
6 ??? 0x00007fff203358fc 0 + 140733733624060
7 ??? 0x00007fff20331443 0 + 140733733606467
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 ??? 0x00007fff203002ba 0 + 140733733405370
1 ??? 0x00007fff2030062c 0 + 140733733406252
2 ??? 0x000000011e99e492 0 + 4808369298
3 ??? 0x000000011e99e2cf 0 + 4808368847
4 ??? 0x000000011e94676a 0 + 4808009578
5 ??? 0x000000011e946e3d 0 + 4808011325
6 ??? 0x000000011e946c74 0 + 4808010868
7 ??? 0x000000011e999e07 0 + 4808351239
8 ??? 0x00007fff203358fc 0 + 140733733624060
9 ??? 0x00007fff20331443 0 + 140733733606467
Thread 18:
0 ??? 0x00007fff20331420 0 + 140733733606432
Thread 19:
0 ??? 0x00007fff20331420 0 + 140733733606432
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000001 rbx: 0x0000000000000065 rcx: 0x00007fff2030304e rdx: 0x0000000000000000
rdi: 0x0000000000000007 rsi: 0x00007fa6be15591f rbp: 0x00007fa6be1558e0 rsp: 0x00007fa6be1558b0
r8: 0x00007fa6be155f48 r9: 0xd397a85e7405c8cc r10: 0x0000000111c03eac r11: 0x0000000000000206
r12: 0x0000000000000001 r13: 0x0000000000000001 r14: 0x00007fa6be15591f r15: 0x0000000000000007
rip: 0x000000010ecdf449 rfl: 0x0000000000010206 cr2: 0x000000010ecdf449
Logical CPU: 3
Error Code: 0x00000014 (no mapping for user instruction read)
Trap Number: 14
Thread 0 instruction stream not available.
Thread 0 last branch register state not available.
Binary Images:
0 - 0xffffffffffffffff +ChimeraX (???) /private/var/folders/*/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX
0x111b2c000 - 0x111bc7fff dyld (852) /usr/lib/dyld
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=848K resident=0K(0%) swapped_out_or_unallocated=848K(100%)
Writable regions: Total=860.9M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=860.9M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
CG backing stores 3240K 6
CG image 164K 9
CoreAnimation 72K 10
CoreGraphics 12K 2
CoreUI image data 2112K 16
Foundation 16K 1
Kernel Alloc Once 8K 1
MALLOC 269.5M 427
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenGL GLSL 384K 5
STACK GUARD 76K 19
Stack 130.1M 20
Stack Guard 56.0M 1
VM_ALLOCATE 64.4M 46
__DATA 224K 2
__DATA_CONST 32K 1
__LINKEDIT 240K 2
__TEXT 624K 1
dylib 2088K 23
dylib (reserved) 60K 4 reserved VM address space (unallocated)
mapped file 753.6M 395
shared memory 7380K 41
=========== ======= =======
TOTAL 1.6G 1047
TOTAL, minus reserved VM space 1.3G 1047
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,2
Processor Name: Dual-Core Intel Core i7
Processor Speed: 3,3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 429.120.4.0.0
SMC Version (system): 2.37f25
Software:
System Software Overview:
System Version: macOS 11.4 (20F71)
Kernel Version: Darwin 20.5.0
Time since boot: 1:19
Graphics/Displays:
Intel Iris Graphics 550:
Chipset Model: Intel Iris Graphics 550
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1927
Revision ID: 0x000a
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (6)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash with trashed stack |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 4 years ago
comment:4 by , 4 years ago
That's not necessarily of running from the .dmg. That's App Translocation, a security measure, namely:
Starting in OS X v10.12, you can no longer provide external code or data alongside your code-signed app in a zip archive or unsigned disk image. An app distributed outside the Mac App Store runs from a randomized path when it is launched and so cannot access such external resources.
follow-up: 5 comment:5 by , 4 years ago
What does "runs from a randomized path" mean? The current working directory is not randomized -- it is / on macOS if I have ChimeraX not set it to ~/Desktop and launch by clicking the icon. I guess it means there is some macOS API that tells where the application is on disk and it gives the random location.
comment:6 by , 4 years ago
I think it's for purposes of loading from libraries, which cares about install paths, not the "current working directory".
Note:
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Looks like they were running ChimeraX directly from the DMG image which might be the cause of the useless stack info.
Current thread 0x0000000111c03e00 (most recent call first):