![[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: | pett | |
|---|---|---|---|
| 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:
See TracTickets
for help on using tickets.
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):