![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 years ago
Last modified 7 years ago
#1869 feedback defect
Crash trying to demote Chain to Sequence
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-13)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [1307]
Path: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 0.9.0 (0.9.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [1307]
User ID: 502
Date/Time: 2019-04-18 09:11:54.266 +0100
OS Version: Mac OS X 10.14.4 (18E226)
Report Version: 12
Anonymous UUID: 93DF4E87-45ED-D785-6E93-DB772A884336
Time Awake Since Boot: 6000 seconds
System Integrity Protection: disabled
Crashed Thread: 0 CrBrowserMain 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: Calling StructureSeq _cpp_demotion method failed.
abort() called
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff648732c6 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff64928bf1 pthread_kill + 284
2 libsystem_c.dylib 0x00007fff64790d8a raise + 26
3 libsystem_platform.dylib 0x00007fff6491db5d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff647dd6a6 abort + 127
6 libc++abi.dylib 0x00007fff61796641 abort_message + 231
7 libc++abi.dylib 0x00007fff617967c7 default_terminate_handler() + 243
8 libobjc.A.dylib 0x00007fff62f0ceeb _objc_terminate() + 105
9 libc++abi.dylib 0x00007fff617a219e std::__terminate(void (*)()) + 8
10 libc++abi.dylib 0x00007fff617a2213 std::terminate() + 51
11 libatomstruct.dylib 0x000000011ab153de atomstruct::AtomicStructure::~AtomicStructure() + 14
12 _ctypes.cpython-37m-darwin.so 0x000000010ac4eebf ffi_call_unix64 + 79
13 _ctypes.cpython-37m-darwin.so 0x000000010ac4f71a ffi_call + 858
14 _ctypes.cpython-37m-darwin.so 0x000000010ac4a813 _ctypes_callproc + 787
15 _ctypes.cpython-37m-darwin.so 0x000000010ac44583 PyCFuncPtr_call + 1043
16 org.python.python 0x000000010212375f _PyObject_FastCallKeywords + 559
17 org.python.python 0x00000001021ed26a call_function + 714
18 org.python.python 0x00000001021e596b _PyEval_EvalFrameDefault + 5707
19 org.python.python 0x0000000102123df3 function_code_fastcall + 195
20 org.python.python 0x00000001021ed271 call_function + 721
21 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
22 org.python.python 0x0000000102123df3 function_code_fastcall + 195
23 org.python.python 0x00000001021ed271 call_function + 721
24 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
25 org.python.python 0x0000000102123df3 function_code_fastcall + 195
26 org.python.python 0x00000001021ed271 call_function + 721
27 org.python.python 0x00000001021e58c0 _PyEval_EvalFrameDefault + 5536
28 org.python.python 0x0000000102123df3 function_code_fastcall + 195
29 org.python.python 0x00000001021ed271 call_function + 721
30 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
31 org.python.python 0x0000000102123df3 function_code_fastcall + 195
32 org.python.python 0x00000001021ed271 call_function + 721
33 org.python.python 0x00000001021e58c0 _PyEval_EvalFrameDefault + 5536
34 org.python.python 0x0000000102123df3 function_code_fastcall + 195
35 org.python.python 0x00000001021e5c45 _PyEval_EvalFrameDefault + 6437
36 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
37 org.python.python 0x00000001021238f6 _PyFunction_FastCallKeywords + 230
38 org.python.python 0x00000001021ed271 call_function + 721
39 org.python.python 0x00000001021e5a09 _PyEval_EvalFrameDefault + 5865
40 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
41 org.python.python 0x00000001021238f6 _PyFunction_FastCallKeywords + 230
42 org.python.python 0x00000001021ed271 call_function + 721
43 org.python.python 0x00000001021e596b _PyEval_EvalFrameDefault + 5707
44 org.python.python 0x0000000102123df3 function_code_fastcall + 195
45 org.python.python 0x00000001021ed271 call_function + 721
46 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
47 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
48 org.python.python 0x00000001021233d2 _PyFunction_FastCallDict + 450
49 QtCore.so 0x000000010fb37828 PyQtSlot::call(_object*, _object*) const + 40
50 QtCore.so 0x000000010fb37727 PyQtSlot::invoke(void**, _object*, void*, bool) const + 391
51 QtCore.so 0x000000010fb38268 PyQtSlotProxy::unislot(void**) + 88
52 QtCore.so 0x000000010fb381da PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
53 QtCore 0x000000010f69f3d6 QMetaObject::activate(QObject*, int, int, void**) + 2230
54 QtWidgets 0x000000010e9e2345 QAction::activate(QAction::ActionEvent) + 309
55 QtCore 0x000000010f69f6aa QMetaObject::activate(QObject*, int, int, void**) + 2954
56 QtCore 0x000000010f697944 QObject::event(QEvent*) + 788
57 QtWidgets 0x000000010e9ebb82 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 306
58 QtWidgets 0x000000010e9ece9f QApplication::notify(QObject*, QEvent*) + 383
59 QtWidgets.so 0x000000010e5bdf8a sipQApplication::notify(QObject*, QEvent*) + 234
60 QtCore 0x000000010f66ea7f QCoreApplication::notifyInternal2(QObject*, QEvent*) + 159
61 QtCore 0x000000010f66fc32 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 850
62 libqcocoa.dylib 0x0000000117c77e8e 0x117c50000 + 163470
63 libqcocoa.dylib 0x0000000117c78741 0x117c50000 + 165697
64 com.apple.CoreFoundation 0x00007fff382dc5e3 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
65 com.apple.CoreFoundation 0x00007fff382dc589 __CFRunLoopDoSource0 + 108
66 com.apple.CoreFoundation 0x00007fff382bff3b __CFRunLoopDoSources0 + 195
67 com.apple.CoreFoundation 0x00007fff382bf505 __CFRunLoopRun + 1189
68 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
69 com.apple.HIToolbox 0x00007fff375ab9db RunCurrentEventLoopInMode + 292
70 com.apple.HIToolbox 0x00007fff375ab61d ReceiveNextEventCommon + 355
71 com.apple.HIToolbox 0x00007fff375ab4a6 _BlockUntilNextEventMatchingListInModeWithFilter + 64
72 com.apple.AppKit 0x00007fff35945ffb _DPSNextEvent + 965
73 com.apple.AppKit 0x00007fff35944d93 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1361
74 com.apple.AppKit 0x00007fff3593eeb0 -[NSApplication run] + 699
75 libqcocoa.dylib 0x0000000117c7753d 0x117c50000 + 161085
76 QtCore 0x000000010f66a742 QEventLoop::exec(QFlags) + 418
77 QtCore 0x000000010f66f172 QCoreApplication::exec() + 402
78 QtWidgets.so 0x000000010e6abdc2 meth_QApplication_exec_(_object*, _object*) + 82
79 org.python.python 0x00000001021243ab _PyMethodDef_RawFastCallKeywords + 251
80 org.python.python 0x000000010212393c _PyCFunction_FastCallKeywords + 44
81 org.python.python 0x00000001021ed209 call_function + 617
82 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
83 org.python.python 0x0000000102123df3 function_code_fastcall + 195
84 org.python.python 0x00000001021ed271 call_function + 721
85 org.python.python 0x00000001021e58da _PyEval_EvalFrameDefault + 5562
86 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
87 org.python.python 0x00000001021238f6 _PyFunction_FastCallKeywords + 230
88 org.python.python 0x00000001021ed271 call_function + 721
89 org.python.python 0x00000001021e596b _PyEval_EvalFrameDefault + 5707
90 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
91 org.python.python 0x00000001021e4280 PyEval_EvalCode + 48
92 org.python.python 0x00000001021e19c3 builtin_exec + 563
93 org.python.python 0x000000010212455e _PyMethodDef_RawFastCallKeywords + 686
94 org.python.python 0x000000010212393c _PyCFunction_FastCallKeywords + 44
95 org.python.python 0x00000001021ed209 call_function + 617
96 org.python.python 0x00000001021e596b _PyEval_EvalFrameDefault + 5707
97 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
98 org.python.python 0x00000001021238f6 _PyFunction_FastCallKeywords + 230
99 org.python.python 0x00000001021ed271 call_function + 721
100 org.python.python 0x00000001021e596b _PyEval_EvalFrameDefault + 5707
101 org.python.python 0x00000001021ede81 _PyEval_EvalCodeWithName + 2721
102 org.python.python 0x00000001021233d2 _PyFunction_FastCallDict + 450
103 org.python.python 0x00000001022424c3 pymain_run_module + 147
104 org.python.python 0x00000001022412d6 pymain_main + 4262
105 org.python.python 0x0000000102240223 Py_Main + 51
106 edu.ucsf.cgl.ChimeraX 0x00000001020fce16 main + 278
107 libdyld.dylib 0x00007fff647383d5 start + 1
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 com.apple.AppKit 0x00007fff3594dd1a _NSEventThread + 175
6 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 2:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6487536e poll + 10
1 QtCore 0x000000010f6c1b40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010f6c31b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x000000010f66a742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001101c4c4a 0x1101a3000 + 138314
5 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
6 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
7 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
8 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
9 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 3:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff6487378e kevent + 10
1 QtWebEngineCore 0x00000001112d1469 0x1101a3000 + 18015337
2 QtWebEngineCore 0x00000001112ce75d 0x1101a3000 + 18003805
3 QtWebEngineCore 0x0000000110dc299f 0x1101a3000 + 12712351
4 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
5 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
6 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
7 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
8 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 4:: Chrome_DBThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110490958 0x1101a3000 + 3070296
10 QtWebEngineCore 0x0000000110490d1f 0x1101a3000 + 3071263
11 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
12 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
13 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
15 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 5:: Chrome_FileThread
0 libsystem_kernel.dylib 0x00007fff6487378e kevent + 10
1 QtWebEngineCore 0x00000001112d1469 0x1101a3000 + 18015337
2 QtWebEngineCore 0x00000001112ce75d 0x1101a3000 + 18003805
3 QtWebEngineCore 0x0000000110dc299f 0x1101a3000 + 12712351
4 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
5 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
6 QtWebEngineCore 0x00000001104909d8 0x1101a3000 + 3070424
7 QtWebEngineCore 0x0000000110490d2f 0x1101a3000 + 3071279
8 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
9 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
10 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 6:: Chrome_FileUserBlockingThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110490a58 0x1101a3000 + 3070552
10 QtWebEngineCore 0x0000000110490d3f 0x1101a3000 + 3071295
11 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
12 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
13 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
15 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 7:: Chrome_ProcessLauncherThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110490ad8 0x1101a3000 + 3070680
10 QtWebEngineCore 0x0000000110490d4c 0x1101a3000 + 3071308
11 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
12 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
13 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
15 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 8:: Chrome_CacheThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110490b58 0x1101a3000 + 3070808
10 QtWebEngineCore 0x0000000110490d59 0x1101a3000 + 3071321
11 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
12 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
13 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
15 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 9:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6487378e kevent + 10
1 QtWebEngineCore 0x00000001112d1469 0x1101a3000 + 18015337
2 QtWebEngineCore 0x00000001112ce75d 0x1101a3000 + 18003805
3 QtWebEngineCore 0x0000000110dc2986 0x1101a3000 + 12712326
4 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
5 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
6 QtWebEngineCore 0x0000000110490bd8 0x1101a3000 + 3070936
7 QtWebEngineCore 0x0000000110490d66 0x1101a3000 + 3071334
8 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
9 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
10 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
12 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 10:: BrowserBlockingWorker1/71171
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 QtWebEngineCore 0x0000000110e12c1f 0x1101a3000 + 13040671
3 QtWebEngineCore 0x0000000110e122e6 0x1101a3000 + 13038310
4 QtWebEngineCore 0x0000000110e1618d 0x1101a3000 + 13054349
5 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
6 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 11:: IndexedDB
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
10 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
11 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
13 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 12:: CompositorTileWorker1/60419
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 QtWebEngineCore 0x00000001119b1cf8 0x1101a3000 + 25226488
3 QtWebEngineCore 0x0000000110e1618d 0x1101a3000 + 13054349
4 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
5 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
6 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
7 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 13:: AudioThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
10 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
11 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
13 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 14:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
10 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
11 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
13 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 15:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6487378e kevent + 10
1 QtWebEngineCore 0x00000001112d1469 0x1101a3000 + 18015337
2 QtWebEngineCore 0x00000001112ce75d 0x1101a3000 + 18003805
3 QtWebEngineCore 0x0000000110dc299f 0x1101a3000 + 12712351
4 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
5 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
6 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
7 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
8 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6487536e poll + 10
1 QtCore 0x000000010f6c1b40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010f6c31b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x000000010f66a742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001101c4c4a 0x1101a3000 + 138314
5 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
6 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
7 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
8 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
9 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 17:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 QtCore 0x000000010f4b058b 0x10f483000 + 185739
3 QtCore 0x000000010f4b0522 QWaitCondition::wait(QMutex*, unsigned long) + 162
4 QtWidgets 0x000000010ec11862 0x10e9da000 + 2324578
5 QtCore 0x000000010f4aefbf 0x10f483000 + 180159
6 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6487536e poll + 10
1 QtCore 0x000000010f6c1b40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010f6c31b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x000000010f66a742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x00000001101c4c4a 0x1101a3000 + 138314
5 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
6 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
7 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
8 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
9 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
11 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 19:: PowerSaveBlocker
0 libsystem_kernel.dylib 0x00007fff6486d22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6486d76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff382c013e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff382bf6ac __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff382bee0e CFRunLoopRunSpecific + 455
5 QtWebEngineCore 0x0000000110dc390f 0x1101a3000 + 12716303
6 QtWebEngineCore 0x0000000110dc32a4 0x1101a3000 + 12714660
7 QtWebEngineCore 0x0000000110dc010e 0x1101a3000 + 12701966
8 QtWebEngineCore 0x0000000110de4531 0x1101a3000 + 12850481
9 QtWebEngineCore 0x0000000110e1836b 0x1101a3000 + 13063019
10 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
11 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
13 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 20:
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 libopenblasp-r0.3.5.dev.dylib 0x0000000102ff8a3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 21:
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 libopenblasp-r0.3.5.dev.dylib 0x0000000102ff8a3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 22:
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 libopenblasp-r0.3.5.dev.dylib 0x0000000102ff8a3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 23:: BrowserBlockingWorker2/171595
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6492956e _pthread_cond_wait + 722
2 QtWebEngineCore 0x0000000110e12c1f 0x1101a3000 + 13040671
3 QtWebEngineCore 0x0000000110e122e6 0x1101a3000 + 13038310
4 QtWebEngineCore 0x0000000110e1618d 0x1101a3000 + 13054349
5 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
6 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 24:: WorkerPool/76339
0 libsystem_kernel.dylib 0x00007fff6487086a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff649295a1 _pthread_cond_wait + 773
2 QtWebEngineCore 0x0000000110dfc2bb 0x1101a3000 + 12948155
3 QtWebEngineCore 0x0000000110e1a6e9 0x1101a3000 + 13072105
4 QtWebEngineCore 0x0000000110e1ac57 0x1101a3000 + 13073495
5 QtWebEngineCore 0x0000000110e11667 0x1101a3000 + 13035111
6 libsystem_pthread.dylib 0x00007fff649262eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff64929249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff6492540d thread_start + 13
Thread 25:
0 libsystem_pthread.dylib 0x00007fff649253f0 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff649253f0 start_wqthread + 0
Thread 27:
0 libsystem_pthread.dylib 0x00007fff649253f0 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010b8a65c0 rcx: 0x0000000102572a48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x0000000102572a80 rsp: 0x0000000102572a48
r8: 0x0000000102572f48 r9: 0xf98407367acd4beb r10: 0x000000010b8a666c r11: 0x0000000000000206
r12: 0x0000000000000307 r13: 0x0000003000000008 r14: 0x0000000000000006 r15: 0x000000000000002d
rip: 0x00007fff648732c6 rfl: 0x0000000000000206 cr2: 0x000000010234c25c
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x10aedf000 - 0x10aef3ff7 +libz.1.2.11.dylib (0) /Applications/ChimeraX.app/Contents/lib/libz.1.2.11.dylib
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0x10e47c000 - 0x10e6feffb +QtWidgets.so (0) /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyQt5/QtWidgets.so
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0x10fa1c000 - 0x10fb5dfff +QtCore.so (0) /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyQt5/QtCore.so
0x10fd3e000 - 0x10fe94fff +QtGui.so (0) /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyQt5/QtGui.so
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0x7fff64781000 - 0x7fff64781ff7 libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff64782000 - 0x7fff64809fff libsystem_c.dylib (1272.250.1) /usr/lib/system/libsystem_c.dylib
0x7fff6480a000 - 0x7fff6480dffb libsystem_configuration.dylib (963.250.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff6480e000 - 0x7fff64811ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff64812000 - 0x7fff64818fff libsystem_darwin.dylib (1272.250.1) /usr/lib/system/libsystem_darwin.dylib
0x7fff64819000 - 0x7fff6481fff7 libsystem_dnssd.dylib (878.250.4) /usr/lib/system/libsystem_dnssd.dylib
0x7fff64820000 - 0x7fff6486bffb libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff6486c000 - 0x7fff64894ff7 libsystem_kernel.dylib (4903.251.3) /usr/lib/system/libsystem_kernel.dylib
0x7fff64895000 - 0x7fff648e0ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff648e1000 - 0x7fff64905fff libsystem_malloc.dylib (166.251.2) /usr/lib/system/libsystem_malloc.dylib
0x7fff64906000 - 0x7fff64910ff7 libsystem_networkextension.dylib (767.250.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff64911000 - 0x7fff64918fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff64919000 - 0x7fff64922fef libsystem_platform.dylib (177.250.1) /usr/lib/system/libsystem_platform.dylib
0x7fff64923000 - 0x7fff6492dff7 libsystem_pthread.dylib (330.250.2) /usr/lib/system/libsystem_pthread.dylib
0x7fff6492e000 - 0x7fff64931ff7 libsystem_sandbox.dylib (851.250.12) /usr/lib/system/libsystem_sandbox.dylib
0x7fff64932000 - 0x7fff64934ff3 libsystem_secinit.dylib (30.220.1) /usr/lib/system/libsystem_secinit.dylib
0x7fff64935000 - 0x7fff6493cff3 libsystem_symptoms.dylib (820.257.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6493d000 - 0x7fff64952fff libsystem_trace.dylib (906.250.5) /usr/lib/system/libsystem_trace.dylib
0x7fff64954000 - 0x7fff64959ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6495a000 - 0x7fff64989ff7 libxpc.dylib (1336.251.2) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 563
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: 339814
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=693.2M resident=0K(0%) swapped_out_or_unallocated=693.2M(100%)
Writable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 23.9M 9
CG image 464K 23
CoreAnimation 336K 32
CoreGraphics 8K 1
CoreImage 208K 24
CoreUI image data 3768K 40
CoreUI image file 360K 6
Foundation 28K 3
Kernel Alloc Once 8K 1
MALLOC 2.4G 259
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 1344K 7 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Memory Tag 242 12K 1
OpenGL GLSL 512K 6
STACK GUARD 108K 27
Stack 164.2M 28
Stack Guard 56.0M 1
VM_ALLOCATE 141.9M 169
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 59.1M 488
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 239.0M 120
__TEXT 454.2M 473
__UNICODE 564K 1
mapped file 88.5M 74
shared memory 704K 16
=========== ======= =======
TOTAL 4.0G 1824
TOTAL, minus reserved VM space 3.6G 1824
Log:
> alias colorcharged color white target s; color :Arg | :Lys | :His red target
s; color :Glu | :Asp blue target s
> alias colorpolar color white target s; color :Gln | :Asn | :His | :Ser |
:Thr | :Tyr | :Cys cornflower blue target s
> alias coloramphipatic color white target s; color :Trp | :Tyr | :Met orange
target s
> alias colorhydrophobic color white target s; color :Ala | :Ile | :Leu | :Met
| :Phe | :Val | :Pro | :Gly grey target s
UCSF ChimeraX version: 0.9 (2019-03-13)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 NVIDIA-12.0.23 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA Corporation
Change History (4)
comment:1 by , 7 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash trying to demote Chain to Sequence |
comment:2 by , 7 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 7 years ago
Hi Eric,
I didn't have sequence shown. I was trying to display the sequence (sequence chain). One problem could be that the pdb was not really a standard pdb. The structure contained a cyclic part.
Best,
Józef
On 18/04/2019, 20:48, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#1869: Crash trying to demote Chain to Sequence
----------------------------------------+----------------------
Reporter: j.r.lewandowski@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Changes (by pett):
* status: accepted => feedback
Comment:
Hi Jozef,
The information automatically supplied with the bug report isn't
really sufficient for me to figure out why the crash occurred. You were
closing a structure or a session when this occurred? Did you have a
sequence or a sequence alignment shown?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1869#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 7 years ago
Does this crash happen reproducibly? If so, can you try the same thing with entry 1bzh (which has a cyclic peptide) and see what happens [doesn't crash for me in limited testing]?
--Eric
Note:
See TracTickets
for help on using tickets.
Hi Jozef,
--Eric