[MacPorts] #46007: pymol crushes on Yosemite after a while

MacPorts noreply at macports.org
Mon Nov 24 16:18:54 PST 2014


#46007: pymol crushes  on Yosemite after a while
----------------------------+--------------------------------
 Reporter:  barak.raveh@…   |      Owner:  macports-tickets@…
     Type:  defect          |     Status:  new
 Priority:  Normal          |  Milestone:
Component:  ports           |    Version:  2.3.3
 Keywords:  pymol NSScreen  |       Port:  pymol
----------------------------+--------------------------------
 Pymol seems to work normally on yosemite but then crushes after a short
 while with message:
 *** Terminating app due to uncaught exception
 'NSInternalInconsistencyException', reason: 'NSScreen reconfig must only
 happen on the main thread.'
 abort() called terminating with uncaught exception of type NSException

 Log below:
 ================

 Process:               Python [1079]
 Path:
 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
 Identifier:            org.python.python
 Version:               2.7.8 (2.7.8)
 Code Type:             X86-64 (Native)
 Parent Process:        bash [688]
 Responsible:           Terminal [685]
 User ID:               501

 Date/Time:             2014-11-24 16:10:56.440 -0800
 OS Version:            Mac OS X 10.10.1 (14B25)
 Report Version:        11
 Anonymous UUID:        C6F9D0BE-F02B-FF6C-5BBB-AAC0CD6EB628


 Time Awake Since Boot: 1100 seconds

 Crashed Thread:        4  Dispatch queue: com.apple.Xplugin.CGEventPort

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

 Application Specific Information:
 *** Terminating app due to uncaught exception
 'NSInternalInconsistencyException', reason: 'NSScreen reconfig must only
 happen on the main thread.'
 abort() called
 terminating with uncaught exception of type NSException

 Application Specific Backtrace 1:
 0   CoreFoundation                      0x00007fff8ff8064c
 __exceptionPreprocess + 172
 1   libobjc.A.dylib                     0x00007fff8bc256de
 objc_exception_throw + 43
 2   CoreFoundation                      0x00007fff8ff8042a +[NSException
 raise:format:arguments:] + 106
 3   Foundation                          0x00007fff8d8fd5b9
 -[NSAssertionHandler
 handleFailureInMethod:object:file:lineNumber:description:] + 195
 4   AppKit                              0x00007fff8b5c6f13 +[NSScreen
 _invalidateIfNeededForReason:] + 139
 5   AppKit                              0x00007fff8b347ffd -[NSApplication
 _reactToDockChanged] + 29
 6   AppKit                              0x00007fff8b27f16c
 _NSCoreDockMessageReceive + 802
 7   HIToolbox                           0x00007fff8ef5fe48
 _ZL12DockCallbackjjPvS_ + 1845
 8   HIServices                          0x00007fff8bbd8c16
 dockClientNotificationProc + 171
 9   CoreGraphics                        0x00007fff92e3fb33
 _ZNK21CGSConnectionNotifier16invoke_callbacksEjPvm + 601
 10  CoreGraphics                        0x00007fff92e3f872
 _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ + 103
 11  CoreGraphics                        0x00007fff92df7fe7
 _ZN21CGSDatagramReadStream22dispatch_next_datagramEv + 779
 12  CoreGraphics                        0x00007fff92df7ccc
 _ZN21CGSDatagramReadStream18dispatch_datagramsEv + 50
 13  CoreGraphics                        0x00007fff92df7ae1
 CGSDatagramReadStreamDispatchDatagramsWithData + 109
 14  CoreGraphics                        0x00007fff92df7897
 CGSSnarfAndDispatchDatagrams + 427
 15  CoreGraphics                        0x00007fff92df75e8
 CGSGetNextEventRecordInternal + 92
 16  CoreGraphics                        0x00007fff92df7533
 CGEventCreateNextEvent + 48
 17  libXplugin.1.dylib                  0x000000010559495c
 ___xp_init_service_cg_event_port_block_invoke + 106
 18  libdispatch.dylib                   0x00007fff94922c13
 _dispatch_client_callout + 8
 19  libdispatch.dylib                   0x00007fff9492d87e
 _dispatch_source_latch_and_call + 721
 20  libdispatch.dylib                   0x00007fff9492662b
 _dispatch_source_invoke + 412
 21  libdispatch.dylib                   0x00007fff94926154
 _dispatch_queue_drain + 571
 22  libdispatch.dylib                   0x00007fff94927ecc
 _dispatch_queue_invoke + 202
 23  libdispatch.dylib                   0x00007fff949256b7
 _dispatch_root_queue_drain + 463
 24  libdispatch.dylib                   0x00007fff94933fe4
 _dispatch_worker_thread3 + 91
 25  libsystem_pthread.dylib             0x00007fff896786cb
 _pthread_wqthread + 729
 26  libsystem_pthread.dylib             0x00007fff896764a1 start_wqthread
 + 13

 Thread 0:: Dispatch queue: com.apple.main-thread
 0   libsystem_kernel.dylib              0x00007fff8db4f3f6 __select + 10
 1   _cmd.so                             0x0000000104cd8eab MainBusyIdle +
 1051
 2   libglut.3.dylib                     0x0000000105524cd8 glutMainLoop +
 153
 3   _cmd.so                             0x0000000104cd7ad6 main_common +
 1238
 4   _cmd.so                             0x0000000104cd7c2c main_shared +
 108
 5   _cmd.so                             0x0000000104ccca2a CmdRunPyMOL +
 90
 6   org.python.python                   0x0000000104680021
 PyEval_EvalFrameEx + 19649
 7   org.python.python                   0x000000010467b052
 PyEval_EvalCodeEx + 1538
 8   org.python.python                   0x0000000104682ad5 fast_function +
 117
 9   org.python.python                   0x000000010467ec1d
 PyEval_EvalFrameEx + 14525
 10  org.python.python                   0x000000010467b052
 PyEval_EvalCodeEx + 1538
 11  org.python.python                   0x000000010467aa46 PyEval_EvalCode
 + 54
 12  org.python.python                   0x00000001046a4884
 PyRun_FileExFlags + 164
 13  org.python.python                   0x00000001046a4401
 PyRun_SimpleFileExFlags + 769
 14  org.python.python                   0x00000001046b9e98 Py_Main + 3096
 15  libdyld.dylib                       0x00007fff88e0a5c9 start + 1

 Thread 1:: Dispatch queue: com.apple.libdispatch-manager
 0   libsystem_kernel.dylib              0x00007fff8db5022e kevent64 + 10
 1   libdispatch.dylib                   0x00007fff94925a6a
 _dispatch_mgr_thread + 52

 Thread 2:
 0   libsystem_kernel.dylib              0x00007fff8db4f3f6 __select + 10
 1   libsystem_pthread.dylib             0x00007fff896782fc _pthread_body +
 131
 2   libsystem_pthread.dylib             0x00007fff89678279 _pthread_start
 + 176
 3   libsystem_pthread.dylib             0x00007fff896764b1 thread_start +
 13

 Thread 3:
 0   libsystem_kernel.dylib              0x00007fff8db4f3f6 __select + 10
 1   org.python.python                   0x0000000104680021
 PyEval_EvalFrameEx + 19649
 2   org.python.python                   0x000000010467b052
 PyEval_EvalCodeEx + 1538
 3   org.python.python                   0x0000000104682ad5 fast_function +
 117
 4   org.python.python                   0x000000010467ec1d
 PyEval_EvalFrameEx + 14525
 5   org.python.python                   0x000000010467b052
 PyEval_EvalCodeEx + 1538
 6   org.python.python                   0x0000000104606b6c function_call +
 364
 7   org.python.python                   0x00000001045e1033 PyObject_Call +
 99
 8   org.python.python                   0x000000010467e980
 PyEval_EvalFrameEx + 13856
 9   org.python.python                   0x0000000104682b72 fast_function +
 274
 10  org.python.python                   0x000000010467ec1d
 PyEval_EvalFrameEx + 14525
 11  org.python.python                   0x0000000104682b72 fast_function +
 274
 12  org.python.python                   0x000000010467ec1d
 PyEval_EvalFrameEx + 14525
 13  org.python.python                   0x000000010467b052
 PyEval_EvalCodeEx + 1538
 14  org.python.python                   0x0000000104606b6c function_call +
 364
 15  org.python.python                   0x00000001045e1033 PyObject_Call +
 99
 16  org.python.python                   0x00000001045ee226
 instancemethod_call + 182
 17  org.python.python                   0x00000001045e1033 PyObject_Call +
 99
 18  org.python.python                   0x00000001046822cd
 PyEval_CallObjectWithKeywords + 93
 19  org.python.python                   0x00000001046bc0c6 t_bootstrap +
 70
 20  libsystem_pthread.dylib             0x00007fff896782fc _pthread_body +
 131
 21  libsystem_pthread.dylib             0x00007fff89678279 _pthread_start
 + 176
 22  libsystem_pthread.dylib             0x00007fff896764b1 thread_start +
 13

 Thread 4 Crashed:: Dispatch queue: com.apple.Xplugin.CGEventPort
 0   libsystem_kernel.dylib              0x00007fff8db4f282 __pthread_kill
 + 10
 1   libsystem_c.dylib                   0x00007fff90b6fb73 abort + 129
 2   libc++abi.dylib                     0x00007fff92d1ba21 abort_message +
 257
 3   libc++abi.dylib                     0x00007fff92d439d1
 default_terminate_handler() + 267
 4   libobjc.A.dylib                     0x00007fff8bc296c6
 _objc_terminate() + 103
 5   libc++abi.dylib                     0x00007fff92d410a1
 std::__terminate(void (*)()) + 8
 6   libc++abi.dylib                     0x00007fff92d41113
 std::terminate() + 51
 7   libobjc.A.dylib                     0x00007fff8bc294ef objc_terminate
 + 9
 8   libdispatch.dylib                   0x00007fff94922c27
 _dispatch_client_callout + 28
 9   libdispatch.dylib                   0x00007fff9492d87e
 _dispatch_source_latch_and_call + 721
 10  libdispatch.dylib                   0x00007fff9492662b
 _dispatch_source_invoke + 412
 11  libdispatch.dylib                   0x00007fff94926154
 _dispatch_queue_drain + 571
 12  libdispatch.dylib                   0x00007fff94927ecc
 _dispatch_queue_invoke + 202
 13  libdispatch.dylib                   0x00007fff949256b7
 _dispatch_root_queue_drain + 463
 14  libdispatch.dylib                   0x00007fff94933fe4
 _dispatch_worker_thread3 + 91
 15  libsystem_pthread.dylib             0x00007fff896786cb
 _pthread_wqthread + 729
 16  libsystem_pthread.dylib             0x00007fff896764a1 start_wqthread
 + 13

 Thread 4 crashed with X86 Thread State (64-bit):
   rax: 0x0000000000000000  rbx: 0x0000000000000006  rcx:
 0x000000010d778748  rdx: 0x0000000000000000
   rdi: 0x000000000000291b  rsi: 0x0000000000000006  rbp:
 0x000000010d778770  rsp: 0x000000010d778748
    r8: 0x0000000000000000   r9: 0x00007fff90b99d90  r10:
 0x000000000c000000  r11: 0x0000000000000206
   r12: 0x000000010d7788d0  r13: 0x0000000000000000  r14:
 0x000000010d779000  r15: 0x000000010d7787b0
   rip: 0x00007fff8db4f282  rfl: 0x0000000000000206  cr2:
 0x00007fff7779cfd8

 Logical CPU:     0
 Error Code:      0x02000148
 Trap Number:     133


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 225.1) <2D502FBB-D2A0-3937-A5C5-385FA65B3874>
 /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
     0x7fff92ae8000 -     0x7fff92aedff7  libunwind.dylib (35.3) <BE7E51A0
 -B6EA-3A54-9CCA-9D88F683A6D6> /usr/lib/system/libunwind.dylib
     0x7fff92af5000 -     0x7fff92afdff7  com.apple.icloud.FindMyDevice
 (1.0 - 1) <D198E170-3610-3727-BC87-73AD249CA097>
 /System/Library/PrivateFrameworks/FindMyDevice.framework/Versions/A/FindMyDevice
     0x7fff92c56000 -     0x7fff92cccfe7  libcorecrypto.dylib (233.1.2)
 <E1789801-3985-3949-B736-6B3378873301> /usr/lib/system/libcorecrypto.dylib
     0x7fff92d1b000 -     0x7fff92d46fff  libc++abi.dylib (125) <88A22A0F-
 87C6-3002-BFBA-AC0F2808B8B9> /usr/lib/libc++abi.dylib
     0x7fff92dc5000 -     0x7fff9361cff3  com.apple.CoreGraphics (1.600.0 -
 772) <6364CBE3-3635-3A53-B448-9D19EF9FEA96>
 /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
     0x7fff9365a000 -     0x7fff93663ff3  com.apple.CommonAuth (4.0 - 2.0)
 <F4C266BE-2E0E-36B4-9DE7-C6B4BF410FD7>
 /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
     0x7fff93849000 -     0x7fff93979fff  com.apple.UIFoundation (1.0 - 1)
 <8E030D93-441C-3997-9CD2-55C8DFAC8B84>
 /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
     0x7fff9397a000 -     0x7fff93989fff  com.apple.LangAnalysis (1.7.0 -
 1.7.0) <D1E527E4-C561-352F-9457-E8C50232793C>
 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
     0x7fff942c2000 -     0x7fff942d4ff7  com.apple.ImageCapture (9.0 -
 9.0) <7FB65DD4-56B5-35C4-862C-7A2DED991D1F>
 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
     0x7fff94324000 -     0x7fff943a1fff  com.apple.CoreServices.OSServices
 (640.3 - 640.3) <28445162-08E9-3E24-84E4-617CE5FE1367>
 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
     0x7fff943a2000 -     0x7fff943dafff  com.apple.RemoteViewServices (2.0
 - 99) <C9A62691-B0D9-34B7-B71C-A48B5F4DC553>
 /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
     0x7fff947cc000 -     0x7fff948affff  libcrypto.0.9.8.dylib (52)
 <7208EEE2-C090-383E-AADD-7E1BD1321BEC> /usr/lib/libcrypto.0.9.8.dylib
     0x7fff948b0000 -     0x7fff94904fff  libc++.1.dylib (120) <1B9530FD-
 989B-3174-BB1C-BDC159501710> /usr/lib/libc++.1.dylib
     0x7fff94905000 -     0x7fff9491bff7  libsystem_asl.dylib (267)
 <F153AC5B-0542-356E-88C8-20A62CA704E2> /usr/lib/system/libsystem_asl.dylib
     0x7fff94921000 -     0x7fff9494bff7  libdispatch.dylib (442.1.4)
 <502CF32B-669B-3709-8862-08188225E4F0> /usr/lib/system/libdispatch.dylib
     0x7fff9494c000 -     0x7fff9494cfff  com.apple.Accelerate.vecLib (3.10
 - vecLib 3.10) <A48738CA-5B6F-3D14-97E9-2BFDFC3DCC06>
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
     0x7fff9494d000 -     0x7fff94972ff7  libPng.dylib (1231)
 <2D5AC0EE-4056-3F76-97E7-BBD415F072B5>
 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
     0x7fff94973000 -     0x7fff94a14ff7  com.apple.Bluetooth (4.3.1 -
 4.3.1f2) <EDC78AEE-28E7-324C-9947-41A0814A8154>
 /System/Library/Frameworks/IOBluetooth.framework/Versions/A/IOBluetooth
     0x7fff94a8a000 -     0x7fff94a8cff7  libsystem_coreservices.dylib (9)
 <41B7C578-5A53-31C8-A96F-C73E030B0938>
 /usr/lib/system/libsystem_coreservices.dylib
     0x7fff94b97000 -     0x7fff94bb3ff7  libsystem_malloc.dylib (53.1.1)
 <19BCC257-5717-3502-A71F-95D65AFA861B>
 /usr/lib/system/libsystem_malloc.dylib
     0x7fff94bb4000 -     0x7fff94bc7ff7  com.apple.CoreBluetooth (1.0 - 1)
 <FA9B43B3-E183-3040-AE25-66EF9870CF35>
 /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth
     0x7fff94bd5000 -     0x7fff94c23fff  libcurl.4.dylib (83.1.2)
 <337A1FF8-E8B1-3173-9F29-C0D4C851D8E1> /usr/lib/libcurl.4.dylib
     0x7fff94c24000 -     0x7fff95077fc7  com.apple.vImage (8.0 - 8.0)
 <33BE7B31-72DB-3364-B37E-C322A32748C5>
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
     0x7fff95078000 -     0x7fff9507aff7  libsystem_sandbox.dylib (358.1.1)
 <DB9962EF-8898-31CC-9B87-E01F8CE74C9D>
 /usr/lib/system/libsystem_sandbox.dylib
     0x7fff956ae000 -     0x7fff956d8fff  GLRendererFloat (11.0.7)
 <3B3B74F4-E63C-3241-8807-E2407C4020B2>
 /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
     0x7fff956e5000 -     0x7fff9577aff7  com.apple.ColorSync (4.9.0 -
 4.9.0) <F06733BD-A10C-3DB3-B050-825351130392>
 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
     0x7fff95790000 -     0x7fff95804fff  com.apple.ApplicationServices.ATS
 (360 - 375) <62828B40-231D-3F81-8067-1903143DCB6B>
 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS

 External Modification Summary:
   Calls made by other processes targeting this process:
     task_for_pid: 1
     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: 531
     thread_create: 0
     thread_set_state: 0

 VM Region Summary:
 ReadOnly portion of Libraries: Total=203.8M resident=106.3M(52%)
 swapped_out_or_unallocated=97.5M(48%)
 Writable regions: Total=179.9M written=31.8M(18%) resident=64.3M(36%)
 swapped_out=0K(0%) unallocated=115.6M(64%)

 REGION TYPE                      VIRTUAL
 ===========                      =======
 ATS (font support)                 32.3M
 ATS (font support) (reserved)         4K        reserved VM address space
 (unallocated)
 CG backing stores                   644K
 CG image                              4K
 CG shared images                    208K
 CoreServices                       1028K
 CoreUI image data                     4K
 Dispatch continuations             8192K
 IOKit                              6796K
 Kernel Alloc Once                     8K
 MALLOC                            104.8M
 MALLOC (admin)                       32K
 MALLOC_LARGE (reserved)            1484K        reserved VM address space
 (unallocated)
 Memory Tag 251                        8K
 OpenGL GLSL                         256K
 STACK GUARD                        56.0M
 Stack                              13.1M
 VM_ALLOCATE                        11.0M
 __DATA                             20.8M
 __GLSLBUILTINS                     2588K
 __IMAGE                             528K
 __LINKEDIT                         74.5M
 __TEXT                            129.3M
 __UNICODE                           544K
 mapped file                        65.4M
 shared memory                        68K
 ===========                      =======
 TOTAL                             529.0M
 TOTAL, minus reserved VM space    527.6M


 Model: MacBookAir4,2, BootROM MBA41.0077.B11, 2 processors, Intel Core i5,
 1.7 GHz, 4 GB, SMC 1.73f66
 Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 384 MB
 Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80CE,
 0x4D34373142353737334448302D4348392020
 Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80CE,
 0x4D34373142353737334448302D4348392020
 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xE9),
 Broadcom BCM43xx 1.0 (5.106.98.100.24)
 Bluetooth: Version 4.3.1f2 15015, 3 services, 19 devices, 1 incoming
 serial ports
 Network Service: Wi-Fi, AirPort, en0
 Serial ATA Device: APPLE SSD SM256C, 251 GB
 USB Device: Hub
 USB Device: Internal Memory Card Reader
 USB Device: Hub
 USB Device: Apple Internal Keyboard / Trackpad
 USB Device: BRCM20702 Hub
 USB Device: Bluetooth USB Host Controller
 USB Device: FaceTime Camera (Built-in)
 Thunderbolt Bus: MacBook Air, Apple Inc., 8.1

-- 
Ticket URL: <https://trac.macports.org/ticket/46007>
MacPorts <https://www.macports.org/>
Ports system for OS X


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