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Crash on start -- Mac OS X #628

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cryos opened this issue Feb 2, 2012 · 2 comments
Open

Crash on start -- Mac OS X #628

cryos opened this issue Feb 2, 2012 · 2 comments

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@cryos
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cryos commented Feb 2, 2012

Hi there -

I hope I am not repeating a previous discussion, but I could not find any previous bug report quite like this.

After successfully using Avogadro for a few days, the program crashed and is no longer able to start. Double-clicking Avogadro.app leads to the program appearing on the dock, a editor window opening, and then "Avogadro quit unexpectedly". Deleting the application from the Applications folder and re-installing did not work. I also tried deleting the .app along with any .plist system files that had "avogadro" in the name before re-installing again, which also did not change anything. Tried re-installing from the nightly build (02/01/2012), but the program still crashes on startup. Notably, roughly the same thing happened on my last MacBook -- I used Avogadro more-or-less successfully for months, then one day it crashed and never opened again. I got a new computer and so never bothered following up.

One possibility: It seems like the program is trying to re-open a file that had been open in a previous session (a window pops up, and sometimes the file path is written at the bottom of that window). I think that I have deleted that file, and maybe the problem is that Avogadro is trying to open a .cml file that is gone since it last ran? That's why I tried to find a .plist file that had history information such as what windows had been open; I was trying to force Avogadro to forget that information!

Any help would be much appreciated.

Alex

Long error report reproduced below:

Process: Avogadro [10278]
Path: /Applications/Avogadro.app/Contents/MacOS/Avogadro
Identifier: net.sourceforge
Version: ??? (1.0.3)
Code Type: X86 (Native)
Parent Process: launchd [136]

Date/Time: 2012-02-02 10:10:48.211 -0800
OS Version: Mac OS X 10.7.2 (11C74)
Report Version: 9

Interval Since Last Report: 2736152 sec
Crashes Since Last Report: 66
Per-App Interval Since Last Report: 2564 sec
Per-App Crashes Since Last Report: 1
Anonymous UUID: E658FD84-2F5B-44AA-83F4-5388C880EFAA

Crashed Thread: 9

Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x000000000003015c

VM Regions Near 0x3015c:
__PAGEZERO 0000000000000000-0000000000001000 [ 4K] ---/--- SM=NUL /Applications/Avogadro.app/Contents/MacOS/Avogadro
--> __TEXT 0000000000001000-000000000008b000 [ 552K] r-x/rwx SM=COW /Applications/Avogadro.app/Contents/MacOS/Avogadro
__DATA 000000000008b000-000000000009c000 [ 68K] rw-/rwx SM=COW /Applications/Avogadro.app/Contents/MacOS/Avogadro

Application Specific Information:
objc[10278]: garbage collection is OFF

Thread 0:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x93087c22 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x930871f6 mach_msg + 70
2 com.apple.CoreFoundation 0x9481f0ea CFRunLoopServiceMachPort + 170
3 com.apple.CoreFoundation 0x94828214 CFRunLoopRun + 1428
4 com.apple.CoreFoundation 0x948278ec CFRunLoopRunSpecific + 332
5 com.apple.CoreFoundation 0x94827798 CFRunLoopRunInMode + 120
6 com.apple.HIToolbox 0x92c63a7f RunCurrentEventLoopInMode + 318
7 com.apple.HIToolbox 0x92f244e9 ZL14RunTransitionsm + 486
8 com.apple.HIToolbox 0x92f2550d TransitionWindowWithOptions + 2867
9 com.apple.HIToolbox 0x92f2630d TransitionWindowAndParent + 113
10 com.apple.HIToolbox 0x92f279e3 ShowSheetWindow + 706
11 QtGui 0x0048c7eb QApplicationPrivate::globalEventProcessor(OpaqueEventHandlerCallRef
, OpaqueEventRef
, void
) + 13499
12 com.apple.HIToolbox 0x92ded920 InvokeEventHandlerUPP(OpaqueEventHandlerCallRef, OpaqueEventRef
, void
, long ()(OpaqueEventHandlerCallRef, OpaqueEventRef_, void_)) + 36
13 com.apple.HIToolbox 0x92c69803 _ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec + 1602
14 com.apple.HIToolbox 0x92c68c80 _ZL30SendEventToEventTargetInternalP14OpaqueEventRefP20OpaqueEventTargetRefP14HandlerCallRec + 482
15 com.apple.HIToolbox 0x92c68a98 SendEventToEventTargetWithOptions + 75
16 com.apple.HIToolbox 0x92c7e6fe _ZL29ToolboxEventDispatcherHandlerP25OpaqueEventHandlerCallRefP14OpaqueEventRefPv + 3152
17 com.apple.HIToolbox 0x92c69cbe _ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec + 2813
18 com.apple.HIToolbox 0x92c68c80 _ZL30SendEventToEventTargetInternalP14OpaqueEventRefP20OpaqueEventTargetRefP14HandlerCallRec + 482
19 com.apple.HIToolbox 0x92c7daa9 SendEventToEventTarget + 76
20 QtGui 0x004a2c34 QEventDispatcherMac::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 596
21 QtCore 0x01318f31 QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 65
22 QtCore 0x0131916d QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) + 189
23 QtCore 0x0131b49e QCoreApplication::exec() + 174
24 net.sourceforge 0x00013c43 main + 6451
25 net.sourceforge 0x00006e96 _start + 216
26 net.sourceforge 0x00006dbd start + 41

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x9308a90a kevent + 10
1 libdispatch.dylib 0x9aa6bc58 _dispatch_mgr_invoke + 969
2 libdispatch.dylib 0x9aa6a6a7 _dispatch_mgr_thread + 53

Thread 2:
0 libsystem_kernel.dylib 0x9308a02e __workq_kernreturn + 10
1 libsystem_c.dylib 0x935eeccf _pthread_wqthread + 773
2 libsystem_c.dylib 0x935f06fe start_wqthread + 30

Thread 3:
0 libsystem_kernel.dylib 0x9308a02e __workq_kernreturn + 10
1 libsystem_c.dylib 0x935eeccf _pthread_wqthread + 773
2 libsystem_c.dylib 0x935f06fe start_wqthread + 30

Thread 4:: Dispatch queue: com.apple.opengl.cvmDoWork
0 libsystem_kernel.dylib 0x93087c22 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x930871f6 mach_msg + 70
2 libCoreVMClient.dylib 0x980b8536 cvmsServ_BuildModularFunction + 219
3 libCoreVMClient.dylib 0x980b973d CVMSBuildModularFunction + 109
4 libCVMSPluginSupport.dylib 0x90cfc46e cvm_deferred_build_modular(void*) + 303
5 libdispatch.dylib 0x9aa6b797 _dispatch_queue_drain + 224
6 libdispatch.dylib 0x9aa6b63c _dispatch_queue_invoke + 47
7 libdispatch.dylib 0x9aa6ae44 _dispatch_worker_thread2 + 187
8 libsystem_c.dylib 0x935eeb24 _pthread_wqthread + 346
9 libsystem_c.dylib 0x935f06fe start_wqthread + 30

Thread 5:
0 libsystem_kernel.dylib 0x9308983e _psynch_cvwait + 10
1 libsystem_c.dylib 0x935f0e78 pthread_cond_wait + 914
2 libsystem_c.dylib 0x9359882a pthread_cond_wait + 48
3 QtCore 0x011f4316 QWaitCondition::wait(QMutex
, unsigned long) + 278
4 QtGui 0x00a6284c QFileInfoGatherer::run() + 540
5 QtCore 0x01259f06 QThreadPrivate::start(void
) + 198
6 libsystem_c.dylib 0x935eced9 _pthread_start + 335
7 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 6:
0 libsystem_kernel.dylib 0x9308a90a kevent + 10
1 QtCore 0x01305dda QKqueueFileSystemWatcherEngine::run() + 74
2 QtCore 0x01259f06 QThreadPrivate::start(void*) + 198
3 libsystem_c.dylib 0x935eced9 _pthread_start + 335
4 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 7:
0 libsystem_kernel.dylib 0x9308983e _psynch_cvwait + 10
1 libsystem_c.dylib 0x935f0e78 pthread_cond_wait + 914
2 libsystem_c.dylib 0x935987f5 pthread_cond_timedwait + 47
3 QtCore 0x011f42f4 QWaitCondition::wait(QMutex
, unsigned long) + 244
4 QtCore 0x01256574 QThreadPoolThread::run() + 500
5 QtCore 0x01259f06 QThreadPrivate::start(void
) + 198
6 libsystem_c.dylib 0x935eced9 _pthread_start + 335
7 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 8:: com.apple.CFSocket.private
0 libsystem_kernel.dylib 0x93089b42 __select + 10
1 com.apple.CoreFoundation 0x94876195 __CFSocketManager + 1557
2 libsystem_c.dylib 0x935eced9 _pthread_start + 335
3 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 9 Crashed:
0 libstdc++.6.dylib 0x95c96f20 std::string::Rep::M_dispose(std::allocator const&) + 32
1 libstdc++.6.dylib 0x95c96f7d std::basic_string<char, std::char_traits, std::allocator >::~basic_string() + 43
2 libopenbabel.4.0.1.dylib 0x00128088 std::pair<std::string, std::string>::~pair() + 26
3 cmlformat.so 0x0a93f415 void std::Destroy<__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, std::allocator<std::pair<std::string, std::string> > >(__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>
, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>
, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, std::allocator<std::pair<std::string, std::string> >) + 23
4 cmlformat.so 0x0a940eb4 std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >::erase(__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >) + 78
5 cmlformat.so 0x0a940f1c std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >::clear() + 30
6 cmlformat.so 0x0a936326 OpenBabel::CMLFormat::DoElement(std::string const&) + 80
7 cdxmlformat.so 0x0a89cd6d OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat_, OpenBabel::OBBase_) + 653
8 cdxmlformat.so 0x0a89b9e7 OpenBabel::XMLMoleculeFormat::ReadMolecule(OpenBabel::OBBase_, OpenBabel::OBConversion_) + 125
9 libopenbabel.4.0.1.dylib 0x00197c51 OpenBabel::OBConversion::Read(OpenBabel::OBBase_, std::istream_) + 323
10 libavogadro.1.0.3.dylib 0x01513922 Avogadro::ReadFileThread::run() + 1850
11 QtCore 0x01259f06 QThreadPrivate::start(void_) + 198
12 libsystem_c.dylib 0x935eced9 _pthread_start + 335
13 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 10:
0 libsystem_c.dylib 0x935c4b28 memmove$VARIANT$sse42 + 363
1 libstdc++.6.dylib 0x95c97adf std::string::Rep::M_clone(std::allocator const&, unsigned long) + 79
2 libstdc++.6.dylib 0x95c97b40 std::string::Rep::M_grab(std::allocator const&, std::allocator const&) + 68
3 libstdc++.6.dylib 0x95c97c38 std::basic_string<char, std::char_traits, std::allocator >::basic_string(std::string const&) + 78
4 cmlformat.so 0x0a93e6d6 std::pair<std::string, std::string>::pair(std::pair<std::string, std::string> const&) + 48
5 cmlformat.so 0x0a93e736 void std::Construct<std::pair<std::string, std::string>, std::pair<std::string, std::string> >(std::pair<std::string, std::string>, std::pair<std::string, std::string> const&) + 28
6 cmlformat.so 0x0a93f485 __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>
, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > > std::__uninitialized_copy_aux<__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>
, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > > >(__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, __gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, false_type) + 31
7 cmlformat.so 0x0a94008d std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >::M_insert_aux(__gnu_cxx::__normal_iterator<std::pair<std::string, std::string>, std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > >, std::pair<std::string, std::string> const&) + 283
8 cmlformat.so 0x0a940236 std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >::push_back(std::pair<std::string, std::string> const&) + 62
9 cmlformat.so 0x0a931bf5 OpenBabel::CMLFormat::TransferElement(std::vector<std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >, std::allocator<std::vector<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > > > >&) + 253
10 cmlformat.so 0x0a936351 OpenBabel::CMLFormat::DoElement(std::string const&) + 123
11 cdxmlformat.so 0x0a89cd6d OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat
, OpenBabel::OBBase
) + 653
12 cdxmlformat.so 0x0a89b9e7 OpenBabel::XMLMoleculeFormat::ReadMolecule(OpenBabel::OBBase_, OpenBabel::OBConversion_) + 125
13 libopenbabel.4.0.1.dylib 0x00197c51 OpenBabel::OBConversion::Read(OpenBabel::OBBase_, std::istream_) + 323
14 libavogadro.1.0.3.dylib 0x01513922 Avogadro::ReadFileThread::run() + 1850
15 QtCore 0x01259f06 QThreadPrivate::start(void*) + 198
16 libsystem_c.dylib 0x935eced9 _pthread_start + 335
17 libsystem_c.dylib 0x935f06de thread_start + 34

Thread 9 crashed with X86 Thread State (32-bit):
eax: 0xffffffff ebx: 0x0a9362e1 ecx: 0xb04a100c edx: 0x02205428
edi: 0xb04a1158 esi: 0x00030154 ebp: 0xb04a1148 esp: 0xb04a1130
ss: 0x00000023 efl: 0x00010213 eip: 0x95c96f20 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000023 gs: 0x0000000f
cr2: 0x0003015c
Logical CPU: 1

Binary Images:
0x1000 - 0x8afe3 +net.sourceforge (??? - 1.0.3) <0D4BF376-9EEB-992E-6DB6-CBBFDE8ED103> /Applications/Avogadro.app/Contents/MacOS/Avogadro
0xdb000 - 0x281fe3 +libopenbabel.4.0.1.dylib (4.0.1 - compatibility 4.0.0) /Applications/Avogadro.app/Contents/lib/libopenbabel.4.0.1.dylib
0x36f000 - 0x428ff7 +QtOpenGL (4.7.1 - compatibility 4.7.0) /Applications/Avogadro.app/Contents/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL
0x46c000 - 0xda4ff7 +QtGui (4.7.1 - compatibility 4.7.0) <81382E59-1147-5F65-7E54-BE36824D49A6> /Applications/Avogadro.app/Contents/Frameworks/QtGui.framework/Versions/4/QtGui
0x1098000 - 0x1185fe7 +QtNetwork (4.7.1 - compatibility 4.7.0) <968AEE79-F97E-C572-1839-E743383181D1> /Applications/Avogadro.app/Contents/Frameworks/QtNetwork.framework/Versions/4/QtNetwork
0x11eb000 - 0x141dfef +QtCore (4.7.1 - compatibility 4.7.0) <64323E9F-8EB6-6D90-7755-84629467EF22> /Applications/Avogadro.app/Contents/Frameworks/QtCore.framework/Versions/4/QtCore
0x14c4000 - 0x1575fff +libavogadro.1.0.3.dylib (1.0.3 - compatibility 1.0.0) /Applications/Avogadro.app/Contents/lib/libavogadro.1.0.3.dylib
0x277f000 - 0x2791fff libTraditionalChineseConverter.dylib (54.0.0 - compatibility 1.0.0) /System/Library/CoreServices/Encodings/libTraditionalChineseConverter.dylib
0x2795000 - 0x27a3ffb libSimplifiedChineseConverter.dylib (54.0.0 - compatibility 1.0.0) /System/Library/CoreServices/Encodings/libSimplifiedChineseConverter.dylib
0x27e9000 - 0x27efff7 +libqgif.dylib (??? - ???) <4EBDE44C-F8E9-D3EC-2E2C-D0824442E003> /Applications/Avogadro.app/Contents/plugins/imageformats/libqgif.dylib
0x3f29000 - 0x3f2fff7 +libqico.dylib (??? - ???) <072A1FE3-2266-E4A6-1202-D4E3688FA617> /Applications/Avogadro.app/Contents/plugins/imageformats/libqico.dylib
0x3f35000 - 0x3f6cff7 +libqjpeg.dylib (??? - ???) /Applications/Avogadro.app/Contents/plugins/imageformats/libqjpeg.dylib
0x3f75000 - 0x3fc1fff +libqmng.dylib (??? - ???) <8B1E6417-857A-E986-30C4-A8C72EF9EF71> /Applications/Avogadro.app/Contents/plugins/imageformats/libqmng.dylib
0x3fd1000 - 0x3fd6ffb +atomindexcolor.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/colors/atomindexcolor.so
0x3fdb000 - 0x3fe0fe7 +chargecolor.so (??? - ???) <9CA661B5-C84F-D5FB-456E-94A4C57CA618> /Applications/Avogadro.app/Contents/lib/avogadro/colors/chargecolor.so
0x3fe5000 - 0x3feafff +customcolor.so (??? - ???) <3F227585-D52A-61DD-6C7E-8A619826ED05> /Applications/Avogadro.app/Contents/lib/avogadro/colors/customcolor.so
0x3ff0000 - 0x3ff5fef +distancecolor.so (??? - ???) <286FFCC9-50F2-DB2D-6900-9816502E9D05> /Applications/Avogadro.app/Contents/lib/avogadro/colors/distancecolor.so
0x7a5c000 - 0x7a63fe3 +residuecolor.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/colors/residuecolor.so
0x7a6a000 - 0x7a6fff3 +axesengine.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/engines/axesengine.so
0x7a75000 - 0x7a8efff +cartoonengine.so (??? - ???) <4809E534-58AF-12CB-90CF-38411053E350> /Applications/Avogadro.app/Contents/lib/avogadro/engines/cartoonengine.so
0x7edb000 - 0x7ee3fff +dipoleengine.so (??? - ???) <3C1959C3-8BDE-2E9C-71F6-0C7C542B8DE3> /Applications/Avogadro.app/Contents/lib/avogadro/engines/dipoleengine.so
0x7eeb000 - 0x7ef2feb +forceengine.so (??? - ???) <2D3383D9-D29C-51FC-F155-711BD36686F6> /Applications/Avogadro.app/Contents/lib/avogadro/engines/forceengine.so
0x98d6000 - 0x98defe7 +hbondengine.so (??? - ???) <64B4E523-E108-28E6-BD74-2949DC8A03D6> /Applications/Avogadro.app/Contents/lib/avogadro/engines/hbondengine.so
0x98e7000 - 0x98f2ff3 +labelengine.so (??? - ???) <34EB4BA8-B2F4-52BA-200F-D853EF08F08D> /Applications/Avogadro.app/Contents/lib/avogadro/engines/labelengine.so
0xa023000 - 0xa072feb +libqtiff.dylib (??? - ???) <7DF69C26-0AC9-0E07-3D65-FF18C94D1A9C> /Applications/Avogadro.app/Contents/plugins/imageformats/libqtiff.dylib
0xa280000 - 0xa285fe3 +overlayengine.so (??? - ???) <400B7A24-3E4F-2D57-CD0C-EFA9DB0AE261> /Applications/Avogadro.app/Contents/lib/avogadro/engines/overlayengine.so
0xa28b000 - 0xa291ff7 +polygonengine.so (??? - ???) <289FF614-2565-E01C-3178-D9F133BDFBAE> /Applications/Avogadro.app/Contents/lib/avogadro/engines/polygonengine.so
0xa297000 - 0xa2a0ff3 +ribbonengine.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/engines/ribbonengine.so
0xa2a9000 - 0xa2b2ffb +ringengine.so (??? - ???) <72290679-8E47-61C4-336C-C2AFA85619A3> /Applications/Avogadro.app/Contents/lib/avogadro/engines/ringengine.so
0xa2bc000 - 0xa2c2ff3 +simplewireengine.so (??? - ???) <537A4118-0A3E-1E62-2C27-C09357FA67BC> /Applications/Avogadro.app/Contents/lib/avogadro/engines/simplewireengine.so
0xa2c9000 - 0xa2d0feb +sphereengine.so (??? - ???) <1EBF0C1B-9ADE-F60A-10B3-1500A7A8FB9A> /Applications/Avogadro.app/Contents/lib/avogadro/engines/sphereengine.so
0xa2d8000 - 0xa2e0feb +stickengine.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/engines/stickengine.so
0xa2e9000 - 0xa2f5ffb +surfaceengine.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/engines/surfaceengine.so
0xa2ff000 - 0xa30afef +wireengine.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/engines/wireengine.so
0xa317000 - 0xa32ffff +animationextension.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/extensions/animationextension.so
0xa347000 - 0xa34ffe7 +fileimportextension.so (??? - ???) <8055D968-7E86-A289-9F9E-0D2134118209> /Applications/Avogadro.app/Contents/lib/avogadro/extensions/fileimportextension.so
0xa357000 - 0xa36eff7 +forcefieldextension.so (??? - ???) <29312744-A77A-035A-5FDA-81AD08CACEAE> /Applications/Avogadro.app/Contents/lib/avogadro/extensions/forcefieldextension.so
0xa383000 - 0xa3c9ff7 +gamessextension.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/extensions/gamessextension.so
0xa3e7000 - 0xa3edff7 +h2methylextension.so (??? - ???) <053DE56E-DE58-7190-ECA5-0A7DEF5B8A17> /Applications/Avogadro.app/Contents/lib/avogadro/extensions/h2methylextension.so
0xa3f3000 - 0xa3f9ff3 +hydrogenextension.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/extensions/hydrogenextension.so
0xa3ff000 - 0xa42cfe3 +inputfileextension.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/extensions/inputfileextension.so
0xa441000 - 0xa44bfff +insertfragmentextension.so (??? - ???) /Applications/Avogadro.app/Contents/lib/avogadro/extensions/insertfragmentextension.so
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0x980b7000 - 0x980baffd libCoreVMClient.dylib (??? - ???) <2D135537-F9A6-33B1-9B01-6ECE7E929C00> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x980bb000 - 0x980d7ff5 com.apple.GenerationalStorage (1.0 - 125) /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage
0x9829e000 - 0x982bbff3 com.apple.openscripting (1.3.3 - ???) <31A51238-0CA1-38C7-9F0E-8A6676EE3241> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x983d4000 - 0x98425ff9 com.apple.ScalableUserInterface (1.0 - 1) /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserInterface
0x98426000 - 0x98448ff1 com.apple.PerformanceAnalysis (1.10 - 10) <45B10D4C-9B3B-37A6-982D-687A6F9EEA28> /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
0x9847f000 - 0x9853ffff com.apple.CoreServices.OSServices (478.29 - 478.29) /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
0x98572000 - 0x986c4fff com.apple.audio.toolbox.AudioToolbox (1.7.1 - 1.7.1) <7646E131-08EE-3D72-ADA2-4A61C562B36E> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x986c5000 - 0x987d4ffb com.apple.DesktopServices (1.6.1 - 1.6.1) <9F02752A-617B-3AC7-BCA1-F040C105EDDE> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
0x98e51000 - 0x98eb8fff libc++.1.dylib (19.0.0 - compatibility 1.0.0) <3AFF3CE8-14AE-300F-8F63-8B7FB9D4DA96> /usr/lib/libc++.1.dylib
0x98eb9000 - 0x98ec1ff3 libunwind.dylib (30.0.0 - compatibility 1.0.0) /usr/lib/system/libunwind.dylib
0x98f04000 - 0x98f04fff com.apple.Carbon (153 - 153) <6FF98F0F-2CDE-3888-A304-4ED447D24CE3> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
0x98f05000 - 0x98f09fff com.apple.CommonPanels (1.2.5 - 94) <3A988595-DE53-34ED-9367-C9A737E2AF38> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x98f0a000 - 0x99998ffe com.apple.AppKit (6.7.2 - 1138.23) /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x99f52000 - 0x9a00fff3 ColorSyncDeprecated.dylib (4.6.0 - compatibility 1.0.0) /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ColorSync.framework/Versions/A/Resources/ColorSyncDeprecated.dylib
0x9a010000 - 0x9a014ff7 com.apple.OpenDirectory (10.7 - 146) <3D3D30CE-6D82-3681-AA98-4E3AEFFA4229> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
0x9a062000 - 0x9a70beeb com.apple.CoreGraphics (1.600.0 - ???) <322FC806-0B9F-3A58-8C88-D477E32A50F8> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x9a70c000 - 0x9aa0efff com.apple.CoreServices.CarbonCore (960.18 - 960.18) <8094724D-591D-3CC2-81DE-4E3029624E11> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x9aa0f000 - 0x9aa0fff0 com.apple.ApplicationServices (41 - 41) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x9aa10000 - 0x9aa68fff com.apple.HIServices (1.10 - ???) <76B50B43-6CFD-3067-A085-11420FD4FAA6> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x9aa69000 - 0x9aa77fff libdispatch.dylib (187.7.0 - compatibility 1.0.0) /usr/lib/system/libdispatch.dylib
0x9aa88000 - 0x9aa93ffb com.apple.speech.recognition.framework (4.0.19 - 4.0.19) <17C11291-5B27-3BE2-8614-7A806745EE8A> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
0x9aa94000 - 0x9aa9fffc com.apple.NetAuth (1.0 - 3.0) /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
0x9ae21000 - 0x9ae57ff7 com.apple.AE (527.7 - 527.7) <7BAFBF18-3997-3656-9823-FD3B455056A4> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x9b309000 - 0x9b314ff3 libCSync.A.dylib (600.0.0 - compatibility 64.0.0) <11726E50-E6FC-3AB0-8750-DDDCCF2B8534> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
0x9b319000 - 0x9b37affb com.apple.audio.CoreAudio (4.0.1 - 4.0.1) <089D78E0-46A6-38DB-9545-7F35CC815939> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x9b37b000 - 0x9b3a9ff7 com.apple.DictionaryServices (1.2.1 - 158.2) /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
0x9b3aa000 - 0x9b4d6ff9 com.apple.CFNetwork (520.2.5 - 520.2.5) <02193949-50A8-3CBC-9920-5FCDB8EBE17A> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
0x9b4d7000 - 0x9b564ff7 com.apple.CoreText (220.11.0 - ???) <4F98D709-75AC-35F0-AD88-8F2C4BD744C0> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText
0x9b565000 - 0x9b9daff7 FaceCoreLight (1.4.7 - compatibility 1.0.0) <312D0F58-B8E7-3F61-8A83-30C95F2EBEAA> /System/Library/PrivateFrameworks/FaceCoreLight.framework/Versions/A/FaceCoreLight
0x9b9e6000 - 0x9ba22ffd libGLImage.dylib (??? - ???) <8251242B-E04E-3467-BD0F-834578B18AC0> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x9bc45000 - 0x9bc4dff5 libcopyfile.dylib (85.1.0 - compatibility 1.0.0) /usr/lib/system/libcopyfile.dylib
0x9bc4e000 - 0x9bc4fff7 libsystem_sandbox.dylib (??? - ???) /usr/lib/system/libsystem_sandbox.dylib
0x9bc8d000 - 0x9bcb6ffe com.apple.opencl (1.50.63 - 1.50.63) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x9bf23000 - 0x9bf4bff7 libxslt.1.dylib (3.24.0 - compatibility 3.0.0) /usr/lib/libxslt.1.dylib
0x9bf98000 - 0x9c007fff com.apple.Heimdal (2.1 - 2.0) /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
0x9c008000 - 0x9c06cfff com.apple.framework.IOKit (2.0 - ???) /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x9c06d000 - 0x9c06dfff libdnsinfo.dylib (395.6.0 - compatibility 1.0.0) <959E5139-EB23-3529-8881-2BCB5724D1A9> /usr/lib/system/libdnsinfo.dylib
0x9c429000 - 0x9c4b0fff com.apple.print.framework.PrintCore (7.1 - 366.1) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0x9c51e000 - 0x9c521ffb com.apple.help (1.3.2 - 42) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x9c522000 - 0x9c556ff3 libTrueTypeScaler.dylib (??? - ???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib
0x9c60d000 - 0x9c611ffd IOSurface (??? - ???) <97E875C2-9F1A-3FBA-B80C-594892A02621> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
0x9c612000 - 0x9c628ffe libxpc.dylib (77.17.0 - compatibility 1.0.0) /usr/lib/system/libxpc.dylib
0x9c63b000 - 0x9c63ffff libGIF.dylib (??? - ???) <06E85451-F51C-31C4-B5A6-180819BD9738> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x9c67f000 - 0x9c6cfff4 libTIFF.dylib (??? - ???) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
0x9c6d0000 - 0x9c720fff libFontRegistry.dylib (??? - ???) <81E03B82-1F31-3702-97DC-BE20298E326F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
0x9c721000 - 0x9c73efff libresolv.9.dylib (46.0.0 - compatibility 1.0.0) <95AE43ED-6C52-3B39-89B6-54C81C62F1FF> /usr/lib/libresolv.9.dylib
0x9c820000 - 0x9c8b7ff3 com.apple.securityfoundation (5.0 - 55005) /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
0x9cb1c000 - 0x9cb5afff libRIP.A.dylib (600.0.0 - compatibility 64.0.0) <0AE59D4F-FFA7-3539-8B86-AD8993894AA0> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
0xba900000 - 0xba91bffd libJapaneseConverter.dylib (54.0.0 - compatibility 1.0.0) <5635DF40-8D8E-3B8C-B075-7B3FC0F184A4> /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib
0xbab00000 - 0xbab21ff6 libKoreanConverter.dylib (54.0.0 - compatibility 1.0.0) <17226124-8E8A-34EB-A2C4-D4A0469CF45B> /System/Library/CoreServices/Encodings/libKoreanConverter.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 71
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: 50624
thread_create: 1
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=169.6M resident=113.9M(67%) swapped_out_or_unallocated=55.7M(33%)
Writable regions: Total=388.5M written=16.8M(4%) resident=57.3M(15%) swapped_out=0K(0%) unallocated=331.2M(85%)

REGION TYPE VIRTUAL
=========== =======
ATS (font support) 33.0M
CG backing stores 16.0M
CG raster data 64K
CG shared images 3576K
CoreGraphics 8K
CoreServices 3356K
IOKit 4328K
MALLOC 301.5M
MALLOC guard page 48K
Memory tag=240 4K
Memory tag=242 12K
Stack 68.6M
VM_ALLOCATE 16.4M
__CI_BITMAP 80K
__DATA 9.9M
__DATA/__OBJC 64K
__IMAGE 1256K
__IMPORT 736K
__LINKEDIT 52.0M
__OBJC 1484K
__PAGEZERO 4K
__TEXT 117.6M
__UNICODE 544K
mapped file 162.0M
shared memory 2004K
shared pmap 10.2M
=========== =======
TOTAL 804.4M

Model: MacBookPro8,1, BootROM MBP81.0047.B24, 2 processors, Intel Core i5, 2.3 GHz, 8 GB, SMC 1.68f98
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 512 MB
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333531533642465238432D48392020
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333531533642465238432D48392020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD6), Broadcom BCM43xx 1.0 (5.100.98.75.18)
Bluetooth: Version 4.0.1f4, 2 service, 18 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: Hitachi HTS545032B9A302, 320.07 GB
Serial ATA Device: MATSHITADVD-R UJ-8A8
USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8509, 0xfa200000 / 3
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2
USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0252, 0xfa120000 / 5
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 4
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821a, 0xfa113000 / 8
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2
USB Device: My Passport 0740, 0x1058 (Western Digital Technologies, Inc.), 0x0740, 0xfd120000 / 4

USB Device: IR Receiver, apple_vendor_id, 0x8242, 0xfd110000 / 3

Reported by: *anonymous

@cryos
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cryos commented Jun 15, 2012

I've tried mightily to reproduce this, but can't. I'm marking this "pending" any further comment, but as far as I can tell, from Apple's side an app that continually crashed on startup will be asked to reset the preferences and not open old windows (at least in 10.7.4 or so.)

Original comment by: @ghutchis

@cryos
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cryos commented Aug 2, 2012

I'm currently experiencing the same problem with Avogadro 1.0.3 on 10.7.4. Avogadro was working fine and then suddenly started crashing on startup. I ran it under gdb and got the following:

dh127098:~ abbiet$ gdb /Applications/Avogadro.app/Contents/MacOS/Avogadro
GNU gdb 6.3.50-20050815 (Apple version gdb-1752) (Sat Jan 28 03:02:46 UTC 2012)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "x86_64-apple-darwin"...Reading symbols for shared libraries .....
warning: Could not find object file "/Developer/SDKs/MacOSX10.4u.sdk/usr/lib/gcc/i686-apple-darwin10/4.0.1/libgcc.a(_eprintf.o)" - no debug information available for "/var/tmp/gcc_40/gcc_40-5493~93/src/gcc/libgcc2.c".

....... done

(gdb) run
Starting program: /Applications/Avogadro.app/Contents/MacOS/Avogadro
Reading symbols for shared libraries +++++++++++........................................................................................................................................... done
Reading symbols for shared libraries . done

"Avogadro version: 1.0.3 Git: 81fcdfb
LibAvogadro version: 1.0.3 Git: 81fcdfb"
BABEL_LIBDIR /Applications/Avogadro.app/Contents/MacOS/../lib/openbabel
Locale: "en_US"
Libavogadro translations not found.
"System has OpenGL support."
"About to test OpenGL capabilities."
"OpenGL capabilities found: "
"Double Buffering."
"Direct Rendering."
"Antialiasing."
Reading symbols for shared libraries . done
Reading symbols for shared libraries warning: Could not find object file "/Developer/SDKs/MacOSX10.4u.sdk/usr/lib/gcc/i686-apple-darwin10/4.0.1/libgcc.a(_eprintf.o)" - no debug information available for "/var/tmp/gcc_40/gcc_40-5493~93/src/gcc/libgcc2.c".

. done
Loading plugins: "/Applications/Avogadro.app/Contents/MacOS/../lib/avogadro"
Searching for plugins in "/Applications/Avogadro.app/Contents/lib/avogadro/colors"
Reading symbols for shared libraries . done
Searching for plugins in "/Applications/Avogadro.app/Contents/lib/avogadro/engines"
Searching for plugins in "/Applications/Avogadro.app/Contents/lib/avogadro/extensions"
Reading symbols for shared libraries . done
Searching for plugins in "/Applications/Avogadro.app/Contents/lib/avogadro/tools"
Searching for plugins in ""
Loading plugins: "/Users/abbiet/Library/Application Support/avogadro/Plugins"
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Reading symbols for shared libraries .. done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
---Type to continue, or q to quit---
---Type to continue, or q to quit---
QStackedLayout::setCurrentWidget: Widget 0x1794af0 not contained in stack
Reading symbols for shared libraries .. done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
GLWidget initialisation...
GLWidget initialised...
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

createObjects()

*** Open Babel Warning in Translate
Cannot perform atom type translation: table cannot find requested types.

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x00000000
[Switching to process 11353 thread 0x7c03]
0x00118adb in std::_Bit_reference::operator= ()
(gdb) bt
#0 0x00118adb in std::_Bit_reference::operator= ()
#1 0x00119e01 in std::__copy<false, std::random_access_iterator_tag>::copy<std::_Bit_iterator, std::_Bit_iterator> ()
#2 0x00119e78 in std::copy<std::_Bit_iterator, std::_Bit_iterator> ()
#3 0x0011c14f in std::vector<bool, std::allocator >::_M_fill_insert ()
#4 0x0011c238 in std::vector<bool, std::allocator >::resize ()
#5 0x001d54ac in OpenBabel::OBAromaticTyper::AssignAromaticFlags ()
#6 0x000f8ae2 in OpenBabel::OBBond::IsAromatic ()
#7 0x001a8379 in OpenBabel::OBSmartsMatcher::EvalBondExpr ()
#8 0x001a8443 in OpenBabel::OBSmartsMatcher::EvalBondExpr ()
#9 0x001a9c94 in OpenBabel::OBSSMatch::Match ()
#10 0x001a9b0e in OpenBabel::OBSSMatch::Match ()
#11 0x001aa35a in OpenBabel::OBSmartsMatcher::match ()
#12 0x001ab34d in OpenBabel::OBSmartsPattern::Match ()
#13 0x000fa9be in OpenBabel::OBBondTyper::AssignFunctionalGroupBonds ()
#14 0x0018840b in OpenBabel::OBMol::PerceiveBondOrders ()
#15 0x1c2d20d5 in OpenBabel::PDBFormat::ReadMolecule ()
#16 0x00195bd9 in OpenBabel::OBConversion::Read ()
#17 0x0150d922 in Avogadro::ReadFileThread::run ()
#18 0x01253f06 in QThreadPrivate::start ()
#19 0x9860bed9 in _pthread_start ()
#20 0x9860f6de in thread_start ()
(gdb)

I tried removing the net.sourceforge.Avogadro.plist file, as I thought the problem might be due to Avogadro trying to open a dodgy file on startup, but this made no difference.

I've kept the original plist file and have the OSX system application report of the crash if they would be useful. I've kept things as they are in case it helps to isolate what the problem is.

Original comment by: jensthomas

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