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Re: Consolidating my Bibliography Chaos

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Re: Consolidating my Bibliography Chaos

Stephan Kurz
Dear all,

thanks to your support and input on how to proceed, I am done with  
merging at least the stuff that I need for my dissertation. I now have  
a master.bib file with 841 publications, more to be merged in later.

Am 09.07.2008 um 17:25 schrieb Stephan Kurz:

> Dear Christiaan and Adam,
>
> thanks for your responses!

>>> - Autofile issues:
>>> Some of my bibs have papers filed (via Autofile, and some are also
>>> still
>>> stored somewhere on the file system of my PowerBook with links in  
>>> the
>>> deprecated local-url field, but that is the minority of the files).
>>> Unfortunately, to different fixed locations on different computers.
>>> What
>>> is the best way to bring these together?
>>
>> I think the easiest way is to fix the .bib files at the local level
>> before merging and then moving the file together with the PDFs to  
>> your
>> joined location.
>
> <snip>

Done that, worked well.

>>> My ideal scenario would be to have a central repository on my
>>> university
>>> server that would sync with my workstations to provide offline
>>> access as
>>> well. That won’t work, so probably I’ll stick to mounting the
>>> university
>>> server (which is no problem from my work computer, but I need a VPN
>>> connection from home).
>>> What will happen if I change the "fixed location" to, say,
>>> "/Volumes/myserver/Papers/" -- can I, say, batch replace the  
>>> location?
>>
>> There is a problem with moving papers to a different volume. BibDesk
>> can automatically follow linked files that are moved outside of
>> BibDesk. But when you "move" them to a different volume the files are
>> actually copied rather than moved, so BibDesk will not be able to  
>> find
>> the files in the new location. On the other hand if you use BibDesk
>> (in particular the manual auto-file feature) to move the files to the
>> new location, this should work. Just set the papers folder in the
>> prefs to "/Volumes/myserver/Papers/" and choose an appropriate
>> filename format, select the items or files you want to move there,  
>> and
>> choose an Auto-File menu item.

> Fine. I will try this. One small follow-up question to be sure:
> What’s going to happen if /Volumes/myserver/ is not mounted?
> Are the links still preserved if I re-save the file after some  
> changes?

<snip>

That worked as well. Unfortunately, it's not very responsive from home  
(not very fast internet connection, and need to use VPN to access  
university server), but it works, and I can access my papers from  
anywhere this way.
All links were preserved in the scenario I thought of before (keeping  
master.bib in an SVN repository on multiple machines, all using BD  
1.3.18) in one direction.

Now I got a serious error that crashes BD every time I try to open the  
version of master.bib that just worked well yesterday night (error log  
below). The one that I prepared on my work computer is still working  
there, but the one to which I added some pubs and linked files that  
were still lurking around on my PowerBook seems to be broken.

Can anyone read the output below? Or may I send my bib file to  
somebody off-list to have a look at it?

Thanks,
Stephan


Process:         BibDesk [5032]
Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
Identifier:      edu.ucsd.cs.mmccrack.bibdesk
Version:         1.3.18 (1202)
Code Type:       X86 (Native)
Parent Process:  launchd [235]

Date/Time:       2008-08-05 12:18:19.261 +0200
OS Version:      Mac OS X 10.5.4 (9E17)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756b2f73
Crashed Thread:  0

Thread 0 Crashed:
0   ...ple.CoreServices.CarbonCore 0x00f0ae78 CleanPath(char const*,  
char*) + 366
1   ...ple.CoreServices.CarbonCore 0x00f0a970 canonpath(char const*,  
char*, int*) + 234
2   ...ple.CoreServices.CarbonCore 0x00f01b29 PathGetObjectInfo(char  
const*, unsigned long, unsigned long, VolumeInfo**, unsigned long*,  
unsigned long*, char*, unsigned long*, unsigned char*) + 465
3   ...ple.CoreServices.CarbonCore 0x00f018ed  
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) + 97
4   ...ple.CoreServices.CarbonCore 0x00f0188a FSPathMakeRefWithOptions  
+ 46
5   edu.ucsd.cs.mmccrack.bibdesk   0x00171a72 BDSKPathToFSRef + 77
6   edu.ucsd.cs.mmccrack.bibdesk   0x001726f9 -[BDSKLinkedAliasFile  
fileRef] + 150
7   edu.ucsd.cs.mmccrack.bibdesk   0x001730a3 -[BDSKLinkedAliasFile  
updateWithPath:] + 294
8   edu.ucsd.cs.mmccrack.bibdesk   0x00171e21 -[BDSKLinkedFile update]  
+ 42
9   com.apple.CoreFoundation       0x944c1c85 -[NSArray  
makeObjectsPerformSelector:] + 565
10  edu.ucsd.cs.mmccrack.bibdesk   0x0005011e -[BibItem(Private)  
createFilesArray] + 783
11  com.apple.CoreFoundation       0x944c1e9c -[NSArray  
makeObjectsPerformSelector:withObject:] + 252
12  edu.ucsd.cs.mmccrack.bibdesk   0x0001e145 -[BibDocument  
setPublicationsWithoutUndo:] + 135
13  edu.ucsd.cs.mmccrack.bibdesk   0x00023853 -[BibDocument  
readFromBibTeXData:fromURL:encoding:error:] + 564
14  edu.ucsd.cs.mmccrack.bibdesk   0x00023391 -[BibDocument  
readFromURL:ofType:encoding:error:] + 2425
15  edu.ucsd.cs.mmccrack.bibdesk   0x00022a12 -[BibDocument  
readFromURL:ofType:error:] + 83
16  com.apple.AppKit               0x96206dea -[NSDocument  
initWithContentsOfURL:ofType:error:] + 311
17  com.apple.AppKit               0x961d69c0 -[NSDocumentController  
makeDocumentWithContentsOfURL:ofType:error:] + 391
18  com.apple.AppKit               0x961d5fe4 -[NSDocumentController  
openDocumentWithContentsOfURL:display:error:] + 420
19  com.omnigroup.OmniAppKit       0x003efc2e -
[NSDocumentController(OAExtensions)  
_replacement_openDocumentWithContentsOfURL:display:error:] + 62
20  edu.ucsd.cs.mmccrack.bibdesk   0x001042f7 -[BDSKDocumentController  
openDocumentWithContentsOfURL:display:error:] + 1213
21  com.apple.AppKit               0x96339523 -
[NSDocumentController(NSInternal) _openFile:] + 143
22  com.apple.AppKit               0x9624a88e -[NSApplication  
_doOpenFile:ok:tryTemp:] + 637
23  com.apple.AppKit               0x961d5e33 -[NSApplication  
_doOpenFiles:] + 242
24  com.apple.AppKit               0x961d5d21 -
[NSApplication(NSAppleEventHandling) _handleAEOpenDocuments:] + 88
25  com.apple.AppKit               0x95ef7eef -
[NSApplication(NSAppleEventHandling) _handleCoreEvent:withReplyEvent:]  
+ 297
26  com.apple.Foundation           0x93cecb6f -[NSAppleEventManager  
dispatchRawAppleEvent:withRawReply:handlerRefCon:] + 655
27  com.apple.Foundation           0x93cec87f  
_NSAppleEventManagerGenericHandler + 223
28  com.apple.AE                   0x900e6648  
aeDispatchAppleEvent(AEDesc const*, AEDesc*, unsigned long, unsigned  
char*) + 144
29  com.apple.AE                   0x900e657e  
dispatchEventAndSendReply(AEDesc const*, AEDesc*) + 44
30  com.apple.AE                   0x900e6425 aeProcessAppleEvent + 177
31  com.apple.HIToolbox           0x940e447d AEProcessAppleEvent + 38
32  com.apple.AppKit               0x95ef5719 _DPSNextEvent + 1189
33  com.apple.AppKit               0x95ef4db8 -[NSApplication  
nextEventMatchingMask:untilDate:inMode:dequeue:] + 128
34  com.apple.AppKit               0x95eeddf3 -[NSApplication run] + 795
35  com.omnigroup.OmniAppKit       0x003c5884 -[OAApplication run] + 580
36  com.apple.AppKit               0x95ebb030 NSApplicationMain + 574
37  edu.ucsd.cs.mmccrack.bibdesk   0x00002bca main + 576
38  edu.ucsd.cs.mmccrack.bibdesk   0x00002970 _start + 210
39  edu.ucsd.cs.mmccrack.bibdesk   0x0000289d start + 41

Thread 1:
0   libSystem.B.dylib             0x93841506  
semaphore_timedwait_signal_trap + 10
1   libSystem.B.dylib             0x9387384f _pthread_cond_wait + 1244
2   libSystem.B.dylib             0x938750d3  
pthread_cond_timedwait_relative_np + 47
3   com.apple.Foundation           0x93d0de8c -[NSCondition  
waitUntilDate:] + 236
4   com.apple.Foundation           0x93d0dca0 -[NSConditionLock  
lockWhenCondition:beforeDate:] + 144
5   ...up.framework.OmniFoundation 0x0051babb -
[NSConditionLock(OFFixes) replacement_lockWhenCondition:beforeDate:] +  
59
6   ...up.framework.OmniFoundation 0x00504139 -
[OFDedicatedThreadScheduler(Private)  
runScheduleInCurrentThreadUntilEmpty:] + 281
7   ...up.framework.OmniFoundation 0x00503c9d -
[OFDedicatedThreadScheduler runScheduleForeverInCurrentThread] + 205
8   com.apple.Foundation           0x93cc7f1d -[NSThread main] + 45
9   com.apple.Foundation           0x93cc7ac4 __NSThread__main__ + 308
10  libSystem.B.dylib             0x938726f5 _pthread_start + 321
11  libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 2:
0   libSystem.B.dylib             0x9384868e __semwait_signal + 10
1   libSystem.B.dylib             0x9387336d pthread_cond_wait
$UNIX2003 + 73
2   libGLProgrammability.dylib     0x94bd4432 glvmDoWork + 162
3   libSystem.B.dylib             0x938726f5 _pthread_start + 321
4   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 3:
0   libSystem.B.dylib             0x9384868e __semwait_signal + 10
1   libSystem.B.dylib             0x9387336d pthread_cond_wait
$UNIX2003 + 73
2   com.apple.QuartzCore           0x92c1ee51 fe_fragment_thread + 54
3   libSystem.B.dylib             0x938726f5 _pthread_start + 321
4   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 4:
0   libSystem.B.dylib             0x938414a6 mach_msg_trap + 10
1   libSystem.B.dylib             0x93848c9c mach_msg + 72
2   com.apple.CoreFoundation       0x944530ce CFRunLoopRunSpecific +  
1790
3   com.apple.CoreFoundation       0x94453cf8 CFRunLoopRunInMode + 88
4   com.apple.Foundation           0x93cfc4a5 -[NSRunLoop(NSRunLoop)  
runMode:beforeDate:] + 213
5   edu.ucsd.cs.mmccrack.bibdesk   0x000f5338 -
[BDSKAsynchronousDOServer runDOServerForPorts:] + 763
6   com.apple.Foundation           0x93cc7f1d -[NSThread main] + 45
7   com.apple.Foundation           0x93cc7ac4 __NSThread__main__ + 308
8   libSystem.B.dylib             0x938726f5 _pthread_start + 321
9   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 5:
0   libSystem.B.dylib             0x938414a6 mach_msg_trap + 10
1   libSystem.B.dylib             0x93848c9c mach_msg + 72
2   com.apple.CoreFoundation       0x944530ce CFRunLoopRunSpecific +  
1790
3   com.apple.CoreFoundation       0x94453cf8 CFRunLoopRunInMode + 88
4   com.apple.Foundation           0x93d2b460 +
[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] +  
320
5   com.apple.Foundation           0x93cc7f1d -[NSThread main] + 45
6   com.apple.Foundation           0x93cc7ac4 __NSThread__main__ + 308
7   libSystem.B.dylib             0x938726f5 _pthread_start + 321
8   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 6:
0   libSystem.B.dylib             0x938915e2 select$DARWIN_EXTSN + 10
1   libSystem.B.dylib             0x938726f5 _pthread_start + 321
2   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 7:
0   libSystem.B.dylib             0x938414a6 mach_msg_trap + 10
1   libSystem.B.dylib             0x93848c9c mach_msg + 72
2   com.apple.CoreFoundation       0x944530ce CFRunLoopRunSpecific +  
1790
3   com.apple.CoreFoundation       0x94453cf8 CFRunLoopRunInMode + 88
4   com.apple.CFNetwork           0x96bc1a32  
CFURLCacheWorkerThread(void*) + 396
5   libSystem.B.dylib             0x938726f5 _pthread_start + 321
6   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 8:
0   libSystem.B.dylib             0x93841506  
semaphore_timedwait_signal_trap + 10
1   libSystem.B.dylib             0x9387384f _pthread_cond_wait + 1244
2   libSystem.B.dylib             0x938750d3  
pthread_cond_timedwait_relative_np + 47
3   com.apple.Foundation           0x93d0de8c -[NSCondition  
waitUntilDate:] + 236
4   com.apple.Foundation           0x93d0dca0 -[NSConditionLock  
lockWhenCondition:beforeDate:] + 144
5   ...up.framework.OmniFoundation 0x0051babb -
[NSConditionLock(OFFixes) replacement_lockWhenCondition:beforeDate:] +  
59
6   com.apple.Foundation           0x93d0dc05 -[NSConditionLock  
lockWhenCondition:] + 69
7   ...up.framework.OmniFoundation 0x004bbb10 -[OFMessageQueue  
nextRetainedInvocationWithBlock:] + 224
8   ...up.framework.OmniFoundation 0x0050819e -[OFQueueProcessor  
processQueueUntilEmpty:forTime:] + 238
9   ...up.framework.OmniFoundation 0x004bc63a -[OFQueueProcessor  
processQueueUntilEmpty:] + 58
10  ...up.framework.OmniFoundation 0x0050861a -[OFQueueProcessor  
processQueueForever] + 42
11  ...up.framework.OmniFoundation 0x005087c5 -
[OFQueueProcessor(Private) processQueueInThread] + 165
12  com.apple.Foundation           0x93cc7f1d -[NSThread main] + 45
13  com.apple.Foundation           0x93cc7ac4 __NSThread__main__ + 308
14  libSystem.B.dylib             0x938726f5 _pthread_start + 321
15  libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 9:
0   libSystem.B.dylib             0x93871f66 kevent + 10
1   libSystem.B.dylib             0x938726f5 _pthread_start + 321
2   libSystem.B.dylib             0x938725b2 thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
   eax: 0xbfffc2e2  ebx: 0x00f0ad15  ecx: 0xbfffcb82  edx: 0x756b2f73
   edi: 0x756b2f73  esi: 0xbfffc2e3  ebp: 0xbfffc308  esp: 0xbfffc270
    ss: 0x0000001f  efl: 0x00010246  eip: 0x00f0ae78   cs: 0x00000017
    ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
   cr2: 0x756b2f73

Binary Images:
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libvDSP.dylib
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<8953865f53e940007a4e4ac5390d3c95> /System/Library/PrivateFrameworks/
DisplayServices.framework/Versions/A/DisplayServices
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(220.1) <8bf7ef71216376d12fcd5ec17e43742c> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
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<9ea4fe135c9e52bd0590eec12c738e82> /usr/lib/libbz2.1.0.dylib
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<4b8f505e32e4f2d67967a276401f9aaf> /System/Library/Frameworks/
Quartz.framework/Versions/A/Quartz
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<a2b462be6c51187eddf7d097ef0e0a04> /System/Library/PrivateFrameworks/
MonitorPanel.framework/Versions/A/MonitorPanel
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<e064f94d969ce25cb7de3cfb980c3249> /System/Library/Frameworks/
Cocoa.framework/Versions/A/Cocoa
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<adbb3a14e8f7da444e16d2fd61862771> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/Metadata.framework/
Versions/A/Metadata
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<7e41e38368974ed048c2f027a961dbd4> /System/Library/Frameworks/
WebKit.framework/Versions/A/WebKit
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<064eb6d96417afa38a80b1735c4113aa> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/
Versions/A/ATS
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Library/Frameworks/vecLib.framework/Versions/A/vecLib
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<fe87a9dede38db00e6c8949942c6bd4f> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/HTMLRendering.framework/
Versions/A/HTMLRendering
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system/libmathCommon.A.dylib
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Frameworks/Quartz.framework/Versions/A/Frameworks/PDFKit.framework/
Versions/A/PDFKit
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(3.5.4) <fe27e80e1a9e86403fd9ed16dcfe4e11> /System/Library/Frameworks/
DirectoryService.framework/Versions/A/DirectoryService
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<5031226ea28b371d8dfdbb32acfb48b5> /usr/lib/libicucore.A.dylib
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<4933ddc7f6618743197aadc85b33b5ab> /usr/lib/libxslt.1.dylib
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(861) /System/Library/QuickTime/QuickTimeImporters.component/Contents/
MacOS/QuickTimeImporters
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Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
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<a53206274b6c2d42691f677863f379ae> /usr/lib/libobjc.A.dylib
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<2fcc8f3bd5bbfc000b476cad8e6a3dd2> /System/Library/Frameworks/
CoreServices.framework/Versions/A/CoreServices
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<8b7831b5f74a950a56cf2d22a2d436f6> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
LangAnalysis.framework/Versions/A/LangAnalysis
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<0f2ba6e891d3761212cf5a5e6134d683> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/
A/CarbonSound
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(861) /System/Library/QuickTime/QuickTimeComponents.component/Contents/
MacOS/QuickTimeComponents
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(3.7.24) <d3180f9edbd9a5e6f283d6156aa3c602> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/
Versions/A/SpeechRecognition
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<093b1b698ca93a0380f5fa262459ea28> /System/Library/Frameworks/
OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
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Frameworks/QTKit.framework/Versions/A/QTKit
0x924bd000 - 0x92549ff7  com.apple.LaunchServices 289.2 (289.2)  
<3577886e3a6d56ee3949850c4fde76c9> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/
Versions/A/LaunchServices
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<1a52b406a3f3d04387c822da4a93c245> /System/Library/Frameworks/
Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/
Versions/A/QuartzComposer
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<f7e78891a6d08265c83dca8e378be1ea> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
HIServices.framework/Versions/A/HIServices
0x92858000 - 0x92858ffd  com.apple.Accelerate.vecLib 3.4.2 (vecLib  
3.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/
Frameworks/vecLib.framework/Versions/A/vecLib
0x92859000 - 0x92881fff  libcups.2.dylib ??? (???)  
<ece20dff2a2c8ed3ae6ef735ef440c37> /usr/lib/libcups.2.dylib
0x92882000 - 0x92898fe7  com.apple.CoreVideo 1.5.1 (1.5.1)  
<ed7bb95fb94817ea3212090aac5c65f3> /System/Library/Frameworks/
CoreVideo.framework/Versions/A/CoreVideo
0x92899000 - 0x928f6ffb  libstdc++.6.dylib ??? (???)  
<04b812dcec670daa8b7d2852ab14be60> /usr/lib/libstdc++.6.dylib
0x928f7000 - 0x92916ffa  libJPEG.dylib ??? (???)  
<0cfb80109d624beb9ceb3c43b6c5ec10> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libJPEG.dylib
0x92985000 - 0x92a6aff3  com.apple.CoreData 100.1 (186)  
<8e28162ef2288692615b52acc01f8b54> /System/Library/Frameworks/
CoreData.framework/Versions/A/CoreData
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<7dac4a7cb0de2f6d08ae71c1249379e3> /System/Library/Frameworks/
AGL.framework/Versions/A/AGL
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<277b460da86bc222785159fe77e2e2ed> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/
Versions/A/SearchKit
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<1b65c05f89e81a499302fd63295b242d> /System/Library/Frameworks/
QuartzCore.framework/Versions/A/QuartzCore
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Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/
Versions/A/vImage
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<f53c808e87d1184c0f9df63aef53ce0b> /usr/lib/libgcc_s.1.dylib
0x92fcb000 - 0x93024ff7  libGLU.dylib ??? (???) /System/Library/
Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x9302d000 - 0x9302dffd  com.apple.Accelerate 1.4.2 (Accelerate  
1.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/
Accelerate
0x9302e000 - 0x930abfef  libvMisc.dylib ??? (???) /System/Library/
Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/
Versions/A/libvMisc.dylib
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<75b0c8d8940a8a27816961dddcac8e0f> /System/Library/Frameworks/
DiskArbitration.framework/Versions/A/DiskArbitration
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<8b26ebf26a009a098484f1ed01ec499c> /System/Library/Frameworks/
SystemConfiguration.framework/Versions/A/SystemConfiguration
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<9b6da3210b7e69e75039cbb0fd4a8482> /System/Library/Frameworks/
Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/
ImageKit
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<91844980804067b07a0b6124310d3f31> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/
Versions/A/NavigationServices
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<6978bbcca4277d6ae9f042beff643f7d> /usr/lib/libsqlite3.0.dylib
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<6d0f80e9d4d81f3f64c876aca005bd53> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libTIFF.dylib
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<4e1161b204b3b1f1047412c16483c39a> /System/Library/Frameworks/
QuickTime.framework/Versions/A/QuickTime
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<a12f397abf2285077b89bd726bff5b18> /usr/lib/libSystem.B.dylib
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<b507b08e484cb89033e9cf23062d77de> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
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(9.0) /System/Library/PrivateFrameworks/
CoreMediaIOServicesPrivate.framework/Versions/A/
CoreMediaIOServicesPrivate
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<94d1a28b351b7dff77becadab0967772> /System/Library/PrivateFrameworks/
DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
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<ad0aa0252e3323d182e17f50defe56fc> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/
DictionaryServices.framework/Versions/A/DictionaryServices
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Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/
ColorSync.framework/Versions/A/ColorSync
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System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
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<bfd4ebea1a7739dd6b523f15dca01a37> /System/Library/Frameworks/
Foundation.framework/Versions/C/Foundation
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<60cfc4b175c4ef60bb8e9036716a29f4> /System/Library/Frameworks/
IOKit.framework/Versions/A/IOKit
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<e36f5c553e5a32f64b7eb458dadadc71> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/
HIToolbox
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Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
ImageCapture.framework/Versions/A/ImageCapture
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<7ef7f5db09ff6dd0135a6165872803cc> /System/Library/Frameworks/
CoreFoundation.framework/Versions/A/CoreFoundation
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<8f910fa65f01d401ad8d04cc933cf887> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/ApplicationServices
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<672d1c7f16a4300addabeff4830f5024> /System/Library/Frameworks/
JavaScriptCore.framework/Versions/A/JavaScriptCore
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<d4234e6f5e5f530bdafb969157f1f17b> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libGIF.dylib
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<22581f8fe9dd2cb261f97a897407ec3e> /System/Library/Frameworks/
Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/
Versions/A/QuartzFilters
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CoreAudio.framework/Versions/A/CoreAudio
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<1baef3d4972ee789d8fa6c1fa44da45c> /usr/lib/libxml2.2.dylib
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<42d8422dc23a18071869fdf7b5d8fab5> /usr/lib/libauto.dylib
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ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/ImageIO
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<c72bd7bd2ce12694c3640a731d1ad878> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/QD.framework/
Versions/A/QD
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<24a448ba4f9f784189bd3183e3474d81> /System/Library/Frameworks/
AddressBook.framework/Versions/A/AddressBook
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<8eb20bcfecc950600aa62dfa07aa47f3> /System/Library/PrivateFrameworks/
CoreMediaPrivate.framework/Versions/A/CoreMediaPrivate
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<475db64244e011cd8811e076035b2632> /System/Library/Frameworks/
OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
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CoreServices.framework/Versions/A/Frameworks/OSServices.framework/
Versions/A/OSServices
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(1.5.1) /System/Library/Frameworks/AudioToolbox.framework/Versions/A/
AudioToolbox
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Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/
Versions/A/libLAPACK.dylib
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Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/
A/CommonPanels
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<c508c60fafca17824c0017b2e4369802> /usr/lib/libiconv.2.dylib
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<bf3fa8927b4b8baae92381a976fd2079> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
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<98a5e3bc0c4fa44bbb09713bb88707fe> /System/Library/Frameworks/
Carbon.framework/Versions/A/Carbon
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<0629b6dcd71f4aac6a891cbe26253e85> /usr/lib/libresolv.9.dylib
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ApplicationServices.framework/Versions/A/Frameworks/
PrintCore.framework/Versions/A/PrintCore
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<125de77ea2434a91364e79a0905a7771> /System/Library/Frameworks/
OpenGL.framework/Versions/A/OpenGL
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<5ddd8539ae2ebfd8e7cc1c57525385c7> /usr/lib/libz.1.dylib
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<c0484bec6e2432b406755591924fe664> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libPng.dylib
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Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/
Versions/A/libBLAS.dylib
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<9fde11f84a72e890bbf2aa8b0b13b79a> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/
Versions/A/CoreText
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Kerberos.framework/Versions/A/Kerberos
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<84b236f43802f4c15011513d18efa101> /System/Library/Frameworks/
AppKit.framework/Versions/C/AppKit
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<d25c63378a5029648ffd4b4669be31bf> /usr/lib/libbsm.dylib
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PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
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<20eadb285da83df96c795c2c5fa20590> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libRadiance.dylib
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<f01d6cbd6a0f24f6c13952ed448e77d6> /System/Library/Frameworks/
Security.framework/Versions/A/Security
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<ce5b085df34a78b7f198aff9db5b52ec> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/
Versions/A/CFNetwork
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<057783867138902b52bc0941fedb74d1> /System/Library/PrivateFrameworks/
Shortcut.framework/Versions/A/Shortcut
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<b9e1ca0b6612e280b6cbea6df0eec5f6> /usr/lib/libsasl2.2.dylib
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System/Library/PrivateFrameworks/InstallServer.framework/Versions/A/
InstallServer
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<2b2854123fed609d1820d2779e2e0963> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/
SecurityHI
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Library/PrivateFrameworks/Backup.framework/Versions/A/Backup
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<a3b573eb950ca583290f7b2b4c486d09> /usr/lib/libffi.dylib
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<9fcf69305c5b48dd8a5cb77107f66c7a> /System/Library/Frameworks/
WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/
WebCore
0xc5000000 - 0xc500fff6 +AGRegex ??? (0.1)  
<761bcd0fa36cea35649d8c8c19f88572> /Applications/BibDesk.app/Contents/
Frameworks/AGRegex.framework/Versions/A/AGRegex
0xfffe8000 - 0xfffebfff  libobjc.A.dylib ??? (???) /usr/lib/
libobjc.A.dylib
0xffff0000 - 0xffff1780  libSystem.B.dylib ??? (???) /usr/lib/
libSystem.B.dylib
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Re: Consolidating my Bibliography Chaos

Stephan Kurz
Stephan Kurz wrote:

<snip>

> Now I got a serious error that crashes BD every time I try to open the  
> version of master.bib that just worked well yesterday night (error log  
> below). The one that I prepared on my work computer is still working  
> there, but the one to which I added some pubs and linked files that  
> were still lurking around on my PowerBook seems to be broken.
>
> Can anyone read the output below? Or may I send my bib file to  
> somebody off-list to have a look at it?

<snip>

> Process:         BibDesk [5032]
> Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
> Identifier:      edu.ucsd.cs.mmccrack.bibdesk
> Version:         1.3.18 (1202)
> Code Type:       X86 (Native)
> Parent Process:  launchd [235]
>
> Date/Time:       2008-08-05 12:18:19.261 +0200
> OS Version:      Mac OS X 10.5.4 (9E17)
> Report Version:  6
>
> Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756b2f73
> Crashed Thread:  0

Strangely enough, BD does not choke on the same file on my G4 PowerBook.
Just got home and tried.

Any ideas?
Stephan

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Re: Consolidating my Bibliography Chaos

Christiaan Hofman
In reply to this post by Stephan Kurz
This is definitely a bug. Though I don't yet see what causes it. And  
what makes it hard is that it crashes in Apple's private code. Any  
idea what configuration triggers this? It would be helpful if you  
could reproduce it with as simple a file as possible, best with a  
single item. I guess it should be an item for which the linked file  
does not exist on the computer? Though that by itself does not give me  
any trouble. So if you can give me as many details as possible about  
what may be non-standard with this linked file?

Christiaan

On 5 Aug 2008, at 12:46 PM, Stephan Kurz wrote:

> <snip>
>
> That worked as well. Unfortunately, it's not very responsive from home
> (not very fast internet connection, and need to use VPN to access
> university server), but it works, and I can access my papers from
> anywhere this way.
> All links were preserved in the scenario I thought of before (keeping
> master.bib in an SVN repository on multiple machines, all using BD
> 1.3.18) in one direction.
>
> Now I got a serious error that crashes BD every time I try to open the
> version of master.bib that just worked well yesterday night (error log
> below). The one that I prepared on my work computer is still working
> there, but the one to which I added some pubs and linked files that
> were still lurking around on my PowerBook seems to be broken.
>
> Can anyone read the output below? Or may I send my bib file to
> somebody off-list to have a look at it?
>
> Thanks,
> Stephan
>
>
> Process:         BibDesk [5032]
> Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
> Identifier:      edu.ucsd.cs.mmccrack.bibdesk
> Version:         1.3.18 (1202)
> Code Type:       X86 (Native)
> Parent Process:  launchd [235]
>
> Date/Time:       2008-08-05 12:18:19.261 +0200
> OS Version:      Mac OS X 10.5.4 (9E17)
> Report Version:  6
>
> Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756b2f73
> Crashed Thread:  0
>
> Thread 0 Crashed:
> 0   ...ple.CoreServices.CarbonCore 0x00f0ae78 CleanPath(char const*,
> char*) + 366
> 1   ...ple.CoreServices.CarbonCore 0x00f0a970 canonpath(char const*,
> char*, int*) + 234
> 2   ...ple.CoreServices.CarbonCore 0x00f01b29 PathGetObjectInfo(char
> const*, unsigned long, unsigned long, VolumeInfo**, unsigned long*,
> unsigned long*, char*, unsigned long*, unsigned char*) + 465
> 3   ...ple.CoreServices.CarbonCore 0x00f018ed
> FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned
> long, FSRef*, unsigned char*) + 97
> 4   ...ple.CoreServices.CarbonCore 0x00f0188a FSPathMakeRefWithOptions
> + 46
> 5   edu.ucsd.cs.mmccrack.bibdesk   0x00171a72 BDSKPathToFSRef + 77
> 6   edu.ucsd.cs.mmccrack.bibdesk   0x001726f9 -[BDSKLinkedAliasFile
> fileRef] + 150
> 7   edu.ucsd.cs.mmccrack.bibdesk   0x001730a3 -[BDSKLinkedAliasFile
> updateWithPath:] + 294
> 8   edu.ucsd.cs.mmccrack.bibdesk   0x00171e21 -[BDSKLinkedFile update]
> + 42
> 9   com.apple.CoreFoundation       0x944c1c85 -[NSArray
> makeObjectsPerformSelector:] + 565
> 10  edu.ucsd.cs.mmccrack.bibdesk   0x0005011e -[BibItem(Private)
> createFilesArray] + 783

<snip rest of trace>



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Re: Consolidating my Bibliography Chaos

Christiaan Hofman


On Tue, Aug 5, 2008 at 11:19 PM, Christiaan Hofman <[hidden email]> wrote:
This is definitely a bug. Though I don't yet see what causes it. And what makes it hard is that it crashes in Apple's private code. Any idea what configuration triggers this? It would be helpful if you could reproduce it with as simple a file as possible, best with a single item. I guess it should be an item for which the linked file does not exist on the computer? Though that by itself does not give me any trouble. So if you can give me as many details as possible about what may be non-standard with this linked file?

Christiaan

And what may perhaps be more important is the .bib file. Where is it located when you open it, is it on the computer itself?

Christiaan
 


On 5 Aug 2008, at 12:46 PM, Stephan Kurz wrote:

<snip>

That worked as well. Unfortunately, it's not very responsive from home
(not very fast internet connection, and need to use VPN to access
university server), but it works, and I can access my papers from
anywhere this way.
All links were preserved in the scenario I thought of before (keeping
master.bib in an SVN repository on multiple machines, all using BD
1.3.18) in one direction.

Now I got a serious error that crashes BD every time I try to open the
version of master.bib that just worked well yesterday night (error log
below). The one that I prepared on my work computer is still working
there, but the one to which I added some pubs and linked files that
were still lurking around on my PowerBook seems to be broken.

Can anyone read the output below? Or may I send my bib file to
somebody off-list to have a look at it?

Thanks,
Stephan


Process:         BibDesk [5032]
Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
Identifier:      edu.ucsd.cs.mmccrack.bibdesk
Version:         1.3.18 (1202)
Code Type:       X86 (Native)
Parent Process:  launchd [235]

Date/Time:       2008-08-05 12:18:19.261 +0200
OS Version:      Mac OS X 10.5.4 (9E17)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756b2f73
Crashed Thread:  0

Thread 0 Crashed:
0   ...ple.CoreServices.CarbonCore      0x00f0ae78 CleanPath(char const*,
char*) + 366
1   ...ple.CoreServices.CarbonCore      0x00f0a970 canonpath(char const*,
char*, int*) + 234
2   ...ple.CoreServices.CarbonCore      0x00f01b29 PathGetObjectInfo(char
const*, unsigned long, unsigned long, VolumeInfo**, unsigned long*,
unsigned long*, char*, unsigned long*, unsigned char*) + 465
3   ...ple.CoreServices.CarbonCore      0x00f018ed
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned
long, FSRef*, unsigned char*) + 97
4   ...ple.CoreServices.CarbonCore      0x00f0188a FSPathMakeRefWithOptions
+ 46
5   edu.ucsd.cs.mmccrack.bibdesk        0x00171a72 BDSKPathToFSRef + 77
6   edu.ucsd.cs.mmccrack.bibdesk        0x001726f9 -[BDSKLinkedAliasFile
fileRef] + 150
7   edu.ucsd.cs.mmccrack.bibdesk        0x001730a3 -[BDSKLinkedAliasFile
updateWithPath:] + 294
8   edu.ucsd.cs.mmccrack.bibdesk        0x00171e21 -[BDSKLinkedFile update]
+ 42
9   com.apple.CoreFoundation            0x944c1c85 -[NSArray
makeObjectsPerformSelector:] + 565
10  edu.ucsd.cs.mmccrack.bibdesk        0x0005011e -[BibItem(Private)
createFilesArray] + 783

<snip rest of trace>




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Re: Consolidating my Bibliography Chaos

Stephan Kurz
Dear Christiaan,

Thanks for your quick response. I have been busy doing other things,  
that's why I only answer today. I have been trying to isolate the  
items that cause BD to crash and found some items that trigger the  
behaviour.

> And what may perhaps be more important is the .bib file. Where is it  
> located when you open it, is it on the computer itself?


It is stored in a local working copy of my SVN repository.

Situation (might help to reproduce) is the following.
I am using BD 1.3.18 on my Intel iMac running OS X 10.5.4
bib-file: stored locally.
AutoFile preferences are set to /Volumes/myserver/somefolder
/Volumes/myserver/somefolder is mounted via smb://
linked files are standard PDF files

There are 3 items in the file. The first two do trigger a crash, and  
the last one doesn't. When I delete the Bdsk-File-1 fields of the  
crasher items: no crash.
That the last item does not crash BD is weird since I added the linked  
files at the same step.
Probably it has to do something with the publication type  
(@incollection)?

If /Volumes/myserver/somefolder is not mounted, no crash happens (that  
also counts for the full bib file with 841 entries), I only get a lot  
of warnings in the style of
"master.bib 71 warning possible runaway string started at line 52"

If I mount /Volumes/myserver/somefolder while BD is open with either  
the small bib or the full one, and afterwards select an item with a  
linked file, BD crashes.




I hope that this helps to narrow it down. Should I file a bug report  
on Sourceforge as well?

All the best, and thanks for your support (and for BibDesk!)
Stephan

Am 05.08.2008 um 23:21 schrieb Christiaan Hofman:

> On Tue, Aug 5, 2008 at 11:19 PM, Christiaan Hofman  
> <[hidden email]> wrote:
> This is definitely a bug. Though I don't yet see what causes it. And  
> what makes it hard is that it crashes in Apple's private code. Any  
> idea what configuration triggers this? It would be helpful if you  
> could reproduce it with as simple a file as possible, best with a  
> single item. I guess it should be an item for which the linked file  
> does not exist on the computer? Though that by itself does not give  
> me any trouble. So if you can give me as many details as possible  
> about what may be non-standard with this linked file?
>
> Christiaan

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small-crash.bib (7K) Download Attachment
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Re: Consolidating my Bibliography Chaos

Christiaan Hofman

On 7 Aug 2008, at 5:42 PM, Stephan Kurz wrote:

> Dear Christiaan,
>
> Thanks for your quick response. I have been busy doing other things,  
> that's why I only answer today. I have been trying to isolate the  
> items that cause BD to crash and found some items that trigger the  
> behaviour.
>
>> And what may perhaps be more important is the .bib file. Where is  
>> it located when you open it, is it on the computer itself?
>
>
> It is stored in a local working copy of my SVN repository.
>
> Situation (might help to reproduce) is the following.
> I am using BD 1.3.18 on my Intel iMac running OS X 10.5.4
> bib-file: stored locally.
> AutoFile preferences are set to /Volumes/myserver/somefolder
> /Volumes/myserver/somefolder is mounted via smb://
> linked files are standard PDF files
>
> There are 3 items in the file. The first two do trigger a crash, and  
> the last one doesn't. When I delete the Bdsk-File-1 fields of the  
> crasher items: no crash.
> That the last item does not crash BD is weird since I added the  
> linked files at the same step.

And all 3 are on your myserver volume?

>
> Probably it has to do something with the publication type  
> (@incollection)?

No, the type is irrelevant.

>
>
> If /Volumes/myserver/somefolder is not mounted, no crash happens  
> (that also counts for the full bib file with 841 entries), I only  
> get a lot of warnings in the style of
> "master.bib 71 warning possible runaway string started at line 52"
>

Those particular warnings are not important in this case.

> If I mount /Volumes/myserver/somefolder while BD is open with either  
> the small bib or the full one, and afterwards select an item with a  
> linked file, BD crashes.
>

It only crashes when you mount when BD is open, or also if you mount  
before launching BD?

> <small-crash.bib>
>
> I hope that this helps to narrow it down. Should I file a bug report  
> on Sourceforge as well?
>

It probably is relevant that the files are on a separate volume. And  
it's important that the .bib file is on your local volume, so that  
should discard some possibilities. However strangely enough your crash  
report seemed to point to resolving your .bib file, so that's strange.  
Do all the crash report look the same (in particular the first 10  
items in the trace)? ATM I still haven't got a clue why it crashes.

Christiaan

> All the best, and thanks for your support (and for BibDesk!)
> Stephan
>
> Am 05.08.2008 um 23:21 schrieb Christiaan Hofman:
>
>> On Tue, Aug 5, 2008 at 11:19 PM, Christiaan Hofman <[hidden email]
>> > wrote:
>> This is definitely a bug. Though I don't yet see what causes it.  
>> And what makes it hard is that it crashes in Apple's private code.  
>> Any idea what configuration triggers this? It would be helpful if  
>> you could reproduce it with as simple a file as possible, best with  
>> a single item. I guess it should be an item for which the linked  
>> file does not exist on the computer? Though that by itself does not  
>> give me any trouble. So if you can give me as many details as  
>> possible about what may be non-standard with this linked file?
>>
>> Christiaan
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
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> https://lists.sourceforge.net/lists/listinfo/bibdesk-users


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Re: Consolidating my Bibliography Chaos

Stephan Kurz
Am 07.08.2008 um 18:38 schrieb Christiaan Hofman:

>> There are 3 items in the file. The first two do trigger a crash, and
>> the last one doesn't. When I delete the Bdsk-File-1 fields of the
>> crasher items: no crash.
>> That the last item does not crash BD is weird since I added the
>> linked files at the same step.
>
> And all 3 are on your myserver volume?

Yes.

>> If I mount /Volumes/myserver/somefolder while BD is open with either
>> the small bib or the full one, and afterwards select an item with a
>> linked file, BD crashes.
>>
>
> It only crashes when you mount when BD is open, or also if you mount
> before launching BD?

In both cases, BD crashes.

>> <small-crash.bib>
>>
>> I hope that this helps to narrow it down. Should I file a bug report
>> on Sourceforge as well?
>
> It probably is relevant that the files are on a separate volume. And
> it's important that the .bib file is on your local volume, so that
> should discard some possibilities. However strangely enough your crash
> report seemed to point to resolving your .bib file, so that's strange.
> Do all the crash report look the same (in particular the first 10
> items in the trace)? ATM I still haven't got a clue why it crashes.

Oops, I did not check that. I have two different crash reports in the  
"thread 0" section. I copied both below.

Stephan

--
Process:         BibDesk [7851]
Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
Identifier:      edu.ucsd.cs.mmccrack.bibdesk
Version:         1.3.18 (1202)
Code Type:       X86 (Native)
Parent Process:  launchd [235]

Date/Time:       2008-08-07 17:36:34.883 +0200
OS Version:      Mac OS X 10.5.4 (9E17)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756c6f56
Crashed Thread:  0

Thread 0 Crashed:
0   ...ple.CoreServices.CarbonCore 0x00f0ae78 CleanPath(char const*,  
char*) + 366
1   ...ple.CoreServices.CarbonCore 0x00f0a970 canonpath(char const*,  
char*, int*) + 234
2   ...ple.CoreServices.CarbonCore 0x00f01b29 PathGetObjectInfo(char  
const*, unsigned long, unsigned long, VolumeInfo**, unsigned long*,  
unsigned long*, char*, unsigned long*, unsigned char*) + 465
3   ...ple.CoreServices.CarbonCore 0x00f018ed  
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) + 97
4   ...ple.CoreServices.CarbonCore 0x00f0188a FSPathMakeRefWithOptions  
+ 46
5   edu.ucsd.cs.mmccrack.bibdesk   0x00171a72 BDSKPathToFSRef + 77
6   edu.ucsd.cs.mmccrack.bibdesk   0x001726f9 -[BDSKLinkedAliasFile  
fileRef] + 150
7   edu.ucsd.cs.mmccrack.bibdesk   0x00172863 -[BDSKLinkedAliasFile  
URL] + 56
8   edu.ucsd.cs.mmccrack.bibdesk   0x0017291d -[BDSKLinkedAliasFile  
displayURL] + 39
9   edu.ucsd.cs.mmccrack.bibdesk   0x00028ee3  
addFileViewObjectForURLToArray + 81
10  com.apple.CoreFoundation       0x943e2cb6 CFArrayApplyFunction + 198
11  edu.ucsd.cs.mmccrack.bibdesk   0x0002b5bb  
addAllFileViewObjectsForItemToArray + 135
12  com.apple.CoreFoundation       0x943e2cb6 CFArrayApplyFunction + 198
13  edu.ucsd.cs.mmccrack.bibdesk   0x0002904c -[BibDocument  
shownFiles] + 286
14  edu.ucsd.cs.mmccrack.bibdesk   0x0002914d -[BibDocument  
numberOfURLsInFileView:] + 34
15  com.mac.amaxwell.fileview     0x006ee827 -[FileView  
numberOfIcons] + 73
16  com.mac.amaxwell.fileview     0x006f8561 -[FileView  
_recalculateGridSize] + 169
17  com.mac.amaxwell.fileview     0x006ede80 -[FileView reloadIcons]  
+ 42
18  edu.ucsd.cs.mmccrack.bibdesk   0x000290ac -[BibDocument  
updateFileViews] + 79
19  edu.ucsd.cs.mmccrack.bibdesk   0x00028200 -[BibDocument  
handleTableSelectionChangedNotification:] + 39
20  com.apple.Foundation           0x93cc754a _nsnote_callback + 106
21  com.apple.CoreFoundation       0x94434aba __CFXNotificationPost +  
362
22  com.apple.CoreFoundation       0x94434d93  
_CFXNotificationPostNotification + 179
23  com.apple.Foundation           0x93cf4a8c -[NSNotificationCenter  
postNotification:] + 124
24  com.apple.Foundation           0x93d27481 postQueueNotifications +  
705
25  com.apple.CoreFoundation       0x944519c2 __CFRunLoopDoObservers +  
466
26  com.apple.CoreFoundation       0x94453424 CFRunLoopRunSpecific +  
2644
27  com.apple.CoreFoundation       0x94453cf8 CFRunLoopRunInMode + 88
28  com.apple.HIToolbox           0x940e1da4  
RunCurrentEventLoopInMode + 283
29  com.apple.HIToolbox           0x940e1bbd ReceiveNextEventCommon +  
374
30  com.apple.HIToolbox           0x940e1a31  
BlockUntilNextEventMatchingListInMode + 106
31  com.apple.AppKit               0x95ef5505 _DPSNextEvent + 657
32  com.apple.AppKit               0x95ef4db8 -[NSApplication  
nextEventMatchingMask:untilDate:inMode:dequeue:] + 128
33  com.apple.AppKit               0x95eeddf3 -[NSApplication run] + 795
34  com.omnigroup.OmniAppKit       0x003c5884 -[OAApplication run] + 580
35  com.apple.AppKit               0x95ebb030 NSApplicationMain + 574
36  edu.ucsd.cs.mmccrack.bibdesk   0x00002bca main + 576
37  edu.ucsd.cs.mmccrack.bibdesk   0x00002970 _start + 210
38  edu.ucsd.cs.mmccrack.bibdesk   0x0000289d start + 41
--

and

--
Process:         BibDesk [5290]
Path:            /Applications/BibDesk.app/Contents/MacOS/BibDesk
Identifier:      edu.ucsd.cs.mmccrack.bibdesk
Version:         1.3.18 (1202)
Code Type:       X86 (Native)
Parent Process:  launchd [235]

Date/Time:       2008-08-07 16:45:47.972 +0200
OS Version:      Mac OS X 10.5.4 (9E17)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000756b2f73
Crashed Thread:  0

Thread 0 Crashed:
0   ...ple.CoreServices.CarbonCore 0x00f0ae78 CleanPath(char const*,  
char*) + 366
1   ...ple.CoreServices.CarbonCore 0x00f0a970 canonpath(char const*,  
char*, int*) + 234
2   ...ple.CoreServices.CarbonCore 0x00f01b29 PathGetObjectInfo(char  
const*, unsigned long, unsigned long, VolumeInfo**, unsigned long*,  
unsigned long*, char*, unsigned long*, unsigned char*) + 465
3   ...ple.CoreServices.CarbonCore 0x00f018ed  
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) + 97
4   ...ple.CoreServices.CarbonCore 0x00f0188a FSPathMakeRefWithOptions  
+ 46
5   edu.ucsd.cs.mmccrack.bibdesk   0x00171a72 BDSKPathToFSRef + 77
6   edu.ucsd.cs.mmccrack.bibdesk   0x001726f9 -[BDSKLinkedAliasFile  
fileRef] + 150
7   edu.ucsd.cs.mmccrack.bibdesk   0x001730a3 -[BDSKLinkedAliasFile  
updateWithPath:] + 294
8   edu.ucsd.cs.mmccrack.bibdesk   0x00171e21 -[BDSKLinkedFile update]  
+ 42
9   com.apple.CoreFoundation       0x944c1c85 -[NSArray  
makeObjectsPerformSelector:] + 565
10  edu.ucsd.cs.mmccrack.bibdesk   0x0005011e -[BibItem(Private)  
createFilesArray] + 783
11  com.apple.CoreFoundation       0x944c1e9c -[NSArray  
makeObjectsPerformSelector:withObject:] + 252
12  edu.ucsd.cs.mmccrack.bibdesk   0x0001e145 -[BibDocument  
setPublicationsWithoutUndo:] + 135
13  edu.ucsd.cs.mmccrack.bibdesk   0x00023853 -[BibDocument  
readFromBibTeXData:fromURL:encoding:error:] + 564
14  edu.ucsd.cs.mmccrack.bibdesk   0x00023391 -[BibDocument  
readFromURL:ofType:encoding:error:] + 2425
15  edu.ucsd.cs.mmccrack.bibdesk   0x00022a12 -[BibDocument  
readFromURL:ofType:error:] + 83
16  com.apple.AppKit               0x96206dea -[NSDocument  
initWithContentsOfURL:ofType:error:] + 311
17  com.apple.AppKit               0x961d69c0 -[NSDocumentController  
makeDocumentWithContentsOfURL:ofType:error:] + 391
18  com.apple.AppKit               0x961d5fe4 -[NSDocumentController  
openDocumentWithContentsOfURL:display:error:] + 420
19  com.omnigroup.OmniAppKit       0x003efc2e -
[NSDocumentController(OAExtensions)  
_replacement_openDocumentWithContentsOfURL:display:error:] + 62
20  edu.ucsd.cs.mmccrack.bibdesk   0x001042f7 -[BDSKDocumentController  
openDocumentWithContentsOfURL:display:error:] + 1213
21  com.apple.AppKit               0x96339523 -
[NSDocumentController(NSInternal) _openFile:] + 143
22  com.apple.AppKit               0x9624a88e -[NSApplication  
_doOpenFile:ok:tryTemp:] + 637
23  com.apple.AppKit               0x961d5e33 -[NSApplication  
_doOpenFiles:] + 242
24  com.apple.AppKit               0x961d5d21 -
[NSApplication(NSAppleEventHandling) _handleAEOpenDocuments:] + 88
25  com.apple.AppKit               0x95ef7eef -
[NSApplication(NSAppleEventHandling) _handleCoreEvent:withReplyEvent:]  
+ 297
26  com.apple.Foundation           0x93cecb6f -[NSAppleEventManager  
dispatchRawAppleEvent:withRawReply:handlerRefCon:] + 655
27  com.apple.Foundation           0x93cec87f  
_NSAppleEventManagerGenericHandler + 223
28  com.apple.AE                   0x900e6648  
aeDispatchAppleEvent(AEDesc const*, AEDesc*, unsigned long, unsigned  
char*) + 144
29  com.apple.AE                   0x900e657e  
dispatchEventAndSendReply(AEDesc const*, AEDesc*) + 44
30  com.apple.AE                   0x900e6425 aeProcessAppleEvent + 177
31  com.apple.HIToolbox           0x940e447d AEProcessAppleEvent + 38
32  com.apple.AppKit               0x95ef5719 _DPSNextEvent + 1189
33  com.apple.AppKit               0x95ef4db8 -[NSApplication  
nextEventMatchingMask:untilDate:inMode:dequeue:] + 128
34  com.apple.AppKit               0x95eeddf3 -[NSApplication run] + 795
35  com.omnigroup.OmniAppKit       0x003c5884 -[OAApplication run] + 580
36  com.apple.AppKit               0x95ebb030 NSApplicationMain + 574
37  edu.ucsd.cs.mmccrack.bibdesk   0x00002bca main + 576
38  edu.ucsd.cs.mmccrack.bibdesk   0x00002970 _start + 210
39  edu.ucsd.cs.mmccrack.bibdesk   0x0000289d start + 41
--

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Re: Consolidating my Bibliography Chaos

Maxwell, Adam R
On 08/07/08 09:50, "Stephan Kurz" <[hidden email]> wrote:

>> It probably is relevant that the files are on a separate volume. And
>> it's important that the .bib file is on your local volume, so that
>> should discard some possibilities. However strangely enough your crash
>> report seemed to point to resolving your .bib file, so that's strange.
>> Do all the crash report look the same (in particular the first 10
>> items in the trace)? ATM I still haven't got a clue why it crashes.
>
> Oops, I did not check that. I have two different crash reports in the
> "thread 0" section. I copied both below.

How long are the paths that cause a crash vs. the one that does not (as in
number of characters)?

Did you check the console log for any other error messages?

--
Adam


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Re: Consolidating my Bibliography Chaos

Stephan Kurz

Am 07.08.2008 um 18:56 schrieb Maxwell, Adam R:

> On 08/07/08 09:50, "Stephan Kurz" <[hidden email]> wrote:
>
>>> It probably is relevant that the files are on a separate volume. And
>>> it's important that the .bib file is on your local volume, so that
>>> should discard some possibilities. However strangely enough your  
>>> crash
>>> report seemed to point to resolving your .bib file, so that's  
>>> strange.
>>> Do all the crash report look the same (in particular the first 10
>>> items in the trace)? ATM I still haven't got a clue why it crashes.
>>
>> Oops, I did not check that. I have two different crash reports in the
>> "thread 0" section. I copied both below.
>
> How long are the paths that cause a crash vs. the one that does not  
> (as in
> number of characters)?

/Volumes/6chars/literatur/Bohme-Fetischismus im 19. Jahrhundert.  
Wissenschaftshistorische Analysen zur Karriere-2000a.pdf
/Volumes/6chars/literatur/Aspalter-Ironieverlust und verleugnete  
Rezeption_ Kontroversen um Romantik-2006a.pdf

the ones above do crash, but not the one below not.

/Volumes/6chars/literatur/Kubac-Notwendige Illusionen. Solidarische  
Anmerkungen zu bildungswissenschaftlicher-2005a.pdf


> Did you check the console log for any other error messages?

There are quite a lot since I tried to reproduce the behaviour for a  
while deleting different parts of my file until I came down to 3  
items, so I just copy the last ones.

Stephan

07.08.08 17:01:26 BibDesk[7625] **** Exception:
Uncaught system exception: signal 11

  **** Stack Trace:
NSExceptionHandlerUncaughtSignalHandler (in ExceptionHandling)
_sigtramp (in libSystem.B.dylib)
0xffffffff
canonpath(char const*, char*, int*) (in CarbonCore)
PathGetObjectInfo(char const*, unsigned long, unsigned long,  
VolumeInfo**, unsigned long*, unsigned long*, char*, unsigned long*,  
unsigned char*) (in CarbonCore)
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) (in CarbonCore)
FSPathMakeRefWithOptions (in CarbonCore)
BDSKPathToFSRef (in BibDesk)
-[BDSKLinkedAliasFile fileRef] (in BibDesk)
-[BDSKLinkedAliasFile updateWithPath:] (in BibDesk)
-[BDSKLinkedFile update] (in BibDesk)
-[NSArray makeObjectsPerformSelector:] (in CoreFoundation)
-[BibItem(Private) createFilesArray] (in BibDesk)
-[NSArray makeObjectsPerformSelector:withObject:] (in CoreFoundation)
-[BibDocument setPublicationsWithoutUndo:] (in BibDesk)
-[BibDocument readFromBibTeXData:fromURL:encoding:error:] (in BibDesk)
-[BibDocument readFromURL:ofType:encoding:error:] (in BibDesk)
-[BibDocument readFromURL:ofType:error:] (in BibDesk)
-[NSDocument initWithContentsOfURL:ofType:error:] (in AppKit)
-[NSDocumentController makeDocumentWithContentsOfURL:ofType:error:]  
(in AppKit)
-[NSDocumentController openDocumentWithContentsOfURL:display:error:]  
(in AppKit)
-[NSDocumentController(OAExtensions)  
_replacement_openDocumentWithContentsOfURL:display:error:] (in  
OmniAppKit)
-[BDSKDocumentController openDocumentWithContentsOfURL:display:error:]  
(in BibDesk)
-[NSDocumentController(NSInternal) _openFile:] (in AppKit)
-[NSApplication _doOpenFile:ok:tryTemp:] (in AppKit)
-[NSApplication _doOpenFiles:] (in AppKit)
-[NSApplication(NSAppleEventHandling) _handleAEOpenDocuments:] (in  
AppKit)
-[NSApplication(NSAppleEventHandling)  
_handleCoreEvent:withReplyEvent:] (in AppKit)
-[NSAppleEventManager  
dispatchRawAppleEvent:withRawReply:handlerRefCon:] (in Foundation)
_NSAppleEventManagerGenericHandler (in Foundation)
aeDispatchAppleEvent(AEDesc const*, AEDesc*, unsigned long, unsigned  
char*) (in AE)
dispatchEventAndSendR
  ****
07.08.08 17:01:29 com.apple.launchd[235]  
([0x0-0x184184].edu.ucsd.cs.mmccrack.bibdesk[7625]) Exited abnormally:  
Segmentation fault
07.08.08 17:11:19 BibDesk[7666] **** Exception:
Uncaught system exception: signal 11

  **** Stack Trace:
NSExceptionHandlerUncaughtSignalHandler (in ExceptionHandling)
_sigtramp (in libSystem.B.dylib)
0xffffffff
canonpath(char const*, char*, int*) (in CarbonCore)
PathGetObjectInfo(char const*, unsigned long, unsigned long,  
VolumeInfo**, unsigned long*, unsigned long*, char*, unsigned long*,  
unsigned char*) (in CarbonCore)
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) (in CarbonCore)
FSPathMakeRefWithOptions (in CarbonCore)
BDSKPathToFSRef (in BibDesk)
-[BDSKLinkedAliasFile fileRef] (in BibDesk)
-[BDSKLinkedAliasFile URL] (in BibDesk)
-[BDSKLinkedAliasFile displayURL] (in BibDesk)
addFileViewObjectForURLToArray (in BibDesk)
CFArrayApplyFunction (in CoreFoundation)
addAllFileViewObjectsForItemToArray (in BibDesk)
CFArrayApplyFunction (in CoreFoundation)
-[BibDocument shownFiles] (in BibDesk)
-[BibDocument numberOfURLsInFileView:] (in BibDesk)
-[FileView numberOfIcons] (in FileView)
-[FileView _recalculateGridSize] (in FileView)
-[FileView reloadIcons] (in FileView)
-[BibDocument updateFileViews] (in BibDesk)
-[BibDocument handleTableSelectionChangedNotification:] (in BibDesk)
_nsnote_callback (in Foundation)
__CFXNotificationPost (in CoreFoundation)
_CFXNotificationPostNotification (in CoreFoundation)
-[NSNotificationCenter postNotification:] (in Foundation)
postQueueNotifications (in Foundation)
__CFRunLoopDoObservers (in CoreFoundation)
CFRunLoopRunSpecific (in CoreFoundation)
CFRunLoopRunInMode (in CoreFoundation)
RunCurrentEventLoopInMode (in HIToolbox)
ReceiveNextEventCommon (in HIToolbox)
BlockUntilNextEventMatchingListInMode (in HIToolbox)
_DPSNextEvent (in AppKit)
-[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] (in  
AppKit)
-[NSApplication run] (in AppKit)
-[OAApplication run] (in OmniAppKit)
NSApplicationMain (in AppKit)
main (in BibDesk)
_start (in BibDesk)
start (in BibDesk)
0x2

  ****
07.08.08 17:21:49 BibDesk[7708] **** Exception:
Uncaught system exception: signal 11

  **** Stack Trace:
NSExceptionHandlerUncaughtSignalHandler (in ExceptionHandling)
_sigtramp (in libSystem.B.dylib)
0xffffffff
canonpath(char const*, char*, int*) (in CarbonCore)
PathGetObjectInfo(char const*, unsigned long, unsigned long,  
VolumeInfo**, unsigned long*, unsigned long*, char*, unsigned long*,  
unsigned char*) (in CarbonCore)
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) (in CarbonCore)
FSPathMakeRefWithOptions (in CarbonCore)
BDSKPathToFSRef (in BibDesk)
-[BDSKLinkedAliasFile fileRef] (in BibDesk)
-[BDSKLinkedAliasFile updateWithPath:] (in BibDesk)
-[BDSKLinkedFile update] (in BibDesk)
-[NSArray makeObjectsPerformSelector:] (in CoreFoundation)
-[BibDocument setFileURL:] (in BibDesk)
-[NSDocument _handleDocumentFileChanges:] (in AppKit)
-[NSArray makeObjectsPerformSelector:withObject:] (in CoreFoundation)
-[NSDocumentController _handleDocumentFileChanges:] (in AppKit)
__NSFireDelayedPerform (in Foundation)
CFRunLoopRunSpecific (in CoreFoundation)
CFRunLoopRunIn
  ****
07.08.08 17:21:55 com.apple.launchd[235]  
([0x0-0x192192].edu.ucsd.cs.mmccrack.bibdesk[7708]) Exited abnormally:  
Segmentation fault
07.08.08 17:36:34 BibDesk[7851] **** Exception:
Uncaught system exception: signal 11

  **** Stack Trace:
NSExceptionHandlerUncaughtSignalHandler (in ExceptionHandling)
_sigtramp (in libSystem.B.dylib)
0xffffffff
canonpath(char const*, char*, int*) (in CarbonCore)
PathGetObjectInfo(char const*, unsigned long, unsigned long,  
VolumeInfo**, unsigned long*, unsigned long*, char*, unsigned long*,  
unsigned char*) (in CarbonCore)
FSPathMakeRefInternal(unsigned char const*, unsigned long, unsigned  
long, FSRef*, unsigned char*) (in CarbonCore)
FSPathMakeRefWithOptions (in CarbonCore)
BDSKPathToFSRef (in BibDesk)
-[BDSKLinkedAliasFile fileRef] (in BibDesk)
-[BDSKLinkedAliasFile URL] (in BibDesk)
-[BDSKLinkedAliasFile displayURL] (in BibDesk)
addFileViewObjectForURLToArray (in BibDesk)
CFArrayApplyFunction (in CoreFoundation)
addAllFileViewObjectsForItemToArray (in BibDesk)
CFArrayApplyFunction (in CoreFoundation)
-[BibDocument shownFiles] (in BibDesk)
-[BibDocument numberOfURLsInFileView:] (in BibDesk)
-[FileView numberOfIcons] (in FileView)
-[FileView _recalculateGridSize] (in FileView)
-[FileView reloadIcons] (in FileView)
-[BibDocument updateFileViews] (in BibDesk)
-[BibDocument handleTableSelectionChangedNotification:] (in BibDesk)
_nsnote_callback (in Foundation)
__CFXNotificationPost (in CoreFoundation)
_CFXNotificationPostNotification (in CoreFoundation)
-[NSNotificationCenter postNotification:] (in Foundation)
postQueueNotifications (in Foundation)
__CFRunLoopDoObservers (in CoreFoundation)
CFRunLoopRunSpecific (in CoreFoundation)
CFRunLoopRunInMode (in CoreFoundation)
RunCurrentEventLoopInMode (in HIToolbox)
ReceiveNextEventCommon (in HIToolbox)
BlockUntilNextEventMatchingListInMode (in HIToolbox)
_DPSNextEvent (in AppKit)
-[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] (in  
AppKit)
-[NSApplication run] (in AppKit)
-[OAApplication run] (in OmniAppKit)
NSApplicationMain (in AppKit)
main (in BibDesk)
_start (in BibDesk)
start (in BibDesk)
0x2

  ****
07.08.08 17:36:38 com.apple.launchd[235]  
([0x0-0x19d19d].edu.ucsd.cs.mmccrack.bibdesk[7851]) Exited abnormally:  
Segmentation fault

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Re: Consolidating my Bibliography Chaos

Christiaan Hofman
On 7 Aug 2008, at 7:14 PM, Stephan Kurz wrote:

>
> Am 07.08.2008 um 18:56 schrieb Maxwell, Adam R:
>
>> On 08/07/08 09:50, "Stephan Kurz" <[hidden email]> wrote:
>>
>>>> It probably is relevant that the files are on a separate volume.  
>>>> And
>>>> it's important that the .bib file is on your local volume, so that
>>>> should discard some possibilities. However strangely enough your
>>>> crash
>>>> report seemed to point to resolving your .bib file, so that's
>>>> strange.
>>>> Do all the crash report look the same (in particular the first 10
>>>> items in the trace)? ATM I still haven't got a clue why it crashes.
>>>
>>> Oops, I did not check that. I have two different crash reports in  
>>> the
>>> "thread 0" section. I copied both below.
>>
>> How long are the paths that cause a crash vs. the one that does not
>> (as in
>> number of characters)?
>
> /Volumes/6chars/literatur/Bohme-Fetischismus im 19. Jahrhundert.
> Wissenschaftshistorische Analysen zur Karriere-2000a.pdf
> /Volumes/6chars/literatur/Aspalter-Ironieverlust und verleugnete
> Rezeption_ Kontroversen um Romantik-2006a.pdf
>

Really? I thought the volume was called kurzs6.

> the ones above do crash, but not the one below not.
>
> /Volumes/6chars/literatur/Kubac-Notwendige Illusionen. Solidarische
> Anmerkungen zu bildungswissenschaftlicher-2005a.pdf
>

It's even the longest one. For the rest I see no relevant difference.  
That's really weird.

>
>> Did you check the console log for any other error messages?
>
> There are quite a lot since I tried to reproduce the behaviour for a
> while deleting different parts of my file until I came down to 3
> items, so I just copy the last ones.
>
> Stephan
>

Well, all crash reports seem to point to the same point in code, in  
BDSKPathToFSRef. But I fail to see why that could lead to a crash, I  
cannot reproduce any crash using the code, trying to reproduce similar  
input. I get the impression it's got something to do with the  
particular volume.

Christiaan

<snip>


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Re: Consolidating my Bibliography Chaos

Stephan Kurz

Am 07.08.2008 um 19:39 schrieb Christiaan Hofman:

> On 7 Aug 2008, at 7:14 PM, Stephan Kurz wrote:
>> Am 07.08.2008 um 18:56 schrieb Maxwell, Adam R:
>>> On 08/07/08 09:50, "Stephan Kurz" <[hidden email]> wrote:
>>>>> It probably is relevant that the files are on a separate volume.
>>>>> And
>>>>> it's important that the .bib file is on your local volume, so that
>>>>> should discard some possibilities. However strangely enough your
>>>>> crash
>>>>> report seemed to point to resolving your .bib file, so that's
>>>>> strange.
>>>>> Do all the crash report look the same (in particular the first 10
>>>>> items in the trace)? ATM I still haven't got a clue why it  
>>>>> crashes.
>>

> Well, all crash reports seem to point to the same point in code, in
> BDSKPathToFSRef. But I fail to see why that could lead to a crash, I
> cannot reproduce any crash using the code, trying to reproduce similar
> input. I get the impression it's got something to do with the
> particular volume.
>
> Christiaan


Ok, it seems that I have now solved the issue. While "solved" is not  
particularly the right word for just resaving it on my home PowerBook  
after editing it, and reopening it on the work iMac.

Strange. It might either have to do with the file (which has not  
changed apart from my additions), or - more likely - with something  
that our server admins might have changed. I did not even notify them  
(probably someone from my university silently reading this list as  
well ;-)), but now everything works as expected.

Sorry for the hassle, still stumped, but happy.

Thank you, especially for all the support from Christiaan!
Stephan

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