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
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makeDocumentWithContentsOfURL:ofType:error:] + 391
18 com.apple.AppKit 0x961d5fe4 -[NSDocumentController
openDocumentWithContentsOfURL:display:error:] + 420
19 com.omnigroup.OmniAppKit 0x003efc2e -
[NSDocumentController(OAExtensions)
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21 com.apple.AppKit 0x96339523 -
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[NSApplication(NSAppleEventHandling) _handleAEOpenDocuments:] + 88
25 com.apple.AppKit 0x95ef7eef -
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aeDispatchAppleEvent(AEDesc const*, AEDesc*, unsigned long, unsigned
char*) + 144
29 com.apple.AE 0x900e657e
dispatchEventAndSendReply(AEDesc const*, AEDesc*) + 44
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31 com.apple.HIToolbox 0x940e447d AEProcessAppleEvent + 38
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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
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[NSConditionLock(OFFixes) replacement_lockWhenCondition:beforeDate:] +
59
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Thread 2:
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1 libSystem.B.dylib 0x9387336d pthread_cond_wait
$UNIX2003 + 73
2 libGLProgrammability.dylib 0x94bd4432 glvmDoWork + 162
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Thread 3:
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1 libSystem.B.dylib 0x9387336d pthread_cond_wait
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Thread 4:
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1 libSystem.B.dylib 0x93848c9c mach_msg + 72
2 com.apple.CoreFoundation 0x944530ce CFRunLoopRunSpecific +
1790
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Thread 5:
0 libSystem.B.dylib 0x938414a6 mach_msg_trap + 10
1 libSystem.B.dylib 0x93848c9c mach_msg + 72
2 com.apple.CoreFoundation 0x944530ce CFRunLoopRunSpecific +
1790
3 com.apple.CoreFoundation 0x94453cf8 CFRunLoopRunInMode + 88
4 com.apple.Foundation 0x93d2b460 +
[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] +
320
5 com.apple.Foundation 0x93cc7f1d -[NSThread main] + 45
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7 libSystem.B.dylib 0x938726f5 _pthread_start + 321
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Thread 6:
0 libSystem.B.dylib 0x938915e2 select$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:
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semaphore_timedwait_signal_trap + 10
1 libSystem.B.dylib 0x9387384f _pthread_cond_wait + 1244
2 libSystem.B.dylib 0x938750d3
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3 com.apple.Foundation 0x93d0de8c -[NSCondition
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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
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10 ...up.framework.OmniFoundation 0x0050861a -[OFQueueProcessor
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11 ...up.framework.OmniFoundation 0x005087c5 -
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12 com.apple.Foundation 0x93cc7f1d -[NSThread main] + 45
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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
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