I just upgraded to Leopard, and it went smoothly. I also upgraded all
william kyngesbury's installers and upgraded R
But when I went to use Rgdal (in R), I couldn't, and naturally, I
thought it might have been to do with changes in the gdal libraries.
It looked like this
> library(rgdal)
Loading required package: sp
Error in dyn.load(file, ...) :
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/rgdal/libs/i386/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/rgdal/libs/
i386/rgdal.so, 6): Library not loaded: /Library/Frameworks/R.framework/
Versions/2.5/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/
rgdal/libs/i386/rgdal.so
Reason: no suitable image found. Did find:
/usr/local/lib/libR.dylib: stat() failed with errno=62
Error: package/namespace load failed for 'rgdal'
>
I then tried to upgrade, but lost the lot! I have attached the crash
log for R (when I tried to upgrade rgdal)
Any ideas?
cheers
Ben
Process: R [1116]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R GUI 1.24-devel (4944)
Code Type: X86 (Native)
Parent Process: launchd [115]
Date/Time: 2008-02-20 14:05:42.721 +0900
OS Version: Mac OS X 10.5.2 (9C31)
Report Version: 6
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Crashed Thread: 2
Application Specific Information:
*** Terminating app due to uncaught exception
'NSPortTimeoutException', reason: 'connection timeout: did not receive
reply'
Thread 0:
0 libSystem.B.dylib 0x9211292f szone_malloc + 182
1 libSystem.B.dylib 0x92112838 malloc_zone_malloc + 81
2 libSystem.B.dylib 0x921127cc malloc + 55
3 libR.dylib 0x0041cfe4 build_trtable + 2737
4 libR.dylib 0x0041edbe re_search_internal + 5107
5 libR.dylib 0x0041eeb0 Rf_regexec + 94
6 libR.dylib 0x003275c7 do_regexpr + 2086
7 libR.dylib 0x003ba55c do_internal + 336
8 libR.dylib 0x0038518e Rf_eval + 1182
9 libR.dylib 0x003874a4 Rf_applyClosure + 663
10 libR.dylib 0x00385085 Rf_eval + 917
11 libR.dylib 0x003857ef Rf_evalList + 125
12 libR.dylib 0x00385262 Rf_eval + 1394
13 libR.dylib 0x003857ef Rf_evalList + 125
14 libR.dylib 0x00385262 Rf_eval + 1394
15 libR.dylib 0x00389576 do_set + 592
16 libR.dylib 0x0038518e Rf_eval + 1182
17 libR.dylib 0x00385f3f do_begin + 58
18 libR.dylib 0x0038518e Rf_eval + 1182
19 libR.dylib 0x0038518e Rf_eval + 1182
20 libR.dylib 0x00385f3f do_begin + 58
21 libR.dylib 0x0038518e Rf_eval + 1182
22 libR.dylib 0x003874a4 Rf_applyClosure + 663
23 libR.dylib 0x00385085 Rf_eval + 917
24 libR.dylib 0x00385f3f do_begin + 58
25 libR.dylib 0x0038518e Rf_eval + 1182
26 libR.dylib 0x003874a4 Rf_applyClosure + 663
27 libR.dylib 0x00385085 Rf_eval + 917
28 libR.dylib 0x003857ef Rf_evalList + 125
29 libR.dylib 0x00385262 Rf_eval + 1394
30 libR.dylib 0x00385f3f do_begin + 58
31 libR.dylib 0x0038518e Rf_eval + 1182
32 libR.dylib 0x0038518e Rf_eval + 1182
33 libR.dylib 0x00385f3f do_begin + 58
34 libR.dylib 0x0038518e Rf_eval + 1182
35 libR.dylib 0x003874a4 Rf_applyClosure + 663
36 libR.dylib 0x00385085 Rf_eval + 917
37 libR.dylib 0x002fd377 do_lapply + 506
38 libR.dylib 0x003ba55c do_internal + 336
39 libR.dylib 0x0038518e Rf_eval + 1182
40 libR.dylib 0x00385f3f do_begin + 58
41 libR.dylib 0x0038518e Rf_eval + 1182
42 libR.dylib 0x003874a4 Rf_applyClosure + 663
43 libR.dylib 0x00385085 Rf_eval + 917
44 libR.dylib 0x00385f3f do_begin + 58
45 libR.dylib 0x0038518e Rf_eval + 1182
46 libR.dylib 0x003874a4 Rf_applyClosure + 663
47 libR.dylib 0x00385085 Rf_eval + 917
48 libR.dylib 0x00389576 do_set + 592
49 libR.dylib 0x0038518e Rf_eval + 1182
50 libR.dylib 0x00385f3f do_begin + 58
51 libR.dylib 0x0038518e Rf_eval + 1182
52 libR.dylib 0x003874a4 Rf_applyClosure + 663
53 libR.dylib 0x00385085 Rf_eval + 917
54 libR.dylib 0x00389576 do_set + 592
55 libR.dylib 0x0038518e Rf_eval + 1182
56 libR.dylib 0x00385f3f do_begin + 58
57 libR.dylib 0x0038518e Rf_eval + 1182
58 libR.dylib 0x00388deb do_for + 585
59 libR.dylib 0x0038518e Rf_eval + 1182
60 libR.dylib 0x00385f3f do_begin + 58
61 libR.dylib 0x0038518e Rf_eval + 1182
62 libR.dylib 0x0038518e Rf_eval + 1182
63 libR.dylib 0x00385f3f do_begin + 58
64 libR.dylib 0x0038518e Rf_eval + 1182
65 libR.dylib 0x003874a4 Rf_applyClosure + 663
66 libR.dylib 0x00385085 Rf_eval + 917
67 libR.dylib 0x00385499 Rf_evalListKeepMissing +
127
68 libR.dylib 0x00385a16 evalArgs + 42
69 libR.dylib 0x00385d1f Rf_DispatchOrEval + 775
70 libR.dylib 0x00452821 do_subset + 79
71 libR.dylib 0x0038518e Rf_eval + 1182
72 libR.dylib 0x00389576 do_set + 592
73 libR.dylib 0x0038518e Rf_eval + 1182
74 libR.dylib 0x00385f3f do_begin + 58
75 libR.dylib 0x0038518e Rf_eval + 1182
76 libR.dylib 0x0038518e Rf_eval + 1182
77 libR.dylib 0x00385f3f do_begin + 58
78 libR.dylib 0x0038518e Rf_eval + 1182
79 libR.dylib 0x003874a4 Rf_applyClosure + 663
80 libR.dylib 0x00385085 Rf_eval + 917
81 libR.dylib 0x00389576 do_set + 592
82 libR.dylib 0x0038518e Rf_eval + 1182
83 libR.dylib 0x00385f3f do_begin + 58
84 libR.dylib 0x0038518e Rf_eval + 1182
85 libR.dylib 0x003874a4 Rf_applyClosure + 663
86 libR.dylib 0x00385085 Rf_eval + 917
87 libR.dylib 0x0034657a protectedEval + 44
88 libR.dylib 0x00346beb R_ToplevelExec + 234
89 libR.dylib 0x00346c2a R_tryEval + 56
90 org.R-project.R 0x0000fbfc -[REngine
evaluateExpressions:] + 296 (REngine.m:281)
91 org.R-project.R 0x0000ff6a -[REngine
executeString:] + 204 (REngine.m:333)
92 org.R-project.R 0x00014a05 -[PackageInstaller
reloadURL:] + 543 (PackageInstaller.m:340)
93 com.apple.AppKit 0x9474ce56 -[NSApplication
sendAction:to:from:] + 112
94 com.apple.AppKit 0x9474cd94 -[NSControl
sendAction:to:] + 108
95 com.apple.AppKit 0x9474cc1a -[NSCell
_sendActionFrom:] + 169
96 com.apple.AppKit 0x9474c273 -[NSCell
trackMouse:inRect:ofView:untilMouseUp:] + 1827
97 com.apple.AppKit 0x9474bac6 -[NSButtonCell
trackMouse:inRect:ofView:untilMouseUp:] + 541
98 com.apple.AppKit 0x9474b380 -[NSControl mouseDown:]
+ 888
99 com.apple.AppKit 0x94749ac3 -[NSWindow sendEvent:] +
5381
100 com.apple.AppKit 0x94716714 -[NSApplication
sendEvent:] + 2780
101 org.R-project.R 0x00007d7d -[RController
doProcessEvents:] + 204 (RController.m:2038)
102 org.R-project.R 0x0000539a -[RController
handleReadConsole:] + 83 (RController.m:959)
103 org.R-project.R 0x0000f35d Re_ReadConsole + 494
(Rcallbacks.m:137)
104 org.R-project.R 0x00016cd6 run_REngineRmainloop +
462 (Rinit.c:381)
105 org.R-project.R 0x0000f73c -[REngine runREPL] + 98
(REngine.m:178)
106 org.R-project.R 0x000020e0 main + 738 (main.m:125)
107 org.R-project.R 0x00001de2 _start + 216
108 org.R-project.R 0x00001d09 start + 41
Thread 1:
0 libSystem.B.dylib 0x921119e6 mach_msg_trap + 10
1 libSystem.B.dylib 0x921191dc mach_msg + 72
2 com.apple.CoreFoundation 0x940d20de CFRunLoopRunSpecific +
1806
3 com.apple.CoreFoundation 0x940d2d18 CFRunLoopRunInMode + 88
4 com.apple.CFNetwork 0x964626cc
CFURLCacheWorkerThread(void*) + 396
5 libSystem.B.dylib 0x92142c55 _pthread_start + 321
6 libSystem.B.dylib 0x92142b12 thread_start + 34
Thread 2 Crashed:
0 com.apple.CoreFoundation 0x9414c0f4
___TERMINATING_DUE_TO_UNCAUGHT_EXCEPTION___ + 4
1 libobjc.A.dylib 0x91ca30fb objc_exception_throw + 40
2 com.apple.Foundation 0x92e391a6 -[NSConnection
sendInvocation:internal:] + 2422
3 com.apple.Foundation 0x92e380d6 -[NSDistantObject
methodSignatureForSelector:] + 1302
4 com.apple.CoreFoundation 0x941517bd ___forwarding___ + 237
5 com.apple.CoreFoundation 0x94151b12 _CF_forwarding_prep_0 + 50
6 org.R-project.R 0x0000415a -[RController
readThread:] + 822 (RController.m:645)
7 com.apple.Foundation 0x92e025ad -[NSThread main] + 45
8 com.apple.Foundation 0x92e02154 __NSThread__main__ + 308
9 libSystem.B.dylib 0x92142c55 _pthread_start + 321
10 libSystem.B.dylib 0x92142b12 thread_start + 34
Thread 3:
0 libSystem.B.dylib 0x92118bce __semwait_signal + 10
1 libSystem.B.dylib 0x92118996 usleep$UNIX2003 + 61
2 com.apple.AppKit 0x946e1cf9 -[NSUIHeartBeat
_heartBeatThread:] + 2042
3 com.apple.Foundation 0x92e025ad -[NSThread main] + 45
4 com.apple.Foundation 0x92e02154 __NSThread__main__ + 308
5 libSystem.B.dylib 0x92142c55 _pthread_start + 321
6 libSystem.B.dylib 0x92142b12 thread_start + 34
Thread 4:
0 libSystem.B.dylib 0x92118bce __semwait_signal + 10
1 libSystem.B.dylib 0x921438cd pthread_cond_wait
$UNIX2003 + 73
2 com.apple.QuartzCore 0x91e6f121 fe_fragment_thread + 54
3 libSystem.B.dylib 0x92142c55 _pthread_start + 321
4 libSystem.B.dylib 0x92142b12 thread_start + 34
Thread 5:
0 libSystem.B.dylib 0x921119e6 mach_msg_trap + 10
1 libSystem.B.dylib 0x921191dc mach_msg + 72
2 com.apple.CoreFoundation 0x940d20de CFRunLoopRunSpecific +
1806
3 com.apple.CoreFoundation 0x940d2d18 CFRunLoopRunInMode + 88
4 com.apple.Foundation 0x92e65ac0 +
[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] +
320
5 com.apple.Foundation 0x92e025ad -[NSThread main] + 45
6 com.apple.Foundation 0x92e02154 __NSThread__main__ + 308
7 libSystem.B.dylib 0x92142c55 _pthread_start + 321
8 libSystem.B.dylib 0x92142b12 thread_start + 34
Thread 2 crashed with X86 Thread State (32-bit):
eax: 0xa064d0f0 ebx: 0x91ca30dc ecx: 0xa064c1a0 edx: 0x007e9000
edi: 0x00000000 esi: 0xb01466d0 ebp: 0xb0146618 esp: 0xb0146618
ss: 0x0000001f efl: 0x00000286 eip: 0x9414c0f4 cs: 0x00000017
ds: 0x0000001f es: 0x0000001f fs: 0x0000001f gs: 0x00000037
cr2: 0x2ec24000
Binary Images:
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<df82fc093e498a9eb5490761cb292218> /System/Library/Frameworks/
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CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
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ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/
Versions/A/CoreText
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Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
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Versions/A/ATS
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<6978bbcca4277d6ae9f042beff643f7d> /usr/lib/libsqlite3.0.dylib
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<b232c018ddd040ec4e2c2af632dd497f> /System/Library/Frameworks/
Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/
libvDSP.dylib
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<e064f94d969ce25cb7de3cfb980c3249> /System/Library/Frameworks/
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OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
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DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
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<9d42e83d860433f9126c4871d1fe0ce8> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
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Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/
HIToolbox
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HIServices.framework/Versions/A/HIServices
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CoreGraphics.framework/Versions/A/CoreGraphics
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Frameworks/vecLib.framework/Versions/A/vecLib
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CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/
Versions/A/CFNetwork
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<d4234e6f5e5f530bdafb969157f1f17b> /System/Library/Frameworks/
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Versions/A/Resources/libGIF.dylib
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Kerberos.framework/Versions/A/Kerberos
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<9b29a5500efe01cc3adea67bbc42568e> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
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CoreServices.framework/Versions/A/Frameworks/
DictionaryServices.framework/Versions/A/DictionaryServices
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<0cfb80109d624beb9ceb3c43b6c5ec10> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libJPEG.dylib
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Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/
A/CarbonSound
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<a3d68f17f37ff55a3e61aca1e3aee522> /System/Library/Frameworks/
OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
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<b8e553df643f2aec68fa968b3b459b2b> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/
Versions/A/OpenScripting
0x96c16000 - 0x96c93fef libvMisc.dylib ??? (???) /System/Library/
Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/
Versions/A/libvMisc.dylib
0x96cac000 - 0x96cbcfff com.apple.speech.synthesis.framework 3.6.59
(3.6.59) <4ffef145fad3d4d787e0c33eab26b336> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
SpeechSynthesis.framework/Versions/A/SpeechSynthesis
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<8e28162ef2288692615b52acc01f8b54> /System/Library/Frameworks/
CoreData.framework/Versions/A/CoreData
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<e01596187e91af5d48653920017b8c8e> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x96e52000 - 0x96f04ffb libcrypto.0.9.7.dylib ??? (???)
<330b0e48e67faffc8c22dfc069ca7a47> /usr/lib/libcrypto.0.9.7.dylib
0xfffe8000 - 0xfffebfff libobjc.A.dylib ??? (???) /usr/lib/
libobjc.A.dylib
0xffff0000 - 0xffff1780 libSystem.B.dylib ??? (???) /usr/lib/
libSystem.B.dylib
--
Ben Madin
REMOTE INFORMATION
t : +61 8 9192 5455
f : +61 8 9192 5535
m : 0448 887 220
Broome WA 6725
[EMAIL PROTECTED]
Out here, it pays to
know...
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