I just tried running R 2.6.2 for Mac OS X and it crashed. The crash log
is attached.
Hopefully this can help with the problem.
Shelah
Shelah Morita wrote:
Hi,
I recently tried to re-install R 2.6.2.dmg from R 2.5 similar to
Brendan below. I also got an installer error associated with tcl/tk. I
removed R and all the associate receipts (including for tcl) and tried
to reinstall, but got the same error.
As you suggested to Brendan, I have looked in /usr/local and
/usr/local/lib. I get the following error with trying to cd to
/usr/local/lib:
-bash: cd: lib: Too many levels of symbolic links
I know that system did not have this problem before I tried to reinstall
R.
But I have not idea how to figure out where the symbolic loop is,
especially if I can't even open the directory.
Can you please help.
Thanks,
Shelah
Brendan,
you have likely an infinite softlink in /usr/local. Please verify that
your /usr/local and /usr/local/lib is in order. If the error still
persists, please send us the installer log from the failed installation.
Cheers,
Simon
PS: Please don't set high-priority flags on your emails, it's
superfluous and considered rude by some.
On Apr 11, 2008, at 7:05 PM, Brendan Casey wrote:
/ Hello,
/>/
/>/ I had problems with rcmdr and tcl/tk before but straightened them
/>/ out. this time, I am really stuck.
/>/
/>/ I was having alot of issues with Rgrphviz so I fiured I would just
/>/ start over. I uninstalled all the R folder, libraries, frameworks,
/>/ and packages. I then downloaded the latest (2008-02-08) version of R
/>/ 2.6.2 for my Mac OSX (10.4.11) I also have X11 installed (1.1.3) and
/>/ was able to run some sort of X11 update from apple. I also tried
/>/ xcode tools download from apple, but it didnt give me an option to
/>/ install X11 again.
/>/
/>/ When I install R from the disk image, it says that there was an error
/>/ with the installation. When i try to install the tcl/tk package
/>/ alone, it also says error with the installation. It seems like its
/>/ installing R and Rgui, but nothing else.
/>/
/>/ After starting R (gui) I installed rcmdr and the dependencies. I
/>/ then started X11 and tried to load rcmdr. Here is what I got:
/>/
/>/ Loading required package: tcltk
/>/ Loading Tcl/Tk interface ... Error in fun(...) :
/>/ Can't find a usable init.tcl in the following directories:
/>/ @TCL_IN_FRAMEWORK@ @TCL_IN_FRAMEWORK@
/>/
/>/ This probably means that Tcl wasn't installed properly.
/>/
/>/ In addition: Warning messages:
/>/ 1: In library() :
/>/ library '/Users/brendancasey/Library/R/2.6/library' contains no
/>/ packages
/>/ 2: In library() :
/>/ library '/Users/brendancasey/Library/R/2.6/library' contains no
/>/ packages
/>/ Error : .onLoad failed in 'loadNamespace' for 'tcltk'
/>/ Error: package 'tcltk' could not be loaded
/>/ ____________________________
/>/ I dont mind uninstalling more folders and starting from scratch (X11,
/>/ R, Rgui, etc), but I am not prepared to reinstall my OS if that is
/>/ what it will take.
/>/
/>/ Can someone please help me with this?
/>/
/>/ Brendan Casey
/>/ bcasey1 at hotmail dot com
/>/ _______________________________________________
/>/ R-SIG-Mac mailing list
/>/ R-SIG-Mac at stat.math.ethz.ch
<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
/>/ https://stat.ethz.ch/mailman/listinfo/r-sig-mac
/>/
/>/
/
--
Shelah Morita Ph.D.
NSF International Research Fellow
Department of Botany and Zoology
University of Stellenbosch
Private Bag X1, Matieland 7602
SOUTH AFRICA
+27 21 808-3232 Office
+27 21 808-2405 Fax
+27 79 774-8372 Cell
+1 202 684-6849 (Voice Mail)
Skype:bellamyia
http://pangonid.net
_ _
( \ !
`.\| ,
<!||)( )(O\______________
/|\ `^
/ / |
**********
Host Name: pango
Date/Time: 2008-04-13 17:11:48.835 +0200
OS Version: 10.4.11 (Build 8S2167)
Report Version: 4
Command: R
Path: /Applications/R.app/Contents/MacOS/R
Parent: WindowServer [65]
Version: R GUI 1.24-devel (4944)
PID: 8302
Thread: 2
Exception: EXC_BREAKPOINT (0x0006)
Code[0]: 0x00000002
Code[1]: 0x00000000
Thread 0:
0 libSystem.B.dylib 0x90037b57 mach_wait_until + 7
1 org.R-project.R 0x00005d9d -[RController handleSystemCommand:]
+ 454 (RController.m:1178)
2 org.R-project.R 0x0000d14f Re_system + 86 (Rcallbacks.m:273)
3 libR.dylib 0x00468366 R_system + 82
4 libR.dylib 0x004c1066 do_system + 656
5 libR.dylib 0x003cb55c do_internal + 336
6 libR.dylib 0x0039618e Rf_eval + 1182
7 libR.dylib 0x00396f3f do_begin + 58
8 libR.dylib 0x0039618e Rf_eval + 1182
9 libR.dylib 0x003984a4 Rf_applyClosure + 663
10 libR.dylib 0x00396085 Rf_eval + 917
11 libR.dylib 0x0039a576 do_set + 592
12 libR.dylib 0x0039618e Rf_eval + 1182
13 libR.dylib 0x00396f3f do_begin + 58
14 libR.dylib 0x0039618e Rf_eval + 1182
15 libR.dylib 0x00399deb do_for + 585
16 libR.dylib 0x0039618e Rf_eval + 1182
17 libR.dylib 0x00396f3f do_begin + 58
18 libR.dylib 0x0039618e Rf_eval + 1182
19 libR.dylib 0x0039618e Rf_eval + 1182
20 libR.dylib 0x00396f3f do_begin + 58
21 libR.dylib 0x0039618e Rf_eval + 1182
22 libR.dylib 0x003984a4 Rf_applyClosure + 663
23 libR.dylib 0x00396085 Rf_eval + 917
24 libR.dylib 0x00399deb do_for + 585
25 libR.dylib 0x0039618e Rf_eval + 1182
26 libR.dylib 0x00396f3f do_begin + 58
27 libR.dylib 0x0039618e Rf_eval + 1182
28 libR.dylib 0x0039618e Rf_eval + 1182
29 libR.dylib 0x00396f3f do_begin + 58
30 libR.dylib 0x0039618e Rf_eval + 1182
31 libR.dylib 0x003984a4 Rf_applyClosure + 663
32 libR.dylib 0x00396085 Rf_eval + 917
33 libR.dylib 0x0035757a protectedEval + 44
34 libR.dylib 0x00357beb R_ToplevelExec + 234
35 libR.dylib 0x00357c2a R_tryEval + 56
36 org.R-project.R 0x0000fbfc -[REngine evaluateExpressions:] +
296 (REngine.m:281)
37 org.R-project.R 0x0000ff6a -[REngine executeString:] + 204
(REngine.m:333)
38 org.R-project.R 0x00015b64 -[PackageInstaller updateAll:] + 212
(PackageInstaller.m:724)
39 com.apple.AppKit 0x9335a968 -[NSApplication sendAction:to:from:]
+ 107
40 com.apple.AppKit 0x9335a8c1 -[NSControl sendAction:to:] + 101
41 com.apple.AppKit 0x9335ca6d -[NSCell _sendActionFrom:] + 168
42 com.apple.AppKit 0x9336f24d -[NSCell
trackMouse:inRect:ofView:untilMouseUp:] + 1271
43 com.apple.AppKit 0x9338ce35 -[NSButtonCell
trackMouse:inRect:ofView:untilMouseUp:] + 848
44 com.apple.AppKit 0x9338c6e5 -[NSControl mouseDown:] + 757
45 com.apple.AppKit 0x93349f8f -[NSWindow sendEvent:] + 5279
46 com.apple.AppKit 0x9333bf28 -[NSApplication sendEvent:] + 5023
47 org.R-project.R 0x00007d7d -[RController doProcessEvents:] +
204 (RController.m:2038)
48 org.R-project.R 0x0000539a -[RController handleReadConsole:] +
83 (RController.m:959)
49 org.R-project.R 0x0000f35d Re_ReadConsole + 494
(Rcallbacks.m:137)
50 org.R-project.R 0x00016cd6 run_REngineRmainloop + 462
(Rinit.c:381)
51 org.R-project.R 0x0000f73c -[REngine runREPL] + 98
(REngine.m:178)
52 org.R-project.R 0x000020e0 main + 738 (main.m:125)
53 org.R-project.R 0x00001de2 _start + 216
54 org.R-project.R 0x00001d09 start + 41
Thread 1:
0 libSystem.B.dylib 0x90009cd7 mach_msg_trap + 7
1 com.apple.CoreFoundation 0x9082d21b CFRunLoopRunSpecific + 2014
2 com.apple.CoreFoundation 0x9082ca36 CFRunLoopRunInMode + 61
3 com.apple.Foundation 0x92851c76 +[NSURLCache _diskCacheSyncLoop:] +
206
4 com.apple.Foundation 0x927f539c forkThreadForFunction + 123
5 libSystem.B.dylib 0x90024227 _pthread_body + 84
Thread 2 Crashed:
0 com.apple.Foundation 0x928284b3 _NSRaiseError + 227
1 com.apple.Foundation 0x92844529 -[NSConnection sendInvocation:] +
1378
2 com.apple.Foundation 0x927fb4d8 -[NSObject(NSForwardInvocation)
forward::] + 469
3 libobjc.A.dylib 0x90a5cba1 _objc_msgForward + 49
4 com.apple.Foundation 0x92843c47 -[NSDistantObject
methodSignatureForSelector:] + 211
5 com.apple.Foundation 0x927fb364 -[NSObject(NSForwardInvocation)
forward::] + 97
6 libobjc.A.dylib 0x90a5cba1 _objc_msgForward + 49
7 org.R-project.R 0x0000415a -[RController readThread:] + 822
(RController.m:645)
8 com.apple.Foundation 0x927f539c forkThreadForFunction + 123
9 libSystem.B.dylib 0x90024227 _pthread_body + 84
Thread 3:
0 libSystem.B.dylib 0x9003f6cf syscall_thread_switch + 7
1 com.apple.AppKit 0x9334424e -[NSUIHeartBeat _heartBeatThread:] +
1399
2 com.apple.Foundation 0x927f539c forkThreadForFunction + 123
3 libSystem.B.dylib 0x90024227 _pthread_body + 84
Thread 2 crashed with X86 Thread State (32-bit):
eax: 0x017a9000 ebx: 0x928283de ecx: 0x90a669f8 edx: 0x0d30fcd0
edi: 0x0d3c9ce0 esi: 0x0d3c9e50 ebp: 0xb019f888 esp: 0xb019f820
ss: 0x0000001f efl: 0x00000246 eip: 0x928284b3 cs: 0x00000017
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
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0x931d9000 - 0x931e4fff com.apple.opengl 1.4.16
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x93254000 - 0x93254fff com.apple.Cocoa 6.4 (???)
/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
0x93256000 - 0x9390cfff com.apple.AppKit 6.4.10 (824.45)
/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x93c8d000 - 0x93d08fff com.apple.CoreData 91 (92.1)
/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
0x93d41000 - 0x93dfafff com.apple.audio.toolbox.AudioToolbox 1.4.7
/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x93e3d000 - 0x93e3dfff com.apple.audio.units.AudioUnit 1.4.2
/System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
0x93e3f000 - 0x94000fff com.apple.QuartzCore 1.4.12
/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x94046000 - 0x94087fff libsqlite3.0.dylib /usr/lib/libsqlite3.0.dylib
0x9408f000 - 0x940c9fff libGLImage.dylib
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x940ce000 - 0x940e4fff com.apple.CoreVideo 1.4.2
/System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
0x94278000 - 0x94287fff libCGATS.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
0x9428e000 - 0x94299fff libCSync.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
0x942e5000 - 0x942fffff libRIP.A.dylib
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
0x94d4d000 - 0x94dfffff com.apple.WebKit 4525.13
/System/Library/Frameworks/WebKit.framework/Versions/A/WebKit
0x94e6a000 - 0x94f31fff com.apple.JavaScriptCore 4525.13
/System/Library/Frameworks/JavaScriptCore.framework/Versions/A/JavaScriptCore
0x94f6d000 - 0x9555ffff com.apple.WebCore 4525.13
/System/Library/Frameworks/WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/WebCore
0x95a47000 - 0x95a49fff com.apple.ExceptionHandling 1.2 (???)
/System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
0x95f49000 - 0x95f77fff libncurses.5.4.dylib /usr/lib/libncurses.5.4.dylib
0x969ba000 - 0x969bafff com.apple.vecLib 3.3.1 (vecLib 3.3.1)
/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
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