From Nomis101 at web.de  Fri Jun 16 12:21:00 2006
From: Nomis101 at web.de (Nomis101 at web.de)
Date: Fri, 16 Jun 2006 12:21:00 +0200
Subject: [Rd] 3 Bugs in R (with R.crash.log) under OSX 10.4.6
Message-ID: <828560331@web.de>

Hi, i'm a biologie-student and nedd R for Analyzing my datas. But i have 3 bis Problems with R. I run R 2.3.1 on a G4 PPC with OSX 10.4.6 and Quicktime 7.1.1.

First Problem:
Open Windows (R-Skript ausf?hren, Arbeitsverzeichnis wechseln...) doesn't close after opening.

Second Problem:
If i make a boxplot with my datas, than copy the boxplot and paste it into "Preview" as an new image and save it as JPEG, then R crashes. The R.crash.log than tells me:

Date/Time:      2006-06-14 21:37:08.869 +0200
OS Version:     10.4.6 (Build 8I127)
Report Version: 4

Command: R
Path:    /Applications/Biologie- und Chemie-Programme/R 2.3.1/R.app/Contents/MacOS/R
Parent:  WindowServer [63]

Version: 1.16 (3198)

PID:    215
Thread: 0

Exception:  EXC_BREAKPOINT (0x0006)
Code[0]:    0x00000001
Code[1]:    0x92991120


Thread 0 Crashed:
0   com.apple.Foundation           	0x92991120 _NSRaiseError + 264
1   com.apple.AppKit               	0x93764d50 -[NSView _drawRect:clip:] + 2472
2   com.apple.AppKit               	0x937641b8 -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 404
3   com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
4   com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
5   com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
6   com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
7   com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
8   com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
9   com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
10  com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
11  com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
12  com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
13  com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
14  com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
15  com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
16  com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
17  com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
18  com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
19  com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
20  com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
21  com.apple.AppKit               	0x938c28e0 -[NSBrowser _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 164
22  com.apple.AppKit               	0x93766f00 _recursiveDisplayInRect2 + 84
23  com.apple.CoreFoundation       	0x907f33c4 CFArrayApplyFunction + 416
24  com.apple.AppKit               	0x937642cc -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 680
25  com.apple.AppKit               	0x93763780 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 196
26  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
27  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
28  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
29  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
30  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
31  com.apple.AppKit               	0x93763d48 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 1676
32  com.apple.AppKit               	0x937843e4 -[NSThemeFrame _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 192
33  com.apple.AppKit               	0x9375d3f4 -[NSView _displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:] + 384
34  com.apple.AppKit               	0x937526e8 -[NSView displayIfNeeded] + 248
35  com.apple.AppKit               	0x93752558 -[NSWindow displayIfNeeded] + 180
36  com.apple.AppKit               	0x93752404 _handleWindowNeedsDisplay + 200
37  com.apple.CoreFoundation       	0x907e373c __CFRunLoopDoObservers + 352
38  com.apple.CoreFoundation       	0x907e39ec __CFRunLoopRun + 436
39  com.apple.CoreFoundation       	0x907e347c CFRunLoopRunSpecific + 268
40  com.apple.HIToolbox            	0x9321d980 RunCurrentEventLoopInMode + 264
41  com.apple.HIToolbox            	0x9321d014 ReceiveNextEventCommon + 380
42  com.apple.HIToolbox            	0x9321ce80 BlockUntilNextEventMatchingListInMode + 96
43  com.apple.AppKit               	0x9371ee84 _DPSNextEvent + 384
44  com.apple.AppKit               	0x9371eb48 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 116
45  org.R-project.R                	0x0000dbf4 -[RController doProcessEvents:] + 104 (RController.m:1824)
46  org.R-project.R                	0x0000b730 -[RController handleReadConsole:] + 88 (RController.m:869)
47  org.R-project.R                	0x0002c0b8 Re_ReadConsole + 108 (Rcallbacks.m:137)
48  org.R-project.R                	0x0003223c run_REngineRmainloop + 300 (Rinit.c:341)
49  org.R-project.R                	0x0002aa1c -[REngine runREPL] + 68 (REngine.m:167)
50  org.R-project.R                	0x0001d340 main + 680 (main.m:101)
51  org.R-project.R                	0x00002e8c _start + 340 (crt.c:272)
52  org.R-project.R                	0x00002d34 start + 60

Thread 1:
0   libSystem.B.dylib              	0x9000b0a8 mach_msg_trap + 8
1   libSystem.B.dylib              	0x9000affc mach_msg + 60
2   com.apple.CoreFoundation       	0x907e3b78 __CFRunLoopRun + 832
3   com.apple.CoreFoundation       	0x907e347c CFRunLoopRunSpecific + 268
4   com.apple.Foundation           	0x9296b598 -[NSConnection sendInvocation:] + 1468
5   com.apple.Foundation           	0x9296a034 -[NSObject(NSForwardInvocation) forward::] + 408
6   libobjc.A.dylib                	0x90a4b0b0 _objc_msgForward + 176
7   com.apple.Foundation           	0x9296a39c -[NSDistantObject methodSignatureForSelector:] + 268
8   com.apple.Foundation           	0x92969f04 -[NSObject(NSForwardInvocation) forward::] + 104
9   libobjc.A.dylib                	0x90a4b0b0 _objc_msgForward + 176
10  org.R-project.R                	0x0000acc0 -[RController readThread:] + 2436 (RController.m:613)
11  com.apple.Foundation           	0x92976194 forkThreadForFunction + 108
12  libSystem.B.dylib              	0x9002ba68 _pthread_body + 96

Thread 2:
0   libSystem.B.dylib              	0x9002c128 semaphore_wait_signal_trap + 8
1   libSystem.B.dylib              	0x90030bec pthread_cond_wait + 480
2   com.apple.Foundation           	0x9297d300 -[NSConditionLock lockWhenCondition:] + 68
3   com.apple.AppKit               	0x937bbaac -[NSUIHeartBeat _heartBeatThread:] + 324
4   com.apple.Foundation           	0x92976194 forkThreadForFunction + 108
5   libSystem.B.dylib              	0x9002ba68 _pthread_body + 96

Thread 3:
0   libSystem.B.dylib              	0x9002edcc kevent + 12
1   com.apple.DesktopServices      	0x9288a2b0 TFSNotificationTask::FSNotificationTaskProc(void*) + 56
2   ...ple.CoreServices.CarbonCore 	0x90bc9260 PrivateMPEntryPoint + 76
3   libSystem.B.dylib              	0x9002ba68 _pthread_body + 96

Thread 4:
0   libSystem.B.dylib              	0x9002c128 semaphore_wait_signal_trap + 8
1   libSystem.B.dylib              	0x90030bec pthread_cond_wait + 480
2   ...ple.CoreServices.CarbonCore 	0x90bc9450 MPWaitOnQueue + 224
3   com.apple.DesktopServices      	0x9288a92c TNodeSyncTask::SyncTaskProc(void*) + 116
4   ...ple.CoreServices.CarbonCore 	0x90bc9260 PrivateMPEntryPoint + 76
5   libSystem.B.dylib              	0x9002ba68 _pthread_body + 96

Thread 0 crashed with PPC Thread State 64:
  srr0: 0x0000000092991120 srr1: 0x000000000202f030                        vrsave: 0x0000000000000000
    cr: 0x24042442          xer: 0x0000000000000004   lr: 0x00000000929910f8  ctr: 0x0000000092952f1c
    r0: 0x0000000000000000   r1: 0x00000000bfffcfe0   r2: 0x00000000a2950508   r3: 0x00000000bfffcb90
    r4: 0x0000000000000000   r5: 0x0000000092952844   r6: 0x00000000bfffcc14   r7: 0x00000000000000ff
    r8: 0x00000000bfffcc00   r9: 0x000000000423a9f0  r10: 0x0000000090a44628  r11: 0x0000000024042442
   r12: 0x0000000092952f1c  r13: 0x0000000000000000  r14: 0x00000000bfffe270  r15: 0x0000000000000001
   r16: 0x0000000000564940  r17: 0x0000000000000000  r18: 0x0000000000000000  r19: 0x0000000000000000
   r20: 0x00000000a37536bc  r21: 0x00000000a3754024  r22: 0x00000000bfffd650  r23: 0x0000000000000001
   r24: 0x00000000bfffd310  r25: 0x0000000000000000  r26: 0x0000000000533c40  r27: 0x0000000000000001
   r28: 0x0000000006908980  r29: 0x00000000a29557f4  r30: 0x0000000006908980  r31: 0x0000000092991028

Binary Images Description:
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  0x157000 -   0x162fff libgcc_s.1.0.dylib 	/Library/Frameworks/R.framework/Versions/2.3/Resources/lib/libgcc_s.1.0.dylib
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0x9029a000 - 0x9034bfff ATS 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
0x9037a000 - 0x90734fff com.apple.CoreGraphics 1.258.30 (???)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x907c1000 - 0x9089afff com.apple.CoreFoundation 6.4.6 (368.27)	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x908e3000 - 0x908e3fff com.apple.CoreServices 10.4 (???)	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
0x908e5000 - 0x909e7fff libicucore.A.dylib 	/usr/lib/libicucore.A.dylib
0x90a41000 - 0x90ac5fff libobjc.A.dylib 	/usr/lib/libobjc.A.dylib
0x90aef000 - 0x90b5dfff com.apple.framework.IOKit 1.4 (???)	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x90b74000 - 0x90b86fff libauto.dylib 	/usr/lib/libauto.dylib
0x90b8d000 - 0x90e65fff com.apple.CoreServices.CarbonCore 681.3 (671.2)	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x90ecb000 - 0x90f4bfff com.apple.CoreServices.OSServices 4.1	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
0x90f95000 - 0x90fd6fff com.apple.CFNetwork 129.16	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
0x90feb000 - 0x91003fff com.apple.WebServices 1.1.2 (1.1.0)	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/WebServicesCore.framework/Versions/A/WebServicesCore
0x91013000 - 0x91094fff com.apple.SearchKit 1.0.5	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
0x910da000 - 0x91104fff com.apple.Metadata 10.4.4 (121.36)	/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
0x91115000 - 0x91123fff libz.1.dylib 	/usr/lib/libz.1.dylib
0x91126000 - 0x912e9fff com.apple.security 4.3 (25966)	/System/Library/Frameworks/Security.framework/Versions/A/Security
0x913ec000 - 0x913f5fff com.apple.DiskArbitration 2.1	/System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
0x913fc000 - 0x91423fff com.apple.SystemConfiguration 1.8.2	/System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
0x91436000 - 0x91441fff libgcc_s.1.dylib 	/usr/lib/libgcc_s.1.dylib
0x91446000 - 0x91466fff libmx.A.dylib 	/usr/lib/libmx.A.dylib
0x9146c000 - 0x91474fff libbsm.dylib 	/usr/lib/libbsm.dylib
0x91478000 - 0x914f3fff com.apple.audio.CoreAudio 3.0.3	/System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x91530000 - 0x91530fff com.apple.ApplicationServices 10.4 (???)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x91532000 - 0x9156afff com.apple.AE 1.5 (297)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x91585000 - 0x91652fff com.apple.ColorSync 4.4.4	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
0x916a7000 - 0x91738fff com.apple.print.framework.PrintCore 4.5 (177.10)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0x9177f000 - 0x91836fff com.apple.QD 3.8.20 (???)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
0x91873000 - 0x918d1fff com.apple.HIServices 1.5.1 (???)	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x918ff000 - 0x91923fff com.apple.LangAnalysis 1.6.1	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x91937000 - 0x9195cfff com.apple.FindByContent 1.5	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/FindByContent.framework/Versions/A/FindByContent
0x9196f000 - 0x919b1fff com.apple.LaunchServices 178	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
0x919cd000 - 0x919e1fff com.apple.speech.synthesis.framework 3.3	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
0x919ef000 - 0x91a2efff com.apple.ImageIO.framework 1.4.6	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
0x91a44000 - 0x91b0cfff libcrypto.0.9.7.dylib 	/usr/lib/libcrypto.0.9.7.dylib
0x91b5a000 - 0x91b6ffff libcups.2.dylib 	/usr/lib/libcups.2.dylib
0x91b74000 - 0x91b91fff libJPEG.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
0x91b96000 - 0x91c05fff libJP2.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
0x91c1c000 - 0x91c20fff libGIF.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x91c22000 - 0x91c69fff libRaw.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRaw.dylib
0x91c6e000 - 0x91cabfff libTIFF.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
0x91cb2000 - 0x91ccbfff libPng.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
0x91cd0000 - 0x91cd3fff libRadiance.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
0x91cd5000 - 0x91cd5fff com.apple.Accelerate 1.2.1 (Accelerate 1.2.1)	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
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0x91ec3000 - 0x91f57fff libvDSP.dylib 	/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
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0x93671000 - 0x9367dfff com.apple.opengl 1.4.7	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x93715000 - 0x93715fff com.apple.Cocoa 6.4 (???)	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
0x93717000 - 0x93d49fff com.apple.AppKit 6.4.6 (824.38)	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x940d6000 - 0x94146fff com.apple.CoreData 80	/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
0x9417f000 - 0x94249fff com.apple.audio.toolbox.AudioToolbox 1.4.1	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x9429d000 - 0x9429dfff com.apple.audio.units.AudioUnit 1.3.3	/System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
0x9429f000 - 0x94453fff com.apple.QuartzCore 1.4.7	/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x944a6000 - 0x944e3fff libsqlite3.0.dylib 	/usr/lib/libsqlite3.0.dylib
0x944eb000 - 0x9453bfff libGLImage.dylib 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x946de000 - 0x946edfff libCGATS.A.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
0x946f5000 - 0x94701fff libCSync.A.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
0x94707000 - 0x94726fff libPDFRIP.A.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libPDFRIP.A.dylib
0x94747000 - 0x9475ffff libRIP.A.dylib 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
0x95a79000 - 0x95b05fff com.apple.WebKit 418	/System/Library/Frameworks/WebKit.framework/Versions/A/WebKit
0x95b60000 - 0x95c55fff com.apple.JavaScriptCore 417.11	/System/Library/Frameworks/WebKit.framework/Versions/A/Frameworks/JavaScriptCore.framework/Versions/A/JavaScriptCore
0x95c91000 - 0x95f9bfff com.apple.WebCore 417.24	/System/Library/Frameworks/WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/WebCore
0x96123000 - 0x9614cfff libxslt.1.dylib 	/usr/lib/libxslt.1.dylib
0x9648d000 - 0x9648ffff com.apple.ExceptionHandling 1.2 (???)	/System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
0x9748f000 - 0x974aefff com.apple.vecLib 3.2.1 (vecLib 3.2.1)	/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib

Problem three:
After the first installation of R, the TukeyHSD-Command works proper. Than, after updating to Quicktime 7.1.1 and a crash of R, the TukeyHSD-Command doesn't work anymore. Everytime i've got the message "syntax error". But i do it in the same way like before.



[Rd] 3 Bugs in R (with R.crash.log) under OSX 10.4.6
Nomis101 at web.de