[R-SIG-Mac] R GUI crashes after installing R-2.7.0 packages from source

Simon Urbanek simon.urbanek at r-project.org
Wed Apr 23 13:55:29 CEST 2008 

On Apr 23, 2008, at 6:08 AM, Gerald Jurasinski wrote:

> Dear List, I repost the following, because I need to run R.app  
> again. But I don't know where to look first (Already made a fresh  
> install)
>

delete your history (~/.Rhistory), that should allow you to use R.app  
again. It seems as if your history contains entries in in different  
encodings and hence fails to load (ungracefully). Fix should follow  
soon.

Cheers,
S


> Dear List,
>
> Last Friday I installed the 2.7.0 developmental leopard builds from http://r.research.att.com/
> And accordingly the newest GUI. Everything went fine. However, than I
> realized that I have to build the packages from source.
> I installed the additional tools from Simons website. Subsequently I
> used the GUI feature "install packages" and checked "from source" to
> install my desired packages. The installing process went along. I
> tested two or three packages, they were running - Fine.
>
> But than, after I closed R and wanted to restart, it crashed on start-
> up. When I wanted to copy the crash report, it crashed the whole  
> system.
> Restart. Tried to start R.gui. Crashed again. Tried to start from the
> terminal. It worked. However, I am used to the gui. I like it a lot.
> After some fiddling around and some more crashes I decided, to let
> experimental R go. Maybe I was too eager to get R 2.7.0 and the new
> quartz-gui? (I am only an intersted user) I removed R completely  
> from my system and installed the
> standard R-2.6.2 from CRAN. However, it still crashes when I try to
> start R.app (I installed the newest GUI version from http://r.research.att.com/though)
> Maybe i did something wrong with gfortran?? Or with some other of the
> installations from the tools website??
>
> A hint is greatly appreciated.
>
> My machine:
>  Model:	MacBook Pro
>  Model-Identification:	MacBookPro3,1
>  CPU:	Intel Core 2 Duo
>  CPU speed:	2.2 GHz
>  L2-Cache:	4 MB
>  Speicher:	2 GB
>  Busgeschwindigkeit:	800 MHz
>  Boot-ROM-Version:	MBP31.0070.B05
>  SMC Version:	1.16f10
>
> My system:
>  System version:	Mac OS X 10.5.2 (9C7010)
>  Kernel-Version:	Darwin 9.2.2
>
> Crash Log:
> Process:         R [1047]
> Path:            /Users/juri/Desktop/_statistics/R.app/Contents/ 
> MacOS/R
> Identifier:      org.R-project.R
> Version:         R GUI 1.24-devel (5041)
> Code Type:       X86 (Native)
> Parent Process:  launchd [178]
>
> Date/Time:       2008-04-21 10:04:51.391 +0200
> OS Version:      Mac OS X 10.5.2 (9C7010)
> Report Version:  6
>
> Exception Type:  EXC_BAD_ACCESS (SIGBUS)
> Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000
> Crashed Thread:  0
>
> Thread 0 Crashed:
> 0   libSystem.B.dylib             	0xffff132f __longcopy + 303
> 1   libSystem.B.dylib             	0xffff086e __memcpy + 206
> 2   com.apple.CoreFoundation      	0x95a1745b
> _CFStringCheckAndGetCharacters + 187
> 3   com.apple.Foundation          	0x91664233 -[NSCFString
> getCharacters:range:] + 67
> 4   com.apple.Foundation          	0x91669424
> _NSNewStringByAppendingStrings + 1044
> 5   com.apple.Foundation          	0x91668f70 -[NSString
> stringByAppendingString:] + 192
> 6   org.R-project.R               	0x00007a24 -[RController
> doLoadHistory:] + 851 (RController.m:1352)
> 7   org.R-project.R               	0x000040a7 -[RController
> awakeFromNib] + 2245 (RController.m:497)
> 8   com.apple.CoreFoundation      	0x95a87a55 -[NSSet
> makeObjectsPerformSelector:] + 181
> 9   com.apple.AppKit              	0x9416eec2 -[NSIBObjectData
> nibInstantiateWithOwner:topLevelObjects:] + 1533
> 10  com.apple.AppKit              	0x941650ec loadNib + 264
> 11  com.apple.AppKit              	0x94164a4d +[NSBundle(NSNibLoading)
> _loadNibFile:nameTable:withZone:ownerBundle:] + 946
> 12  com.apple.AppKit              	0x94164690 +[NSBundle(NSNibLoading)
> loadNibFile:externalNameTable:withZone:] + 171
> 13  com.apple.AppKit              	0x941645ce +[NSBundle(NSNibLoading)
> loadNibNamed:owner:] + 391
> 14  org.R-project.R               	0x00002d50 main + 298 (main.m:65)
> 15  org.R-project.R               	0x00002c0a _start + 216
> 16  org.R-project.R               	0x00002b31 start + 41
>
> Thread 1:
> 0   libSystem.B.dylib             	0x9337b9e6 mach_msg_trap + 10
> 1   libSystem.B.dylib             	0x933831dc mach_msg + 72
> 2   com.apple.CoreFoundation      	0x959ff0de CFRunLoopRunSpecific +
> 1806
> 3   com.apple.CoreFoundation      	0x959ffd18 CFRunLoopRunInMode + 88
> 4   com.apple.CFNetwork           	0x90b566cc
> CFURLCacheWorkerThread(void*) + 396
> 5   libSystem.B.dylib             	0x933acc55 _pthread_start + 321
> 6   libSystem.B.dylib             	0x933acb12 thread_start + 34
>
> Thread 2:
> 0   libSystem.B.dylib             	0x9337b9e6 mach_msg_trap + 10
> 1   libSystem.B.dylib             	0x933831dc mach_msg + 72
> 2   com.apple.CoreFoundation      	0x959ff0de CFRunLoopRunSpecific +
> 1806
> 3   com.apple.CoreFoundation      	0x959ffd18 CFRunLoopRunInMode + 88
> 4   com.apple.Foundation          	0x916a13ed -[NSConnection
> sendInvocation:internal:] + 3005
> 5   com.apple.Foundation          	0x916a0569 -[NSDistantObject
> forwardInvocation:] + 329
> 6   com.apple.CoreFoundation      	0x95a7eaaa ___forwarding___ + 986
> 7   com.apple.CoreFoundation      	0x95a7eb12 _CF_forwarding_prep_0  
> + 50
> 8   org.R-project.R               	0x00004d46 -[RController
> readThread:] + 250 (RController.m:599)
> 9   com.apple.Foundation          	0x9166a5ad -[NSThread main] + 45
> 10  com.apple.Foundation          	0x9166a154 __NSThread__main__ + 308
> 11  libSystem.B.dylib             	0x933acc55 _pthread_start + 321
> 12  libSystem.B.dylib             	0x933acb12 thread_start + 34
>
> Thread 0 crashed with X86 Thread State (32-bit):
>  eax: 0x00040000  ebx: 0x00000070  ecx: 0x000d607e  edx: 0xfffc0000
>  edi: 0x00040000  esi: 0xffc2b000  ebp: 0xbfffec5c  esp: 0xbfffec50
>   ss: 0x0000001f  efl: 0x00010246  eip: 0xffff132f   cs: 0x00000017
>   ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
>  cr2: 0x00000000
>
> Binary Images:
>    0x1000 -    0x40fe3 +org.R-project.R R GUI 1.24-devel (5041)
> <f2da233bbf2e43ceaaa645d5a7a86333> /Users/juri/Desktop/_statistics/
> R.app/Contents/MacOS/R
>  0x1a5000 -   0x1a7fff  com.apple.ExceptionHandling 1.5 (10) /System/
> Library/Frameworks/ExceptionHandling.framework/Versions/A/
> ExceptionHandling
>  0x1ae000 -   0x1af7e4 +libRblas.dylib ??? (???)
> <5f6f8bca6ef245f4be68d4698af55518> /Library/Frameworks/R.framework/
> Versions/2.6/Resources/lib/libRblas.dylib
>  0x1b4000 -   0x1bbfed +libgcc_s.1.dylib ??? (???) /Library/
> Frameworks/R.framework/Versions/2.6/Resources/lib/libgcc_s.1.dylib
>  0x1de000 -   0x204fff +libreadline.5.2.dylib ??? (???) /Library/
> Frameworks/R.framework/Versions/2.6/Resources/lib/libreadline. 
> 5.2.dylib
>  0x2f4000 -   0x50c04d +libR.dylib ??? (???)
> <802714feef234f589fabd136dacd0dcc> /Library/Frameworks/R.framework/
> Versions/2.6/Resources/lib/libR.dylib
>  0x5e8000 -   0x673fff +libgfortran.2.dylib ??? (???) /Library/
> Frameworks/R.framework/Versions/2.6/Resources/lib/libgfortran.2.dylib
>  0xe82000 -   0xf8cfef  com.apple.RawCamera.bundle 2.0.4 (2.0.4) /
> System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
> 0x8fe00000 - 0x8fe2da53  dyld 96.2 (???)
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> 0x90003000 - 0x9008cfe3  com.apple.DesktopServices 1.4.5 (1.4.5)
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> 0x9024d000 - 0x9024dfff  com.apple.Carbon 136 (136)
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> Versions/A/libvMisc.dylib
> 0x958f2000 - 0x9597eff7  com.apple.LaunchServices 286.5 (286.5)
> <33c3ae54abb276b61a99d4c764d883e2> /System/Library/Frameworks/
> CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/
> Versions/A/LaunchServices
> 0x9597f000 - 0x9598bfe7  com.apple.opengl 1.5.6 (1.5.6)
> <d599b1bb0f8a8da6fd125e2587b27776> /System/Library/Frameworks/
> OpenGL.framework/Versions/A/OpenGL
> 0x9598c000 - 0x9598cffd  com.apple.Accelerate 1.4.2 (Accelerate
> 1.4.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/
> Accelerate
> 0x9598d000 - 0x95abffef  com.apple.CoreFoundation 6.5.1 (476.10)
> <d5bed2688a5eea11a6dc3a3c5c17030e> /System/Library/Frameworks/
> CoreFoundation.framework/Versions/A/CoreFoundation
> 0x95b3e000 - 0x95c23ff3  com.apple.CoreData 100.1 (186)
> <8e28162ef2288692615b52acc01f8b54> /System/Library/Frameworks/
> CoreData.framework/Versions/A/CoreData
> 0x95c24000 - 0x95c44ff2  libGL.dylib ??? (???) /System/Library/
> Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
> 0x95c45000 - 0x95d39ff4  libiconv.2.dylib ??? (???)
> <c508c60fafca17824c0017b2e4369802> /usr/lib/libiconv.2.dylib
> 0x95d6c000 - 0x95d87ffb  libPng.dylib ??? (???)
> <b6abcac36ec7654ff3e1cfa786b0117b> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
> Versions/A/Resources/libPng.dylib
> 0x95dad000 - 0x963fdfff  com.apple.WebCore 5525.13 (5525.13)
> <c4293b0cc1f8614190058683137459c6> /System/Library/Frameworks/
> WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/
> WebCore
> 0x963fe000 - 0x963feffd  com.apple.vecLib 3.4.2 (vecLib 3.4.2) / 
> System/
> Library/Frameworks/vecLib.framework/Versions/A/vecLib
> 0x963ff000 - 0x96401ff5  libRadiance.dylib ??? (???)
> <20eadb285da83df96c795c2c5fa20590> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
> Versions/A/Resources/libRadiance.dylib
> 0x96402000 - 0x964d0ff7  com.apple.JavaScriptCore 5525.13 (5525.13)
> <04772ff1212d98f31c613dde4d123698> /System/Library/Frameworks/
> JavaScriptCore.framework/Versions/A/JavaScriptCore
> 0x964d1000 - 0x96500ff7  libncurses.5.4.dylib ??? (???)
> <3b2ac2ca8190942b6b81d2a7012ea859> /usr/lib/libncurses.5.4.dylib
> 0x96501000 - 0x96506fff  com.apple.CommonPanels 1.2.4 (85)
> <ea0665f57cd267609466ed8b2b20e893> /System/Library/Frameworks/
> Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/ 
> Versions/
> A/CommonPanels
> 0x96525000 - 0x9654dfff  libcups.2.dylib ??? (???)
> <2f0a710a9128882efb2ed92ad139b58c> /usr/lib/libcups.2.dylib
> 0x9654e000 - 0x965fefff  edu.mit.Kerberos 6.0.12 (6.0.12)
> <3dd13466876a8fe4549cfc1354233ec3> /System/Library/Frameworks/
> Kerberos.framework/Versions/A/Kerberos
> 0x96868000 - 0x96868ff8  com.apple.Cocoa 6.5 (???)
> <e064f94d969ce25cb7de3cfb980c3249> /System/Library/Frameworks/
> Cocoa.framework/Versions/A/Cocoa
> 0x96869000 - 0x968fcfff  com.apple.ink.framework 101.3 (86)
> <bf3fa8927b4b8baae92381a976fd2079> /System/Library/Frameworks/
> Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
> 0x969bb000 - 0x96a15ff7  com.apple.CoreText 2.0.1 (???)
> <07494945ad1e3f5395599f42748457cc> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/ 
> CoreText.framework/
> Versions/A/CoreText
> 0x96b4e000 - 0x96b5efff  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
> 0x96b5f000 - 0x96b66ff7  libCGATS.A.dylib ??? (???)
> <9b29a5500efe01cc3adea67bbc42568e> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/
> CoreGraphics.framework/Versions/A/Resources/libCGATS.A.dylib
> 0x96b67000 - 0x96c21fe3  com.apple.CoreServices.OSServices 224.4
> (224.4) <ff5007ab220908ac54b6c661e447d593> /System/Library/Frameworks/
> CoreServices.framework/Versions/A/Frameworks/OSServices.framework/
> Versions/A/OSServices
> 0x96d80000 - 0x96d9fffa  libJPEG.dylib ??? (???)
> <0cfb80109d624beb9ceb3c43b6c5ec10> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
> Versions/A/Resources/libJPEG.dylib
> 0x96da0000 - 0x96da4fff  libmathCommon.A.dylib ??? (???) /usr/lib/
> system/libmathCommon.A.dylib
> 0x96dce000 - 0x96e8bfff  com.apple.WebKit 5525.13 (5525.13)
> <6534b17c7310ea608c9f3ca41df9b4a4> /System/Library/Frameworks/
> WebKit.framework/Versions/A/WebKit
> 0x96e8c000 - 0x96fb0fe3  com.apple.audio.toolbox.AudioToolbox 1.5.1
> (1.5.1) /System/Library/Frameworks/AudioToolbox.framework/Versions/A/
> AudioToolbox
> 0x97130000 - 0x97136fff  com.apple.print.framework.Print 218.0.2
> (220.1) <8bf7ef71216376d12fcd5ec17e43742c> /System/Library/Frameworks/
> Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/ 
> Print
> 0x97137000 - 0x97142fe7  libCSync.A.dylib ??? (???)
> <df82fc093e498a9eb5490761cb292218> /System/Library/Frameworks/
> ApplicationServices.framework/Versions/A/Frameworks/
> CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib
> 0x9714f000 - 0x97156ffe  libbsm.dylib ??? (???)
> <d25c63378a5029648ffd4b4669be31bf> /usr/lib/libbsm.dylib
> 0x97157000 - 0x97186fe3  com.apple.AE 402.2 (402.2)
> <e01596187e91af5d48653920017b8c8e> /System/Library/Frameworks/
> CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/ 
> AE
> 0x9719b000 - 0x971a2fe9  libgcc_s.1.dylib ??? (???)
> <f53c808e87d1184c0f9df63aef53ce0b> /usr/lib/libgcc_s.1.dylib
> 0xfffe8000 - 0xfffebfff  libobjc.A.dylib ??? (???) /usr/lib/
> libobjc.A.dylib
> 0xffff0000 - 0xffff1780  libSystem.B.dylib ??? (???) /usr/lib/
> libSystem.B.dylib
>
> ——————————————————
>
> Dr. Gerald Jurasinski
> Landscape Ecology and Land Evaluation
> Institute Management of Rural Areas
> Faculty of Agricultural and Environmental Sciences
> University of Rostock
> Justus-von-Liebig-Weg 6
> 18059 Rostock
> Germany
>
> gerald.jurasinski at uni-rostock.de
> http://www.auf.uni-rostock.de/loe
> +49 381 4983225 (tel)
> +49 381 4983222 (fax)
>
> ——————————————————
>
> gerald jurasinski
> fahnenstraße 8
> 18057 rostock
> terhorab at mac.com
> +49 381 8774550
>
>

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