On Thu, 6 Nov 2008, Steve Lianoglou wrote:
Hi,
Early last week, I installed the 64-bit leopard build for R provided here:
http://r.research.att.com/
I've realized that when R.app is running in the background (and sitting
idle), it eventually beach-balls. When I switch over to see what's happening,
I see that R is crashed, and it's giving me options to:
* abort
* save workspace then abort
* 1 or 2 others
Sorry, I didn't copy the issue down exactly because I hastily quit it and
reinstalled R 2.7.2 to get back to work. I'm not sure if it's R itself, or
the R.app GUI ... I can mess around w/ it a bit later next week once I get
passed some deadlines.
I wonder if it's the R.app gui that's the problem, and not R itself. I'm
running R 2.8 via the terminal now to see if it eventually
hangs/core-dumps/whatever.
That is the behaviour of R's segfault handler, but from the log it looks
like code in R.app caused it running in a callback from R itself.
Are other people working with 64-bit R/R.apphaving these issues? Is the best
path to using 64-bit R via custom compilation? Maybe ignore R.app for now?
What are you folks doing?
I only use 64-bit command-line R and my own compilation of R. The latter
seems pretty much rock-solid.
Thanks,
-steve
Crash log:
Process: R [3009]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 2.8.0 GUI 1.26 (5256)
Code Type: X86-64 (Native)
Parent Process: launchd [171]
Date/Time: 2008-11-05 17:18:21.279 -0500
OS Version: Mac OS X 10.5.5 (9F33)
Report Version: 6
Exception Type: EXC_CRASH (SIGSEGV)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 1
Thread 0:
0 libSystem.B.dylib 0x00007fffffe01259 __longcopy + 89
1 libSystem.B.dylib 0x00007fffffe00882 __memcpy + 226
2 com.apple.security 0x00007fff83612bea
Security::NameValuePair::CloneData(Security::CssmData const&) + 60
3 com.apple.security 0x00007fff83612d2a
Security::NameValuePair::NameValuePair(Security::CssmData const&) + 108
4 com.apple.security 0x00007fff83612e94
Security::NameValueDictionary::NameValueDictionary(Security::CssmData const&)
+ 136
5 com.apple.security 0x00007fff8352436d
Security::KeychainCore::CCallbackMgr::consume(unsigned int, unsigned int,
Security::CssmData const&) + 41
6 com.apple.security 0x00007fff8360985a
Security::SecurityServer::NotificationPort::receive(Security::MachPlusPlus::Message
const&) + 360
7 com.apple.security 0x00007fff83627767
Security::MachPlusPlus::CFAutoPort::cfCallback(__CFMachPort*, void*, long,
void*) + 49
8 com.apple.CoreFoundation 0x00007fff83301a87
__CFMachPortPerform + 119
9 com.apple.CoreFoundation 0x00007fff833233cc
CFRunLoopRunSpecific + 3516
10 com.apple.HIToolbox 0x00007fff816eeea2
RunCurrentEventLoopInMode + 278
11 com.apple.HIToolbox 0x00007fff816eecd8
ReceiveNextEventCommon + 322
12 com.apple.HIToolbox 0x00007fff816eeb83
BlockUntilNextEventMatchingListInMode + 79
13 com.apple.AppKit 0x00007fff83d94c44 _DPSNextEvent +
603
14 com.apple.AppKit 0x00007fff83d94583 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 136
15 org.R-project.R 0x00000001000077d6 -[RController
doProcessEvents:] + 182
16 org.R-project.R 0x00000001000049f0 -[RController
handleReadConsole:] + 144
17 org.R-project.R 0x000000010000dd61 Re_ReadConsole +
449
18 org.R-project.R 0x0000000100019260
run_REngineRmainloop + 896
19 org.R-project.R 0x00000001000109e7 -[REngine runREPL]
+ 119
20 org.R-project.R 0x0000000100001f99 main + 729
21 org.R-project.R 0x0000000100001c94 start + 52
Thread 1 Crashed:
0 libSystem.B.dylib 0x00007fff810c75f6 mach_msg_trap + 10
1 libSystem.B.dylib 0x00007fff810cec2f mach_msg + 59
2 com.apple.CoreFoundation 0x00007fff83322c6f
CFRunLoopRunSpecific + 1631
3 com.apple.CFNetwork 0x00007fff828f7fa3
CFURLCacheWorkerThread(void*) + 321
4 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
5 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 2:
0 libSystem.B.dylib 0x00007fff811135c6
select$DARWIN_EXTSN + 10
1 com.apple.Foundation 0x00007fff8011ee25 __NSThread__main__
+ 1157
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 3:
0 libSystem.B.dylib 0x00007fff810c7656
semaphore_timedwait_signal_trap + 10
1 libSystem.B.dylib 0x00007fff810f66ce _pthread_cond_wait
+ 1207
2 com.apple.Foundation 0x00007fff801621e4 -[NSCondition
waitUntilDate:] + 228
3 com.apple.Foundation 0x00007fff80162012 -[NSConditionLock
lockWhenCondition:beforeDate:] + 130
4 com.apple.AppKit 0x00007fff83dfcb7d -[NSUIHeartBeat
_heartBeatThread:] + 417
5 com.apple.Foundation 0x00007fff8011ee25 __NSThread__main__
+ 1157
6 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
7 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 4:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 5:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 6:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 7:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 8:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 9:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 10:
0 libSystem.B.dylib 0x00007fff810ce5be __semwait_signal +
10
1 com.apple.QuartzCore 0x00007fff80548a5d fe_fragment_thread
+ 54
2 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
3 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 11:
0 libSystem.B.dylib 0x00007fff810c75f6 mach_msg_trap + 10
1 libSystem.B.dylib 0x00007fff810cec2f mach_msg + 59
2 com.apple.CoreFoundation 0x00007fff83322c6f
CFRunLoopRunSpecific + 1631
3 com.apple.Foundation 0x00007fff8017e440
+[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 288
4 com.apple.Foundation 0x00007fff8011ee25 __NSThread__main__
+ 1157
5 libSystem.B.dylib 0x00007fff810f5913 _pthread_start +
316
6 libSystem.B.dylib 0x00007fff810f57d5 thread_start + 13
Thread 1 crashed with X86 Thread State (64-bit):
rax: 0x0000000010004005 rbx: 0x0000000000000000 rcx: 0x0000000113945918
rdx: 0x0000000000000000
rdi: 0x0000000113945a10 rsi: 0x0000000003000006 rbp: 0x0000000113945970
rsp: 0x0000000113945918
r8: 0x0000000000003603 r9: 0x0000000000000000 r10: 0x0000000000000450
r11: 0x0000000000000202
r12: 0x0000000000003603 r13: 0x0000000000000450 r14: 0x0000000113945a10
r15: 0x0000000003000006
rip: 0x00007fff810c75f6 rfl: 0x0000000000000202 cr2: 0x000000007bb0b000
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<cc8eece8c0097b254c758bd4e8df9537> /usr/lib/libauto.dylib
0x7fff82ae2000 - 0x7fff82ae2fff com.apple.Carbon 136 (136)
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/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
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(2.2.1) <e75fe224700767869227cc903bef8ed9>
/System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
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<86be7909f46cc044a887cbb60ab7826d>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
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(2.0.4) <47dcdc0b5986b2c157e0b6dae48ce464>
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5.5.3 (245.3) <bffd62913cdf70462983c58b27be7a07>
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/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
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<4257ab268996bbeb93b47946df181cdc>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
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<d53437c1faeb42624f1d71202caa9cad>
/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
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/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
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<08b6a34eb05414f6d173b2deafbadf76> /usr/lib/libxml2.2.dylib
0x7fff82f58000 - 0x7fff82fbbfef libGLU.dylib ??? (???)
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
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786.6 (786.6) <7048aee00133f19029108600e9ede844>
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
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(Accelerate 1.4.2)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
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(476.15) <4b970007410b71eca926819f3959548f>
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0x7fff834e6000 - 0x7fff834f4ff9 com.apple.helpdata 1.0.1 (14.2)
/System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
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<8f5631ff238ad1bad2e031fe5e7442d2>
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<0674c4e3353c677c9f58df3297ae559b>
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x7fff8371d000 - 0x7fff83762fef libRIP.A.dylib ??? (???)
<10b9428084c1632994eb4f3d686f99a9>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
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/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
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(vecLib 3.4.2)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff83829000 - 0x7fff83d49fc6 libGLProgrammability.dylib ??? (???)
<cab03de441b8787bc90c5199ec79ce2b>
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff83d4a000 - 0x7fff83d54fff
com.apple.speech.recognition.framework 3.7.24 (3.7.24)
<a49d89814bff9aff6d477c00e426e158>
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
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<c750765812bf8e2dfdce523e1e13d5cb>
/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x7fff8467e000 - 0x7fff846f2fe7 libstdc++.6.dylib ??? (???)
<379a6a2dc6e21ba77310b3d2d9ea30ac> /usr/lib/libstdc++.6.dylib
0x7fff846f3000 - 0x7fff84736fef com.apple.QD 3.11.54 (???)
<cac2d6ee11c5db967bdf180747256122>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
0x7fff84737000 - 0x7fff84755fff libPng.dylib ??? (???)
<4017eab74319a648dfd73b7d503e557d>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
0x7fff84756000 - 0x7fff84780fff libcups.2.dylib ??? (???)
<b548bfb490ecbb8543a6992d592aa876> /usr/lib/libcups.2.dylib
0x7fff84781000 - 0x7fff847d5fe3 com.apple.HIServices 1.7.0 (???)
<ab682a94bbb2418c772570a5f5e13849>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
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/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x7fffffe00000 - 0x7fffffe01780 libSystem.B.dylib ??? (???)
/usr/lib/libSystem.B.dylib
0xfffffffffffec000 - 0xfffffffffffeffff libobjc.A.dylib ??? (???)
/usr/lib/libobjc.A.dylib
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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