[R-SIG-Mac] 64-bit build of R crashes while idle
Steve Lianoglou
mailinglist.honeypot at gmail.com
Thu Nov 6 17:25:42 CET 2008
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.
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?
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
Binary Images:
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(32) <f1ae7e34fb008524b502ed0185b32794> /System/Library/Frameworks/
CoreServices.framework/Versions/A/CoreServices
0x7fff82a5e000 - 0x7fff82aaefe7 com.apple.Metadata 10.5.2
(398.22) <1fc60b4568a7ffbec4273f656d61ab58> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/Metadata.framework/
Versions/A/Metadata
0x7fff82aaf000 - 0x7fff82ae1ff7 libauto.dylib ??? (???)
<cc8eece8c0097b254c758bd4e8df9537> /usr/lib/libauto.dylib
0x7fff82ae2000 - 0x7fff82ae2fff com.apple.Carbon 136 (136)
<256825542105f42e564bafddb77b6a8b> /System/Library/Frameworks/
Carbon.framework/Versions/A/Carbon
0x7fff82ae3000 - 0x7fff82be6feb com.apple.CoreData 100.1
(186) <074abc7f43f81f7885e4d0674a8be4bc> /System/Library/Frameworks/
CoreData.framework/Versions/A/CoreData
0x7fff82be7000 - 0x7fff82bedfff com.apple.DiskArbitration
2.2.1 (2.2.1) <e75fe224700767869227cc903bef8ed9> /System/Library/
Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
0x7fff82bee000 - 0x7fff82c31fef libTIFF.dylib ??? (???)
<86be7909f46cc044a887cbb60ab7826d> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libTIFF.dylib
0x7fff82c32000 - 0x7fff82d6efe9 com.apple.ImageIO.framework
2.0.4 (2.0.4) <47dcdc0b5986b2c157e0b6dae48ce464> /System/Library/
Frameworks/ApplicationServices.framework/Versions/A/Frameworks/
ImageIO.framework/Versions/A/ImageIO
0x7fff82d6f000 - 0x7fff82daefef com.apple.framework.IOKit
1.5.1 (???) <56d5528f3623ad4d9c68751018e658c3> /System/Library/
Frameworks/IOKit.framework/Versions/A/IOKit
0x7fff82daf000 - 0x7fff82db1fff
com.apple.print.framework.Print 218.0.2 (220.1)
<2b847a0a1cd885f596a4d10409d50ba3> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x7fff82db2000 - 0x7fff82e21ff9
com.apple.print.framework.PrintCore 5.5.3 (245.3)
<bffd62913cdf70462983c58b27be7a07> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
PrintCore.framework/Versions/A/PrintCore
0x7fff82e22000 - 0x7fff82e22ff8
com.apple.ApplicationServices 34 (34)
<29a6f07deb1ef821735e2c18ef1e9fa5> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/ApplicationServices
0x7fff82e23000 - 0x7fff82e45fff libJPEG.dylib ??? (???)
<4257ab268996bbeb93b47946df181cdc> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libJPEG.dylib
0x7fff82e46000 - 0x7fff82e46ff8 com.apple.Cocoa 6.5 (???)
<d53437c1faeb42624f1d71202caa9cad> /System/Library/Frameworks/
Cocoa.framework/Versions/A/Cocoa
0x7fff82e47000 - 0x7fff82e4affb com.apple.help 1.1 (36)
<625c2d6bb29ee822f9dce6322d08df47> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x7fff82e4b000 - 0x7fff82e4ffff libGIF.dylib ??? (???)
<66436b84211fe0e723051eab15af0aca> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/Resources/libGIF.dylib
0x7fff82e50000 - 0x7fff82e61fff
com.apple.speech.synthesis.framework 3.7.1 (3.7.1)
<7b000af113e7f602b9e0b1fd383005fc> /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/
SpeechSynthesis.framework/Versions/A/SpeechSynthesis
0x7fff82e62000 - 0x7fff82f57fff libxml2.2.dylib ??? (???)
<08b6a34eb05414f6d173b2deafbadf76> /usr/lib/libxml2.2.dylib
0x7fff82f58000 - 0x7fff82fbbfef libGLU.dylib ??? (???) /
System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
libGLU.dylib
0x7fff82fbc000 - 0x7fff832b7fe3
com.apple.CoreServices.CarbonCore 786.6 (786.6)
<7048aee00133f19029108600e9ede844> /System/Library/Frameworks/
CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/
Versions/A/CarbonCore
0x7fff832b8000 - 0x7fff832b8ffd com.apple.Accelerate 1.4.2
(Accelerate 1.4.2) /System/Library/Frameworks/Accelerate.framework/
Versions/A/Accelerate
0x7fff832b9000 - 0x7fff833f0fff com.apple.CoreFoundation
6.5.4 (476.15) <4b970007410b71eca926819f3959548f> /System/Library/
Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff833f1000 - 0x7fff834e5fff libobjc.A.dylib ??? (???)
<118dc1ae05e685ad64290352fc94f1f0> /usr/lib/libobjc.A.dylib
0x7fff834e6000 - 0x7fff834f4ff9 com.apple.helpdata 1.0.1
(14.2) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/
HelpData
0x7fff834f5000 - 0x7fff834fafff com.apple.CommonPanels 1.2.4
(85) <8f5631ff238ad1bad2e031fe5e7442d2> /System/Library/Frameworks/
Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/
A/CommonPanels
0x7fff834fb000 - 0x7fff83701ffb com.apple.security 5.0.4
(34102) <18f1b986b1c5c26b98da0c096b29f559> /System/Library/Frameworks/
Security.framework/Versions/A/Security
0x7fff83702000 - 0x7fff8371cfff com.apple.openscripting
1.2.8 (???) <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
0x7fff83763000 - 0x7fff83827fe2 com.apple.vImage 3.0 (3.0) /
System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vImage.framework/Versions/A/vImage
0x7fff83828000 - 0x7fff83828ffd com.apple.Accelerate.vecLib
3.4.2 (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
0x7fff83d55000 - 0x7fff8467dfef com.apple.AppKit 6.5.3
(949.34) <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
0x7fff847d6000 - 0x7fff847d9fff com.apple.securityhi 3.0
(30817) <d7c8cb3ade97482c5dbe4f68b32396cd> /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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