Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to <7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? best, Steve #---------------- Crash log ------------------------ Process: R [231] Path: /Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0xffff07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x00009ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x000076df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x00002538 main + 296 14 org.R-project.R 0x000023d6 start + 54 Thread 1: 0 libSystem.B.dylib 0x9744946e __semwait_signal + 10 1 libSystem.B.dylib 0x97473dcd pthread_cond_wait$UNIX2003 + 73 2 com.apple.JavaScriptCore 0x947e0842 WTF::TCMalloc_PageHeap::scavengerThread() + 578 3 com.apple.JavaScriptCore 0x947e086f WTF::TCMalloc_PageHeap::runScavengerThread(void*) + 15 4 libSystem.B.dylib 0x97473155 _pthread_start + 321 5 libSystem.B.dylib 0x97473012 thread_start + 34 Thread 2: 0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 1 libSystem.B.dylib 0x97449a7c mach_msg + 72 2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 4 com.apple.CFNetwork 0x94d48264 CFURLCacheWorkerThread(void*) + 388 5 libSystem.B.dylib 0x97473155 _pthread_start + 321 6 libSystem.B.dylib 0x97473012 thread_start + 34 Thread 3: 0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 1 libSystem.B.dylib 0x97449a7c mach_msg + 72 2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 4 com.apple.Foundation 0x9447ecad -[NSConnection sendInvocation:internal:] + 3005 5 com.apple.Foundation 0x9447de29 -[NSDistantObject forwardInvocation:] + 329 6 com.apple.CoreFoundation 0x96ab784a ___forwarding___ + 986 7 com.apple.CoreFoundation 0x96ab78b2 _CF_forwarding_prep_0 + 50 8 org.R-project.R 0x0000da65 -[RController readThread:] + 245 9 com.apple.Foundation 0x94447dfd -[NSThread main] + 45 10 com.apple.Foundation 0x944479a4 __NSThread__main__ + 308 11 libSystem.B.dylib 0x97473155 _pthread_start + 321 12 libSystem.B.dylib 0x97473012 thread_start + 34 Thread 0 crashed with X86 Thread State (32-bit): eax: 0x3c706f74 ebx: 0x96a690fe ecx: 0x00000001 edx: 0x00000007 edi: 0x00067ee2 esi: 0xf1c0a03d ebp: 0xbfffe6f8 esp: 0xbfffe6f0 ss: 0x0000001f efl: 0x00010282 eip: 0xffff07c7 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00067ee2 #---------------------------------------------------------------------- -- View this message in context: http://old.nabble.com/R-2.10-memory-leak-on-OS-X-tp26422294p26422294.html Sent from the R help mailing list archive at Nabble.com.
Just a couple of suggestions. One would be to send your question to R-sig-mac. The other would be to try starting R from the command line instead of the gui, and see if the problem occurs in that context. That might provide a little bit of debugging information, and might also let you continue working until the problem is solved. And, two other fairly common OS X suggestions are (1) remove the application's preferences file. Sometimes that clears up weird problems. And (2) temporarily create a new user and run the app as that user. It it works there, you know the problem is with the user's environment, not with the application. Neither of these suggestions is specific to R. -Don At 7:45 PM -0800 11/19/09, Stropharia wrote:>Dear R users, > >I am running R 2.10.0 on OS X 10.5.8. > >I had been running 2.10 successfully for about a week (and have used >previous R versions for 2+ years on the same computer) until 2 days ago it >failed to start up for me. Now when I try to start R, the application tries >to initiate for several minutes then crashes. Looking at the activity >monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to ><7Mb in the first 10-15 seconds of attempting to start the program. At this >point I either have to force quit R (as everything starts to freeze up) or >wait several minutes for it to crash. > >I have erased the application and reinstalled it 4 times now - with exactly >the same result. I looked around in the Library and System folders to see if >any other files needed to be removed, but couldn't find any. I have also >restarted the computer and repaired permissions multiple times - and then >reinstalled R, with no luck. The exact same thing happens if I start R64. > >I did not updated OS X or R, or install any other programs, just prior to >this first happening and am at a loss to explain what's going on. I have >copied the first part of one of the crash logs below. Does anyone have any >ideas for to remedy this? > >best, > >Steve > > >#---------------- Crash log ------------------------ >Process: R [231] >Path: /Applications/R.app/Contents/MacOS/R >Identifier: org.R-project.R >Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) >Code Type: X86 (Native) >Parent Process: launchd [101] > >Date/Time: 2009-11-18 23:15:45.570 -0500 >OS Version: Mac OS X 10.5.8 (9L31a) >Report Version: 6 >Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E > >Exception Type: EXC_BAD_ACCESS (SIGBUS) >Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000067ee2 >Crashed Thread: 0 > >Thread 0 Crashed: >0 libSystem.B.dylib 0xffff07c7 __memcpy + 39 >(cpu_capabilities.h:246) >1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + >4052 >2 com.apple.Foundation 0x94446eb7 >-[NSString(NSStringOtherEncodings) >getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 >3 com.apple.Foundation 0x94446a1a >_NSNewStringByAppendingStrings >+ 538 >4 com.apple.Foundation 0x94446760 -[NSString >stringByAppendingString:] + 192 >5 org.R-project.R 0x00009ce8 -[RController >doLoadHistory:] >+ 808 >6 org.R-project.R 0x000076df -[RController >awakeFromNib] + >2319 >7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet >makeObjectsPerformSelector:] + 181 >8 com.apple.AppKit 0x92efed8e -[NSIBObjectData >nibInstantiateWithOwner:topLevelObjects:] + 1533 >9 com.apple.AppKit 0x92ef4fba loadNib + 264 >10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) >_loadNibFile:nameTable:withZone:ownerBundle:] + 946 >11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) >loadNibFile:externalNameTable:withZone:] + 171 >12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) >loadNibNamed:owner:] + 391 >13 org.R-project.R 0x00002538 main + 296 >14 org.R-project.R 0x000023d6 start + 54 > >Thread 1: >0 libSystem.B.dylib 0x9744946e __semwait_signal + 10 >1 libSystem.B.dylib 0x97473dcd pthread_cond_wait$UNIX2003 + >73 >2 com.apple.JavaScriptCore 0x947e0842 >WTF::TCMalloc_PageHeap::scavengerThread() + 578 >3 com.apple.JavaScriptCore 0x947e086f >WTF::TCMalloc_PageHeap::runScavengerThread(void*) + 15 >4 libSystem.B.dylib 0x97473155 _pthread_start + 321 >5 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 2: >0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 >1 libSystem.B.dylib 0x97449a7c mach_msg + 72 >2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 >3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 >4 com.apple.CFNetwork 0x94d48264 >CFURLCacheWorkerThread(void*) >+ 388 >5 libSystem.B.dylib 0x97473155 _pthread_start + 321 >6 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 3: >0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 >1 libSystem.B.dylib 0x97449a7c mach_msg + 72 >2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 >3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 >4 com.apple.Foundation 0x9447ecad -[NSConnection >sendInvocation:internal:] + 3005 >5 com.apple.Foundation 0x9447de29 -[NSDistantObject >forwardInvocation:] + 329 >6 com.apple.CoreFoundation 0x96ab784a ___forwarding___ + 986 >7 com.apple.CoreFoundation 0x96ab78b2 _CF_forwarding_prep_0 + 50 >8 org.R-project.R 0x0000da65 -[RController readThread:] + >245 >9 com.apple.Foundation 0x94447dfd -[NSThread main] + 45 >10 com.apple.Foundation 0x944479a4 __NSThread__main__ + 308 >11 libSystem.B.dylib 0x97473155 _pthread_start + 321 >12 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x3c706f74 ebx: 0x96a690fe ecx: 0x00000001 edx: 0x00000007 > edi: 0x00067ee2 esi: 0xf1c0a03d ebp: 0xbfffe6f8 esp: 0xbfffe6f0 > ss: 0x0000001f efl: 0x00010282 eip: 0xffff07c7 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > cr2: 0x00067ee2 >#---------------------------------------------------------------------- >-- >View this message in context: >http://*old.nabble.com/R-2.10-memory-leak-on-OS-X-tp26422294p26422294.html >Sent from the R help mailing list archive at Nabble.com. > >______________________________________________ >R-help at r-project.org mailing list >https://*stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- --------------------------------- Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 macq at llnl.gov
At 7:45 PM -0800 11/19/09, Stropharia wrote:>Dear R users, > >I am running R 2.10.0 on OS X 10.5.8. > >I had been running 2.10 successfully for about a week (and have used >previous R versions for 2+ years on the same computer) until 2 days ago it >failed to start up for me. Now when I try to start R, the application tries >to initiate for several minutes then crashes. Looking at the activity >monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to ><7Mb in the first 10-15 seconds of attempting to start the program. At this >point I either have to force quit R (as everything starts to freeze up) or >wait several minutes for it to crash.Try deleting the .Rhistory file which is probably found in your home directory. (This is the help that Bryon Ellis gave me 10 months ago when I had a similar problem.). Bill> >I have erased the application and reinstalled it 4 times now - with exactly >the same result. I looked around in the Library and System folders to see if >any other files needed to be removed, but couldn't find any. I have also >restarted the computer and repaired permissions multiple times - and then >reinstalled R, with no luck. The exact same thing happens if I start R64. > >I did not updated OS X or R, or install any other programs, just prior to >this first happening and am at a loss to explain what's going on. I have >copied the first part of one of the crash logs below. Does anyone have any >ideas for to remedy this? > >best, > >Steve > > >#---------------- Crash log ------------------------ >Process: R [231] >Path: /Applications/R.app/Contents/MacOS/R >Identifier: org.R-project.R >Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) >Code Type: X86 (Native) >Parent Process: launchd [101] > >Date/Time: 2009-11-18 23:15:45.570 -0500 >OS Version: Mac OS X 10.5.8 (9L31a) >Report Version: 6 >Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E > >Exception Type: EXC_BAD_ACCESS (SIGBUS) >Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000067ee2 >Crashed Thread: 0 > >Thread 0 Crashed: >0 libSystem.B.dylib 0xffff07c7 __memcpy + 39 >(cpu_capabilities.h:246) >1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + >4052 >2 com.apple.Foundation 0x94446eb7 >-[NSString(NSStringOtherEncodings) >getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 >3 com.apple.Foundation 0x94446a1a >_NSNewStringByAppendingStrings >+ 538 >4 com.apple.Foundation 0x94446760 -[NSString >stringByAppendingString:] + 192 >5 org.R-project.R 0x00009ce8 -[RController >doLoadHistory:] >+ 808 >6 org.R-project.R 0x000076df -[RController >awakeFromNib] + >2319 >7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet >makeObjectsPerformSelector:] + 181 >8 com.apple.AppKit 0x92efed8e -[NSIBObjectData >nibInstantiateWithOwner:topLevelObjects:] + 1533 >9 com.apple.AppKit 0x92ef4fba loadNib + 264 >10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) >_loadNibFile:nameTable:withZone:ownerBundle:] + 946 >11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) >loadNibFile:externalNameTable:withZone:] + 171 >12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) >loadNibNamed:owner:] + 391 >13 org.R-project.R 0x00002538 main + 296 >14 org.R-project.R 0x000023d6 start + 54 > >Thread 1: >0 libSystem.B.dylib 0x9744946e __semwait_signal + 10 >1 libSystem.B.dylib 0x97473dcd pthread_cond_wait$UNIX2003 + >73 >2 com.apple.JavaScriptCore 0x947e0842 >WTF::TCMalloc_PageHeap::scavengerThread() + 578 >3 com.apple.JavaScriptCore 0x947e086f >WTF::TCMalloc_PageHeap::runScavengerThread(void*) + 15 >4 libSystem.B.dylib 0x97473155 _pthread_start + 321 >5 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 2: >0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 >1 libSystem.B.dylib 0x97449a7c mach_msg + 72 >2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 >3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 >4 com.apple.CFNetwork 0x94d48264 >CFURLCacheWorkerThread(void*) >+ 388 >5 libSystem.B.dylib 0x97473155 _pthread_start + 321 >6 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 3: >0 libSystem.B.dylib 0x97442286 mach_msg_trap + 10 >1 libSystem.B.dylib 0x97449a7c mach_msg + 72 >2 com.apple.CoreFoundation 0x96a37e7e CFRunLoopRunSpecific + 1790 >3 com.apple.CoreFoundation 0x96a38aa8 CFRunLoopRunInMode + 88 >4 com.apple.Foundation 0x9447ecad -[NSConnection >sendInvocation:internal:] + 3005 >5 com.apple.Foundation 0x9447de29 -[NSDistantObject >forwardInvocation:] + 329 >6 com.apple.CoreFoundation 0x96ab784a ___forwarding___ + 986 >7 com.apple.CoreFoundation 0x96ab78b2 _CF_forwarding_prep_0 + 50 >8 org.R-project.R 0x0000da65 -[RController readThread:] + >245 >9 com.apple.Foundation 0x94447dfd -[NSThread main] + 45 >10 com.apple.Foundation 0x944479a4 __NSThread__main__ + 308 >11 libSystem.B.dylib 0x97473155 _pthread_start + 321 >12 libSystem.B.dylib 0x97473012 thread_start + 34 > >Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x3c706f74 ebx: 0x96a690fe ecx: 0x00000001 edx: 0x00000007 > edi: 0x00067ee2 esi: 0xf1c0a03d ebp: 0xbfffe6f8 esp: 0xbfffe6f0 > ss: 0x0000001f efl: 0x00010282 eip: 0xffff07c7 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > cr2: 0x00067ee2 >#---------------------------------------------------------------------- >-- >View this message in context: >http://old.nabble.com/R-2.10-memory-leak-on-OS-X-tp26422294p26422294.html >Sent from the R help mailing list archive at Nabble.com. > >______________________________________________ >R-help at r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r It is 5 minutes to midnight http://www.thebulletin.org