[R-SIG-Mac] [R] R 2.10 memory leak on OS X
Rob Goedman
robjgoedman at me.com
Fri Nov 20 05:46:34 CET 2009
Steve,
Do you have a .Rhistory and/or a .Rdata file in your home/working dirs?
If so, can you rename them temporarily and restart R again?
Or you can send me your ~/Library/Preferences/org.R-project.R.plist file.
Regards,
Rob
On Nov 19, 2009, at 7:45 PM, 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
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>
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