[R] R 2.10 memory leak on OS X

Don MacQueen macq at llnl.gov
Fri Nov 20 05:01:01 CET 2009


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
>#----------------------------------------------------------------------
>--
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>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.
>
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>and provide commented, minimal, self-contained, reproducible code.


-- 
---------------------------------
Don MacQueen
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
macq at llnl.gov




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