[R-SIG-Mac] [R] R 2.10 'memory leak'? on OS X

Fri Nov 20 18:15:20 CET 2009

Steve,

They are not always in the same place, this depends on the settings in your 'Startup'  preferences. The preferences are saved in below plist file, hence I requested to send that file (or you can double click the file and it will open in the Property List Editor). Based on the info in that file it is possible to find out where the files are stored
and temporarily rename them in a Terminal.

Rob

On Nov 19, 2009, at 8:46 PM, Rob Goedman wrote:

> 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 20, 2009, at 7:38 AM, Stropharia wrote:

> 
> Thanks Duncan,
> 
> I managed to get R to start through the terminal this way. Still no luck
> getting the R.app to start. Is it possible to directly access (and then
> trash or modify) the .RData and .RProfile files? I assume they would be
> recreated if I could then open the R.app. Having searched for them on
> spotlight and in the /user/library folder, I don't see them anywhere - are
> they always located in the same place on OS X?
> 
> thanks,
> 
> Steve
> 
> 
> Duncan Murdoch-2 wrote:
>> 
>> On 20/11/2009 12:33 AM, 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?
>> 
>> 
>> It sounds like one of your user-specific startup files is causing the 
>> problem, e.g. .RData, or .Rprofile.  Did you try starting R with option 
>> --vanilla?  That will skip them.
>> 
>> Duncan Murdoch
>> 
>>> 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
>>> #----------------------------------------------------------------------
>> 
>> ______________________________________________
>> 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.
>> 
>> 
> 
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> 
> ______________________________________________
> 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.