[R] R 2.10 'memory leak'? on OS X

Stropharia stevenworthington at hotmail.com
Fri Nov 20 21:45:11 CET 2009 

Thanks a lot Duncan and David, the remedy was to delete the files .Rhistory
and .RData via the terminal - with "rm . Rhistory" etc. (By default they are
hidden on OS X.) Now R.app opens fine.

best,

Steve



David Winsemius wrote:
> 
> Probably best further discussed on R-SIG-Mac list:
> 
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> ... since that is where the tricks of convincing MacOSX to display  
> system files is discussed and a semi-regular basis:
> 
> https://stat.ethz.ch/pipermail/r-sig-mac/2009-November/006768.html
> 
> https://stat.ethz.ch/pipermail/r-sig-mac/2009-March/005925.html
> 
> -- 
> David.
> 
> On Nov 20, 2009, at 10:38 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.
>>>
>>>
>>
>> -- 
>> View this message in context:
>> http://old.nabble.com/R-2.10-%27memory-leak%27--on-OS-X-tp26422775p26443494.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.
> 
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
> 
> ______________________________________________
> 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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