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

Duncan Murdoch murdoch at stats.uwo.ca
Fri Nov 20 17:01:13 CET 2009


On 20/11/2009 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?
>   

.RProfile won't be recreated:  it's where you put your own startup 
customizations.  It sounds as though .RData is a more likely culprit.

.RData is created when you quit and reply Yes to the question about 
saving.  I forget if there are special rules on a Mac about where the 
saving occurs, but on other systems it's in the current working 
directory.  On startup, R will look there and in the user's home 
directory. 

You probably want to ask on R-sig-mac for some Mac specific advice.

Duncan Murdoch
> 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
> >> #----------------------------------------------------------------------
> > 
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> > 
> > 
>
>




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