[R-SIG-Mac] R crash on startup in OS X

[Simon Urbanek]

On Oct 21, 2009, at 4:53 PM, Jordan Thomson wrote:

> Hi guys,
>
> I've started from scratch with R 2.9.2 and now have R.app in my  
> Applications folder.
> The Framework folder is in the proper place and I can find the  
> libR.dylib file using Finder.  However, when I run the command in  
> Terminal that Simon suggested it returns this error, even though the  
> path is correct and the file is there:
>
> /Library/Frameworks/R.framework/Versions/2.9/Resources/lib/
> file:       cannot open (/Library/Frameworks/R.framework/Versions/ 
> 2.9/Resources/lib/
> file)
> /Library/Frameworks/R.framework/Versions/2.9/Resources/lib/
> libR.dylib: cannot open (/Library/Frameworks/R.framework/Versions/ 
> 2.9/Resources/lib/
> libR.dylib)
> [Process completed]
>
> Sorry this is a pain... any other suggestions?!
>

Well, if I were you I'd run
sudo rm -rf /Library/Frameworks/R.framework
and re-install R (using the installer). But if you want to try to  
figure out what's happening try this -- what does ls -l say? Run
id
ls -l /Library/Frameworks
ls -l /Library/Frameworks/R.framework
ls -l /Library/Frameworks/R.framework/Versions
ls -l /Library/Frameworks/R.framework/Versions/2.9/Resources/lib

Cheers,
Simon


> Cheers,
>
> Jordy
>
>
> ----- Original Message -----
> From: "Steve Lianoglou" <mailinglist.honeypot at gmail.com>
> To: "Jordan Thomson" <jathomso at sfu.ca>
> Cc: r-sig-mac at stat.math.ethz.ch
> Sent: Wednesday, October 21, 2009 1:10:29 PM GMT -08:00 US/Canada  
> Pacific
> Subject: Re: [R-SIG-Mac] R crash on startup in OS X
>
>
> On Oct 21, 2009, at 3:55 PM, Jordan Thomson wrote:
>
>> Hi Steve,
>>
>> Thanks for the quick reply.  The Framework folder and contents are
>> all there at /Library/Frameworks/R.framework/Versions/2.9, including
>> the library file (libR.dylib).  For some reason, however, R still
>> won't load that library and crashes on launch.
>>
>> I'm not sure why that would be.  Do you have any other suggestions?
>
> Hmm ... so I'm not sure what just happened since it wasn't there
> before (did you reinstall just now or something?).
>
> I see Simon just responded to you, so definitely do what he suggests,
> but it seems something is wonky.
>
> To minimize the back and forths, you might consider trashing the R.app
> you have in your *Academic* folder and reinstalling the R version you
> like from the appropriate *.dmg/*.pkg (eg. the new 2.10 RC is up at r.research.att.com
>  if you're interested in that).
>
> If I recall correctly, the installer should put a new R.app in your /
> Applications folder. You should be able to move that wherever you like
> if you really don't want it there and it should "just work".
>
> -steve
>
>> Thanks for your time,
>>
>> Jordy
>>
>>
>>
>> ----- Original Message -----
>> From: "Steve Lianoglou" <mailinglist.honeypot at gmail.com>
>> To: "Jordan Thomson" <jathomso at sfu.ca>
>> Cc: r-sig-mac at stat.math.ethz.ch
>> Sent: Wednesday, October 21, 2009 12:20:12 PM GMT -08:00 US/Canada
>> Pacific
>> Subject: Re: [R-SIG-Mac] R crash on startup in OS X
>>
>> Hi Jordan,
>>
>> On Oct 21, 2009, at 3:05 PM, Jordan Thomson wrote:
>>
>>> Hello,
>>>
>>> I'm having trouble running the latest version of R (2.9.2) in Mac OS
>>> X 10.4.11.  Once installed, the program crashes on launch, with the
>>> crash log giving the following error:
>>>
>>> Library not loaded: /Library/Frameworks/R.framework/Versions/2.9/
>>> Resources/lib/libR.dylib
>>> Referenced from: /Users/jordythomson/Desktop/All Things Academic/
>>> Courses and TA Files/R Workshop/R.app/Contents/MacOS/R
>>> Reason: image not found
>>>
>>>
>>> The folder R is trying to access no longer exists.  I had an older
>>> version of R there but uninstalled it and deleted the folder some
>>> time ago.
>>
>> Perhaps I'm misunderstanding you, but I'm not sure how this is
>> possible?
>>
>> Your new version of R (2.9.2) is installed in precisely that
>> folder ... the R.app file in your ../All Things Academic/../.. is
>> simply referencing the R "system" installed in /Library/Frameworks/
>> R.framework/....
>>
>> So, in short, you need /Library/Frameworks/R.framework/Versions/2.9
>> and its contents to be there to have a working R on your system.
>>
>> Does that help?
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  |  Memorial Sloan-Kettering Cancer Center
>>  |  Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>   |  Memorial Sloan-Kettering Cancer Center
>   |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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