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

[Kent Manley]

There is a also a utility to fix permissions under Applications- 
 >Utility->Disk Utility that will go through the library frameworks  
and at the very least, let you know the permissions have changed and  
what they should be, and at the very best, fix these.

Is it possible you installed the R under one user name (and/or  
upgraded after the initial install), and now are working under another  
username?

Good luck,
Kent

On Oct 21, 2009, at 6:52 PM, Simon Urbanek wrote:

>
> 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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