R crash on startup in OS X

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