[R-SIG-Mac] Naive question about permissions

[peter dalgaard]

On Oct 20, 2012, at 07:40 , Paul Hewson wrote:

> Thanks very much all, I'm still sure this is mac naivety on my part, but I'm still curious how I've managed to foul up what seems like such a simple procedure.

It still might not be you... 

I think you still need to tell us a few more details, e.g. the OSX version. However, since you say that the macbook is "institutional", is there a chance that someone tampered with permissions for your login shell? or that the OS has "security features" in place that are getting in the way? Is, BTW, any of this stuff on networked or otherwise specially mounted drives? -- sometimes there's a noexec setting for the entire drive. 

Can you do this:

~ pd$ /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R
Fatal error: R home directory is not defined

(It has to fail like that as the environment is not set up properly, but it would be informative as to whether the program can be started at all.)

> 
> 
> John's longer point - I'm going to check out removing and re-installing.   I had to enter a system password and checkbox that I wanted all users to be able to use R.   I can certainly use R GUI as myself so don't entirely understand how I gave R gui different ownerships/permissions that R console.
> 
> Regarding the other questions (my naive and presumably wrong thought was that I need to put myself as a user in group admin, but I'm not sure that's entirely correct).
> 
> 
> John's question
> R.home() gives
> "/Library/Frameworks/R.framework/Resources"
> Checking permissions gives 
> pm6-0068:~ phewson$ ls -l /Library/Frameworks/R.framework
> total 40
> lrwxr-xr-x  1 root  admin   24 18 Oct 11:16 Headers -> Versions/Current/Headers
> lrwxr-xr-x  1 root  admin   30 18 Oct 11:16 Libraries -> Versions/Current/Resources/lib
> lrwxr-xr-x  1 root  admin   31 18 Oct 11:16 PrivateHeaders -> Versions/Current/PrivateHeaders
> lrwxr-xr-x  1 root  admin   18 18 Oct 11:16 R -> Versions/Current/R
> lrwxr-xr-x  1 root  admin   26 18 Oct 11:16 Resources -> Versions/Current/Resources
> drwxrwxr-x  5 root  admin  170 18 Oct 21:22 Versions
> 
> 
> Simon's question, yes typing R in the console gives me a the dialog box, but the console does also gives me the following:
> /usr/bin/R: line 259: /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R: Permission denied
> /usr/bin/R: line 259: /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R: Undefined error: 
> (same for R vanilla)
> 
> Davor's question yields:
> phewson$ ls -l /Library/Frameworks/R.framework/Resources/bin
> total 10176
> -rwxrwxr-x  1 root  admin     1828 22 Jun 20:16 BATCH
> -rwxrwxr-x  1 root  admin     2112 22 Jun 20:16 COMPILE
> -rwxrwxr-x  1 root  admin      823 22 Jun 20:16 INSTALL
> -rwxrwxr-x  1 root  admin     1579 22 Jun 20:16 LINK
> lrwxr-xr-x  1 root  admin        3 18 Oct 11:18 R -> R64
> -rwxrwxr-x  1 root  admin     8773 18 Oct 11:18 R32
> -rwxrwxrwx  1 root  admin     8775 18 Oct 11:18 R64
> -rwxrwxr-x  1 root  admin      158 22 Jun 20:16 REMOVE
> -rwxrwxr-x  1 root  admin     1374 22 Jun 20:16 Rcmd
> -rwxrwxr-x  1 root  admin      312 22 Jun 20:16 Rd2pdf
> -rwxrwxr-x  1 root  admin      359 22 Jun 20:16 Rdconv
> -rwxrwxr-x  1 root  admin      258 22 Jun 20:16 Rdiff
> -rwxrwxr-x  1 root  admin      310 22 Jun 20:16 Rprof
> -rwxrwxr-x  1 root  admin    37992 22 Jun 20:18 Rscript
> -rwxrwxr-x  1 root  admin      155 22 Jun 20:16 SHLIB
> -rwxrwxr-x  1 root  admin      318 22 Jun 20:16 Stangle
> -rwxrwxr-x  1 root  admin      316 22 Jun 20:16 Sweave
> -rwxrwxr-x  1 root  admin    41048  5 Nov  2011 arch
> -rwxrwxr-x  1 root  admin      317 22 Jun 20:16 build
> -rwxrwxr-x  1 root  admin      317 22 Jun 20:16 check
> -rwxrwxr-x  1 root  admin     7486 22 Jun 20:16 config
> drwxrwxr-x  4 root  admin      136 22 Jun 20:16 exec
> -rwxrwxr-x  1 root  admin     3600 22 Jun 20:16 f77_f2c
> -rwxrwxr-x  1 root  admin  2326336 22 Jun 20:18 fc-cache
> -rwxrwxr-x  1 root  admin    13760 22 Jun 20:16 javareconf
> -rwxrwxr-x  1 root  admin   274347 22 Jun 20:16 libtool
> -rwxrwxr-x  1 root  admin     3494 22 Jun 20:16 mkinstalldirs
> -rwxrwxr-x  1 root  admin      413 22 Jun 20:16 pager
> -rwxrwxr-x  1 root  admin  2385276 22 Jun 20:18 qpdf
> -rwxrwxr-x  1 root  admin     4121 22 Jun 20:16 rtags
> 
> Best
> paul
> -=-=-=-=-=-=-=-=-=-=-=-=
> Dr. Paul Hewson
> Editor, Teaching Statistics (www.teachingstatistics.co.uk)
> Associate Professor (Senior Lecturer) in Statistics
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> -=-=-=-=-=-=-=-=-=-=-=-=
> ________________________________________
> From: Davor Cubranic [cubranic at stat.ubc.ca]
> Sent: 20 October 2012 03:40
> To: Paul Hewson
> Cc: r-sig-mac at r-project.org
> Subject: Re: [R-SIG-Mac] Naive question about permissions
> 
> On 12-10-19 02:28 PM, Paul Hewson wrote:
>> As I say, I think I've tracked the symlink itself as well as the
>> files it links to /usr/bin/R is itself a symlink to R64.    All three
>> users have an x when you do ls -l , they don't all have r and w.
> 
> Can you show us the output of running:
> ls -l /Library/Frameworks/R.framework/Resources/bin
> 
> Davor
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
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Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com