[R-SIG-Mac] Naive question about permissions

Paul Hewson paul.hewson at plymouth.ac.uk
Thu Nov 15 12:12:29 CET 2012 

Dear All,
Sorry for cluttering up the list and whatnot, and thanks for the
support.   As noted, the clue was in the PopUp menu telling me I
couldn't use R.

On the offchance someone in the future hits this email trail, I've been
told by the sysadmin who fixed this:

"I simply allowed the frameworks and commands to be able to run as they
are not in the normal path.  The /usr/bin/R  is alias to inside the
frameworks folder in /Library, and not /usr/bin on /Volumes/System/"

Best

Paul

On 20/10/12 13:34, Simon Urbanek wrote:
> 
> On Oct 20, 2012, at 1:40 AM, 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.
>>
>>
>> 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)
>>
> 
> Are you running any anti-virus software or other haxxies? The thing is
> that R will not show any dialog box since it is a console tool, so the
> dialog box has to come from some other software that may be causing the
> issue in the first place ...
> 
> 
>> 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
>> School of Computing and Mathematics
>> University of Plymouth
>> Drake Circus
>> Plymouth PL4 8AA
>>
>> tel (01752) 586870
>> fax (01752) 586900
>> VoIP: sip:pjhewson at ekiga.net
>>
>> email: paul.hewson at plymouth.ac.uk
>> web: http://www.plymouth.ac.uk/staff/phewson
>> -=-=-=-=-=-=-=-=-=-=-=-=
>> ________________________________________
>> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
> 

-- 
=+=+=+=+=+=+=+=+=+=+=+=
Dr Paul Hewson
Editor, Teaching Statistics (www.teachingstatistics.co.uk)
Associate Professor (SL) Statistics
School of Computing & Maths
Plymouth University
Drake Circus
Plymouth PL4 8AA
++44 (0)1752 586870

More information about the R-SIG-Mac mailing list