[R-SIG-Mac] Naive question about permissions

Paul Hewson paul.hewson at plymouth.ac.uk
Sat Oct 20 09:32:20 CEST 2012 

Hi,
OS X Lion 10.7.4 (11E53)
mac book pro 15 in ch Mid 2010
Entirely stand alone, no networked drives.   I **should** have admin
rights (I can install software for example), but the nuances of
permissions go beyond both myself at the moment as well as the tech
support I've been pestering.

If I run
/Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R
I get the permission denied error

If I run
sudo /Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R
I get the Fatal error: R home directory is not defined.

(as I'm missing tab completion I also cd'd into /Lib etc. /x86_64 where
sudo R ran fine.

Best
Paul


On 20/10/12 07:27, peter dalgaard wrote:
> 
> 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
>> 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
> 
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 
> 
> 
> 
> 
> 
> 
> 

-- 
=+=+=+=+=+=+=+=+=+=+=+=
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

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