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:[email protected] >> >> email: [email protected] >> web: http://www.plymouth.ac.uk/staff/phewson >> -=-=-=-=-=-=-=-=-=-=-=-= >> ________________________________________ >> From: Davor Cubranic [[email protected]] >> Sent: 20 October 2012 03:40 >> To: Paul Hewson >> Cc: [email protected] >> 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 >> [email protected] >> 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 _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
