Hello, I have just been given an institutional macbook - I'm very used to linux, but some apple things are baffling me (like the lack of sudo apt-get update and upgrade for example). I've installed roasted marshmallows, it's very nice. However, I can't run it from command line (or aquamacs) due to some permissions error. I've checked both R, the R64 and the symlink as described on the FAQ page. All the permissions look OK (everyone seems to have x). The only thing I can think of is that I'm not in the admin group (and can't seem to put myself in that group). Could this be a chmod issue or am I barking up the wrong tree completely. Paul =+=+=+=+=+=+=+=+=+=+=+= 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
Naive question about permissions
11 messages · Paul Hewson, Richard M. Heiberger, Simon Urbanek +2 more
Paul,
On Oct 19, 2012, at 3:52 PM, Paul Hewson wrote:
Hello, I have just been given an institutional macbook - I'm very used to linux, but some apple things are baffling me (like the lack of sudo apt-get update and upgrade for example).
It's called softwareupdate on OS X ... apt is specific to Debian, so, yes, OS X is not Debian :) Just install Debian on the MacBook if you don't want to be baffled, it's possible and some people that buy Macs just for the hardware do it.
I've installed roasted marshmallows, it's very nice. However, I can't run it from command line (or aquamacs) due to some permissions error. I've checked both R, the R64 and the symlink as described on the FAQ page. All the permissions look OK (everyone seems to have x). The only thing I can think of is that I'm not in the admin group (and can't seem to put myself in that group). Could this be a chmod issue or am I barking up the wrong tree completely.
We can't tell because you omitted all useful information ... (what error? where? how do you start it?) Cheers, Simon
Paul =+=+=+=+=+=+=+=+=+=+=+= 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 R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
typing R in the console gets the error "you don't have permission to use the application R". the message is on a dialog box that pops up. the R gui though is marvellous, works fine. Problem is I can't run r from aquamacs (same error message), or from make. R will though run as sudo, but that seems like a naughty workround. But at least it suggests all the paths etc. are correct. Fairly sure this is all dumb newbie mac user, but I hope I'm not the first. I couldn't see anything on any helplists anywhere. The only thing close was to run the "repair permissions" which I've done and a email from you a couple of years ago about mac installer setting permissions. 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. Thanks paul =+=+=+=+=+=+=+=+=+=+=+= 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
On 19 Oct 2012, at 22:05, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:
Paul, On Oct 19, 2012, at 3:52 PM, Paul Hewson wrote:
Hello, I have just been given an institutional macbook - I'm very used to linux, but some apple things are baffling me (like the lack of sudo apt-get update and upgrade for example).
It's called softwareupdate on OS X ... apt is specific to Debian, so, yes, OS X is not Debian :) Just install Debian on the MacBook if you don't want to be baffled, it's possible and some people that buy Macs just for the hardware do it.
I've installed roasted marshmallows, it's very nice. However, I can't run it from command line (or aquamacs) due to some permissions error. I've checked both R, the R64 and the symlink as described on the FAQ page. All the permissions look OK (everyone seems to have x). The only thing I can think of is that I'm not in the admin group (and can't seem to put myself in that group). Could this be a chmod issue or am I barking up the wrong tree completely.
We can't tell because you omitted all useful information ... (what error? where? how do you start it?) Cheers, Simon
Paul =+=+=+=+=+=+=+=+=+=+=+= 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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On Oct 19, 2012, at 5:28 PM, Paul Hewson wrote:
typing R in the console gets the error "you don't have permission to use the application R". the message is on a dialog box that pops up. the R gui though is marvellous, works fine. Problem is I can't run r from aquamacs (same error message), or from make.
What exactly happens when you run R in Terminal? Do you still get a dialog box? It's a console application after all ...
R will though run as sudo, but that seems like a naughty workround. But at least it suggests all the paths etc. are correct. Fairly sure this is all dumb newbie mac user, but I hope I'm not the first.
To my best knowledge yes, you are - this is not something that usually happens with the CRAN binary .. it's rather odd unless you have some custom setting ... try R --vanilla just in case ... Cheers, Simon
I couldn't see anything on any helplists anywhere. The only thing close was to run the "repair permissions" which I've done and a email from you a couple of years ago about mac installer setting permissions. 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. Thanks paul =+=+=+=+=+=+=+=+=+=+=+= 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 On 19 Oct 2012, at 22:05, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:
Paul, On Oct 19, 2012, at 3:52 PM, Paul Hewson wrote:
Hello, I have just been given an institutional macbook - I'm very used to linux, but some apple things are baffling me (like the lack of sudo apt-get update and upgrade for example).
It's called softwareupdate on OS X ... apt is specific to Debian, so, yes, OS X is not Debian :) Just install Debian on the MacBook if you don't want to be baffled, it's possible and some people that buy Macs just for the hardware do it.
I've installed roasted marshmallows, it's very nice. However, I can't run it from command line (or aquamacs) due to some permissions error. I've checked both R, the R64 and the symlink as described on the FAQ page. All the permissions look OK (everyone seems to have x). The only thing I can think of is that I'm not in the admin group (and can't seem to put myself in that group). Could this be a chmod issue or am I barking up the wrong tree completely.
We can't tell because you omitted all useful information ... (what error? where? how do you start it?) Cheers, Simon
Paul =+=+=+=+=+=+=+=+=+=+=+= 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 R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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
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) 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
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
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
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
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
1 day later
Right, thanks. Finally sank in. The dialog box looks to me like the Finder icon (I don't know what that means yet, but it doesn't look like the gatekeeper thing which is in newer versions of os x ). There is sophos on the system and it beyond me to do anything I think. Anyway, you've given me something to discus with our technical support (like turning sophos off for 2 minutes while I check if that's the problem). I will email back when it's fixed. Thanks Paul =+=+=+=+=+=+=+=+=+=+=+= 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
On 20 Oct 2012, at 13:34, "Simon Urbanek" <simon.urbanek at r-project.org> 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