[R-SIG-Mac] similar problems installing Rcmdr with R.

[John Fox]

Dear Mark,

> -----Original Message-----
> From: Hebblewhite, Mark [mailto:Mark.Hebblewhite at umontana.edu]
> Sent: Wednesday, September 25, 2013 3:17 AM
> To: Simon Urbanek; John Fox
> Cc: r-sig-mac at r-project.org; 'Rodney Sparapani'
> Subject: Re: [R-SIG-Mac] similar problems installing Rcmdr with R.
> 
> Yes, originally,
> 
> 
> 1) sudo chmod a+rx/usr/local/* did not work but
> 
> 2) sudo zsh
> chmod -R 755/usr/local
> 
> did work.
> 
> However, at your advice, Simon, I've gone and entered
> 
> 3) sudo chmod -R a+rX /usr/local
> 
> 
> in terminal, and now Rcmdr works.
> 
> Is there something else I should do to 'reverse' the 2nd incorrect
> command?
> 
> Incidentally, this is obviously a broader problem and I encountered
> similar problems with other packages like adehabitat.

Of course. As I explained earlier, the problem was that the tcltk package
couldn't load, not with the Rcmdr directly, and the adehabitat package also
uses the tcltk package.

> 
> Thanks SO much for all your assistance and help, especially for
> updating
> the help files for Rcmdr John. I will ask some of my current graduate
> students to test it out on their Mac's too.

They likely won't experience the same problem as you did, unless they too
have incorrect permissions set for the /usr/local directory or
subdirectories of it. Most people who follow the Rcmdr Mac OS X installation
notes won't experience a problem. Anyway, I have some troubleshooting tips
there now that cover the issue that arose on your Mac. If you turn up other
problems not currently covered by the notes, I'd appreciate learning about
them.

Best,
 John

> 
> thanks again!
> 
> Mark Hebblewhite
> 
> 
> 
> 
> On 9/25/13 8:30 AM, "Simon Urbanek" <simon.urbanek at r-project.org>
> wrote:
> 
> >
> >On Sep 24, 2013, at 8:34 PM, John Fox <jfox at mcmaster.ca> wrote:
> >
> >> Dear Mark,
> >>
> >>> -----Original Message-----
> >>> From: Hebblewhite, Mark [mailto:Mark.Hebblewhite at umontana.edu]
> >>> Sent: Tuesday, September 24, 2013 12:32 PM
> >>> To: John Fox
> >>> Cc: r-sig-mac at r-project.org
> >>> Subject: Re: [R-SIG-Mac] similar problems installing Rcmdr with R.
> >>>
> >>> Yes, the solution proposed by Rodney Sparapani below worked to fix
> my
> >>> problem, but was a slightly different command than proposed to
> Sarah
> >>> earlier.
> >>>
> >>>
> >>> Thanks very much Rodney! It will be challenging to fix this
> problem,
> >>> however, for other 'naïve' users of MAC if the solution is
> different
> >>> each
> >>> time.
> >>>
> >>
> >> Just to be clear:
> >>
> >> 	sudo chmod a+rx /usr/local/*
> >>
> >> didn't work, but
> >>
> >> 	sudo zsh
> >> 	chmod -R 755 /usr/local
> >>
> >> did work?
> >>
> >
> >
> >The later is bad, do NOT use it! It will set exec permissions on
> >*everything* even files are are not supposed to be executable.
> >You probably want
> >
> >sudo chmod -R a+rX /usr/local
> >
> >Cheers,
> >Simon
> >
> >
> >
> >> Frankly, I don't get that, since the first command should insure
> that
> >> everyone has (at least) read and execute permission (i.e., level 5).
> >>
> >> I think that I'll add a trouble-shooting section to the Rcmdr Mac
> >> installation notes, but I would like to understand why one approach
> >>worked
> >> here and not the other.
> >>
> >> Best,
> >> John
> >>
> >>> Thanks very much John, Simon and Rodney!
> >>>
> >>> On 09/24/2013 07:45 AM, Hebblewhite, Mark wrote:
> >>>> 7. From previous posts on this list serve
> >>>> [http://grokbase.com/t/r/r-sig-mac/138nv3tj17/unable-to-load-
> rcmdr-
> >>> with-r-
> >>>> 3
> >>>> -0-1-on-a-mac-os-x-10-8-3] I followed this set of instructions to
> see
> >>>> whether there were problems with my permissions:
> >>>>
> >>>>>> system("ls -ld /usr/local /usr/local/lib
> /usr/local/lib/libtcl*")
> >>>> ls: /usr/local/lib: Permission denied
> >>>> ls: /usr/local/lib/libtcl*: Permission denied
> >>>> drwx------  8 root  wheel  272 Sep 24 10:21 /usr/local
> >>>>
> >>>>
> >>>> 8. But in my disk utilities I can see no clear disk permissions
> >>> related to
> >>>> R. I ran repair disk permissions earlier today and there was 1 R
> >>> problem
> >>>> but that¹s been apparently fixed.
> >>>
> >>> Hi Mark:
> >>>
> >>> I am assuming you came to Mac from Windows, rather than UNIX/Linux,
> >>> right?  On Mac OS X (and UNIX/Linux in general), you need to have
> >>> permission to read/write/execute files.  But, I think you can fix
> >>> this rather easily.  In a terminal...
> >>> % sudo zsh
> >>> # chmod -R 755 /usr/local
> >>>
> >>>
> >>>>
> >>
> >>
> >