[R-SIG-Mac] Experiences with El Capitan

Spencer Graves spencer.graves at prodsyse.com
Tue Oct 13 04:58:36 CEST 2015 


On 10/12/2015 8:51 PM, Kevin Ushey wrote:
> The simplest way to fix your issue is to symlink R to /usr/local/bin, e.g.
>
>      ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/R


This worked.  Thanks.  Spencer


... but not completely:  "R CMD build" worked.  "R CMD check" ended with:


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
   pdflatex is not available


	
>
> Or, as Professor Ripley said in his initial post, R installers from
> 3.2.2 on El Capitan will now install a symlink at /usr/local/bin/R, so
> you might want to just re-install or update R.
>
> Updating the CLT is normally just a matter of downloading the latest


What's CLT?  Central Limit Theorem?  Charlotte Douglas International 
Airport?


> version of Xcode from the App Store, if I understand correctly. (You


	  I requested "Xcode" at the App Store.  It asked for my Apple password 
then went away.  I rebooted and still got "pdflatex is not available".


> may need to read + confirm a license agreement on your next run of the
> clang compiler -- try running 'clang' after installing Xcode to see if
> you're prompted)


$ clang
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


	  Thanks again for your prompt reply.  Other suggestions?  (All this 
worked before I upgraded to OS X 10.11.)  Spencer

>
> Kevin
>
> On Mon, Oct 12, 2015 at 6:33 PM, Spencer Graves
> <spencer.graves at prodsyse.com> wrote:
>>
>> On 10/5/2015 2:46 PM, Simon Urbanek wrote:
>>> On Oct 5, 2015, at 3:34 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>>>
>>>> peter dalgaard <pdalgd at gmail.com> writes:
>>>>
>>>>> <Round of applause, please!>
>>>> Agreed.
>>>>
>>>> I just would like to dd that in the case of using homebrew, which
>>>> installs everything under /usr/local/... which did not cause any
>>>> problems at all. I moved the contents of /usr/local to an other location
>>>> before upgrade because the upgrade to Yosemite took because of a large
>>>> /usr/local several hours instead of about half an hour, moved it back
>>>> afterwards and everything worked fins without problems.
>>>>
>>>> One question concerning mixed usage of homebrew and the Official R
>>>> installers:
>>>>
>>>> do the Official R installers fail if an R binary already exist, or do
>>>> they raise a warning?
>>>>
>>>> To make this easier, would it be possible, to install the binaries under
>>>> /usr/local/bin/R.X.Y.Z and then just create links in /usr/local/bin ?
>>>> Tghis would make the whole process more transparent and easier to switch
>>>> between different versions and means of installation.
>>>>
>>> R installer never installs any R binaries outside of the framework/app.
>>> The only thing we provide on 10.10 is a softlink for R and Rscript in
>>> /usr/local/bin into the framework (removing anything else in that name if it
>>> exists). In earlier OS X versions this applies to /usr/bin instead.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> Thanks for the clarifications,
>>>>
>>>> Rainer
>>>>
>>>>> -pd
>>>>>
>>>>>> On 04 Oct 2015, at 18:53 , Prof Brian Ripley <ripley at stats.ox.ac.uk>
>>>>>> wrote:
>>>>>>
>>>>>> The machine which provides the 'r-devel-osx-x86_64-clang' checks on
>>>>>> the CRAN check farm has been upgraded from Yosemite to El Capitan
>>>>>> and a complete round of checks has been run.
>>>>>>
>>>>>>
>>>>>> 1) There is a lot of misinformation around about 'System Integrity
>>>>>> Protection' aka 'rootless'.
>>>>>>
>>>>>> Upgrading to El Capitan moves files which are not allowed under /usr
>>>>>> to /Library/SystemMigration/usr, so you will be able to see what was
>>>>>> lost. This includes /usr/bin/R, /usr/bin/Rscript (but the installer
>>>>>> installs these under /usr/local/bin on El Capitan as from R 3.2.2),
>>>>>> /usr/X11R6, /usr/texbin .  Contrary to reports from betas, the link
>>>>>> /usr/X11 is preserved.
>>>>>>
>>>>>> If an installer tries to create a disallowed file such as
>>>>>> /usr/bin/R, this is silently ignored (at least in the cases we
>>>>>> tested).  So you can install e.g. R 3.1.3 but the executables will
>>>>>> not appear in the default Terminal path (more details in the current
>>>>>> manual).
>>>>>>
>>>>>>
>>>>>> 2) After updating you need to re-install the Command Line Tools and
>>>>>> R (to get the links in /usr/local).  I did not need to re-install
>>>>>> Java nor XQuartz.
>>
>>
>>        How do you suggest I "re-install the Command Line Tools and R"?
>>
>>
>>        I upgraded to 10.11 days ago but only now tried "R CMD build" and got,
>> "-bash: R: command not found". How can I get past this?
>>
>>
>>        Thanks,
>>        Spencer
>>
>>
>> p.s.  Thanks very much for all your work, including the comments on this
>> thread.
>>
>>
>>>>>> 3) All the 'Mavericks' binary packages tested worked.  The source
>>>>>> packages of rJava and rgl (only) cannot be installed and the
>>>>>> maintainers have patched versions available.
>>>>>>
>>>>>>
>>>>>> There is updated information in the latest 'R Installation and
>>>>>> Administration' manual in R-patched and R-devel (in the sources, or
>>>>>> the online versions at https://cran.r-project.org/manuals.html will
>>>>>> update in a day or two).
>>>>>>
>>>>>> --
>>>>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>>>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>>>> 1 South Parks Road, Oxford OX1 3TG, UK
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> --
>>>> Rainer M. Krug
>>>> email: Rainer<at>krugs<dot>de
>>>> PGP: 0x0F52F982
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
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