[R-SIG-Mac] Experiences with El Capitan

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Tue Oct 13 05:21:43 CEST 2015 

CLT = command line tools.  Otherwise you only have the compilers from the Xcode interface.

in order to have tex2dvi, you need a tex distribution installed.  I do remember if Simon has one on his R mac site, nut you can do an install from say  (as the RStudio help says):

> To build manuals and vignettes you'll also need to install the MacTeX LaTeX distribution (or another version of LaTeX for the Mac). You can download MacTeX from here: http://www.tug.org/mactex/downloading.html.


HTH,

Roy

> On Oct 12, 2015, at 7:58 PM, Spencer Graves <spencer.graves at prodsyse.com> wrote:
> 
> 
> 
> 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
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> _______________________________________________
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> 
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**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
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Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

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