[R-SIG-Mac] Experiences with El Capitan

Spencer Graves spencer.graves at prodsyse.com
Tue Oct 13 11:53:08 CEST 2015 


On 10/12/2015 10:21 PM, Roy Mendelssohn - NOAA Federal wrote:
> 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,


       Yes, it didn't just help, it fixed the problem.  Thanks.  (My 
Father once said, "That not only hit the spot, it erased it.")


        Best Wishes,
       Spencer
>
> 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 athttps://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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> **********************
> "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
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> e-mail:Roy.Mendelssohn at noaa.gov  www:http://www.pfeg.noaa.gov/
>
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> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
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