[R-SIG-Mac] Experiences with El Capitan

[Kevin Ushey]

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

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

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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