[R-SIG-Mac] Experiences with El Capitan

[Simon Urbanek]

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.
>>> 
>>> 
>>> 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
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