[R-SIG-Mac] Experiences with El Capitan

[Rainer M Krug]

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.

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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