[R-SIG-Mac] Experiences with El Capitan

[Simon Urbanek]

On Oct 6, 2015, at 3:12 AM, Rainer M Krug <Rainer at krugs.de> wrote:

> Simon Urbanek <simon.urbanek at r-project.org> writes:
> 
>> 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.
> 
> OK - thanks for the clarification.
> 
> Maybe I am overly careful, but I would very much prefer that the user is
> asked how to proceed if something would be overwritten.
> 
> Due to e.g. homebrew /usr/local/bin becomes used quite a bit, so an
> approach which does not overwrite existing files / links in
> /usr/local/bin would be, in my opinion, a plus.
> 
> Homebrew does for example installs the files, but does issue an error if
> the links in e.g. /usr/local/bin would overwrite existing files / links.
> 

Homebrew doesn't really abide by any Apple rules and it's command line tool, so whatever it does is quite irrelevant here. Users use Homebrew entirely at their own risk. R is using the standard Apple Installer and for obvious reasons AI doesn't pester the user about making low-level decisions (since 99% of users just want it to work - just imagine AI asking about every file when you upgrade OS X ;)). Also if you mix native R and Homebrew R you're already in trouble, so you better know what you're doing.

That said, one thing we could do would be to re-name whatever we find to replace so you can move it back if you so desire. (Of course if you install it twice your backup is gone etc.).

Cheers,
Simon




> Cheers,
> 
> Rainer
> 
>> 
>> 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
>>> _______________________________________________
>>> 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