[R-SIG-Mac] Experiences with El Capitan

[Rainer M Krug]

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.

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
>> _______________________________________________
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>> R-SIG-Mac at r-project.org
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-- 
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
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