[R-SIG-Mac] Experiences with El Capitan

[Spencer Graves]

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
>>>>
>>>> _______________________________________________
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>>>> 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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