[R-SIG-Mac] Experiences with El Capitan

Rainer M Krug Rainer at krugs.de
Tue Oct 6 15:40:07 CEST 2015 

Simon Urbanek <simon.urbanek at r-project.org> writes:

> 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 ;)).

That would be fun...

I see the differences between the Apple rules and homebrew - and as far
as I know in /usr/local/bin open for everybody, so you are right that
there is nobody to blame for anything. But especially because of this
nature, I would consider it as an advantage if R would not just delete
existing links but rename / move them as you suggets below - especially
as one of the main players in /usr/local/bin (homebrew) is refusing to overwrite,
unless you tell it to do so.

> Also if you mix native R and Homebrew R you're already in trouble, so
> you better know what you're doing.

Completely agree - but still - there might be reasons to do so (although I don't
know which reason ...).

>
> 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.).

Renaming would be a step in the right direction. And backups could be
numbered, so none would be lost, even after multiple installs.

This brings back the question of R-x.y links - but I think that is a
different question.

Cheers,

Rainer


>
> 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
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>> 
>> -- 
>> Rainer M. Krug
>> email: Rainer<at>krugs<dot>de
>> PGP: 0x0F52F982
>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
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email:      Rainer at krugs.de

Skype:      RMkrug

PGP: 0x0F52F982
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