[R-SIG-Mac] Experiences with El Capitan

[Prof Brian Ripley]

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