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, rip...@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@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
