[R-SIG-Mac] Updating to Mavericks

[Prof Brian Ripley]

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some) 
with the CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz.  The Mavericks update re-populates /usr/X11 with 
links which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava.  Try any of the 
rJava examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

- Re-install the Xcode command-line tools.  Xcode for Mavericks has 
moved most things inside Xcode (specifically under 
/Applications/Xcode.app/Contents/Developer) and the command-line tools 
previously installed seemed almost to work, but not entirely.

xcode-select --install

seems to be the recommended way to do so under Mavericks.


If you previously had them installed, the Xcode 4.6.3 compilers (such as 
llvm-g++-4.2) should still work.  Otherwise you could select clang as 
your compiler: see 
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages 
. There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these 
are clang-based but are not quite the same as clang/clang++.  Although 
g++ reports

% g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/usr/include/c++/4.2.1

it looks at the libcxx headers at
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ 
.  And the packages which do not compile under clang++ do not compile 
under g++ .

Packages using a C++ interface may need re-compiling if you use clang++ 
(or g++) as your C++ compiler.  The external software at 
http://r.research.att.com/libs/ which I know does is gdal and zeromq. It 
would be prudent to compile Rcpp with the same compiler as a Rcpp-using 
package, although not always necessary.


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595