[R-SIG-Mac] Updating to Mavericks

peter dalgaard pdalgd at gmail.com
Thu Oct 31 15:57:14 CET 2013

Thanks Brian.

One more item: If building from SVN, you may need to run "svn upgrade" in the source directory (at top level).

I suppose that's a consequence of upgrading Xcode rather than Mavericks per se, but might as well mention it here.

Do we have any authoritative advice as to what should go into config.site? Mine seems to work unchanged, but I'm not sure I have a clue about what they are doing anymore.


On 30 Oct 2013, at 15:38 , Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

> 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
> _______________________________________________
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Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

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