[R-SIG-Mac] Updating to Mavericks
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Oct 31 23:19:24 CET 2013
On 31/10/2013 14:57, peter dalgaard wrote:
> 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.
Yes. A quick poll of systems I have access to has svn 1.6.x on 10.7,
1.7.x on 10.8 and 10.9. As AFAICS it is part of Xcode, it depends on
the version you had installed and I believe those machines were all
> 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.
% cat config.site
F77="gfortran-4.2 -arch x86_64 -mtune=native"
CFLAGS="-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion"
Those are rather picky C flags, of course: intended to pick up issues
with long vectors.
gcc/g++ are not the same as clang/clang++, although the only differences
I have detected are what they report themselves as. As I don't know if
there are any material differences I chose to use clang explicitly.
Similarly calling gfortran-4.2 explicitly to avoid any other versions
(and I would even consider using /usr/local/bin/gfortran-4.2).
> 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
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
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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