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
fully updated.
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.
I have
% cat config.site
CC="clang -mtune=native"
OBJC=$CC
F77="gfortran-4.2 -arch x86_64 -mtune=native"
FC=$F77
CXX="clang++ -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).
-pd
On 30 Oct 2013, at 15:38 , Prof Brian Ripley <rip...@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, rip...@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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--
Brian D. Ripley, rip...@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@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
