Hi Simon,
R uses the Apple compiler, but I'm not hard-coding the full path. In
your case apparently your PATH has /usr/local/bin before the system
paths, so it overrides the default. Another (simpler?) way to solve
this is to simply move /usr/local/bin at the end of your PATH
(recommended) and all should be well without changing any config
files.
I actually wanted to avoid doing this because I tend to install newer
versions of standard things into /usr/local/* that I'd like to use
instead of the default ones in /usr/bin/* so I was looking for a back
door ...
As for the rest of your comments (which I'll keep below for
posterity), they're spot on. Thanks for the thorough and informative
feedback. I've nuked all traces of the HPC compilers and will now just
explicitly compile w/ /usr/bin/g++-4.2 when necessary ... that's a
simple-enough sol'n for me until Apple decides to set some gcc >= 4.2
as the default compiler.
Thanks again,
-steve
This kind of leads me into another related question, then. So, I
actually d/l'd the HPC compiler so I can compile w/ -fopenmp (to
use OpenMP for some easy parallelization).
You can use -fopenmp with Apple's compilers as well, just make sure
you make the gcc-4.2 compilers the default (sudo gcc_select 4.2 if
you have gcc_spect on your system, otherwise change the symlinks
like ln -sf gcc-4.2 /usr/bin/gcc etc. - or specify them directly as
you did). Apple's gcc-4.2 compilers are supported by the CRAN binary.
Does this mean that I shouldn't do that w/ a vanilla R install and
perhaps recompile R from source w/ the HPC compiler? And if Simon
doesn't like using the HPC compiler, then should we stay away from
this in general?
In general, yes. As you have seen yourself the HPC compilers are not
complete, so they cannot build universal binaries. Also they don't
use Apple's driver, so all Apple-specific flags will fail. I didn't
check the last HPC release, but before they were partially broken
causing miscompilations, included wrong binaries (i.e. even the
compiler for Tiger would include symbols for Leopard so the binary
would not work), etc. I was trying to contact the maintainer a few
times, but without avail, so I don't think it's well supported,
either.
Cheers,
Simon
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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