You will want to recompile R with the new compiler. Then, whenever you
compile a package, it will use the same compiler as R was compiled with.
Mixing compilers might be possible using the hints from Duncan, but I
am pretty sure it is discouraged.
In the past Simon has discouraged use of the HPC compilers. I don't
remember the reasons, but I respect the source of the information :)
He knows way more about mac compilers than I do. Of course, this was a
while back and things might have changed.
Kasper
On May 5, 2009, at 10:05 , Steve Lianoglou wrote:
Hi all,
I'm wondering if/where I can go to tell R to use a specific version
of my gcc compiler when installing packages from source, via
`install.packages("...", type='source')` or when running `R CMD
INSTALL some_source_packge.tar.gz` from the command line.
The reason I ask is because I've downloaded gcc-4.4 from HPC/OSX[1],
and it unfortunately puts the compilers in /usr/local/bin/gcc, w/o
version info (it would be nice if it were /usr/local/bin/gcc-4.4). R
tries to use this when compiling, but these compilers do not support
the "-arch=..." flags, so it bombs.
I've been hunting around in the tools:::.install_packges code and
also the "R Installation and Adminstration"[2] document, but can't
find what I'm looking for. I have a feeling that perhaps I can put
something into my ~/.R/Makevars, or ~/.R/Makevars-i386-apple-
darwin8.11.1 file, but I'm just taking stabs at the dark, so not
having much luck.
I can work around this by temporarily removing /usr/local/bin from
my path when trying to `R CMD INSTALL` packages by source, but I was
hoping there might be a more elegant solution. The fact that
installing by source gets the `make` command from the system
environment makes me a bit hopeful, but I'm not really sure.
Thanks for any help,
-steve
[1] HPC/OSX: http://hpc.sourceforge.net/
[2] R Install/admin:
http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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