Thanks Duncan & Kasper, I've been able to squeeze out of my problem ...
Duncan:
You can pass configure args with the configure.args parameter to
install.packages. I'm not sure how many you need to set, but you'll
likely need to set CC, CPP, CXX, F77, FC, OBJC, and maybe some of
the associated flags. You can see the list using "R CMD config" in
the console.
The R CMD config was the trick. I actually put set those flags in my
~/.R/Makevars-PLATFORM file, as it seems the build step is picking
these up so I don't have to pass them into the configure.args param.
For the record, since I'm on a first generation MBP, the name of that
file is "Makevars-i386-apple-darwin8.11.1", and it looks like:
CC=/usr/bin/gcc
CPP=/usr/bin/cpp
CXX=/usr/bin/g++
CXXCPP=/usr/bin/cpp
OBJC=/usr/bin/gcc
Kasper:
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.
Thanks for the preemptive warning. On the computer where I'm having
this problem, R is actually installed from the official cran
installer, so I just needed to set it to use the apple gcc by default.
I have to assume that this R was also built w/ Apple's gcc, so perhaps
R doesn't use the same compiler by default, as you suggest? I'm not
sure.
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.
Yeah, I'd trust that source of information as well :-)
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). 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?
Thanks,
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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