Sorry to spam, but I just wanted to post this follow up just in case
someone asks google about this later.
I found that I can get the R's default settings for the ones I needed
to override (CC, CPP, etc.) by typing `R CMD config SETTING` at the
command line. So, for instance, to find out what R had config'd for CPP:
$ R CMD config CPP
gcc -arch i386 -std=gnu99 -E
So I used that to redefine my Makevars, only now I have an absolute to
gcc/g++ so that I can get the ones from Apple, and not the one in my /
usr/local/bin. So, the contents of my Makevars file is now:
CC=/usr/bin/gcc -arch i386 -std=gnu99
CPP=/usr/bin/gcc -arch i386 -std=gnu99 -E
CXX=/usr/bin/g++ -arch i386
CXXCPP=/usr/bin/g++ -arch i386 -E
OBJC=/usr/bin/gcc -arch i386 -std=gnu99
-steve
On May 5, 2009, at 3:03 PM, Steve Lianoglou wrote:
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
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
