[R-SIG-Mac] Compiling packages with specific gcc

[Steve Lianoglou]

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