R help - Sep 2012 - Where is the R configuration file or how to override R compilers

I have a question about how one can modify or override the compilers
that R uses for package installations?  Or if perhaps this configuration
is in some editable file somewhere.

Initially I built the version of R 2.15.1 on Solaris SPARC (virtual T4),
but found out the build was done as 32 bit.  After some research, I
found that the pre-compiled GCC version I had only allowed for 32 bit.
I wanted 64 bit.  Therefore I ended up download the SunStudio compilers
(12.1 version) and was able to export the compiler commands (per the R
manual) and get a 64 bit version running.  The problem I have now is
that I am trying to install the GBM package from CRAN (and from source
as well.)  What I find is that something keeps trying to run "c++"
during compilation.  Since I only have the SUN compiler the file is
named "CC" not "c++".  How do I override this?

I've tried the following with no success:
1. EXPORT CXX to point to my CC compiler (eg export
CXX='/opt/SUNWspro/bin/CC')
2. Create an alias to c++ (eg alias c++='/opt/SUNWspro/bin/CC')
3. I even tried to create a symlink for g++: ln -s /opt/SUNWspro/bin/CC
c++

However none of these seem to work and I get the following
error:
># /usr/local/bin/R CMD INSTALL  /export/home/downloads>
* installing to library '/usr/local/lib/R/library'
* installing *source* package 'gbm' ...
** package 'gbm' successfully unpacked and MD5 sums checked
** libs
c++ -m64 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include
-KPIC   -c adaboost.cpp -o adaboost.o
bash: c++: command not found
*** Error code 127
make: Fatal error: Command failed for target `adaboost.o'
ERROR: compilation failed for package 'gbm'
* removing '/usr/local/lib/R/library/gbm'

Is there some environment variable or config file I can temporarily
override this setting?  My first thought was that I can try to build GCC
from source, but I've spent two days trying to get that to work no
success.  In addition, trying to download the version from sun-freeware
did not appear to work as well.  Therefore that's why I am looking at
this direction to see if there is a way I can get this package
installed?  I will note that if I manually compile the GBM source using
"CC" it compiles fine.  I just think something in R is overriding
this.
I tried installing from both the CRAN download as well as GBM source and
get the same error.  I don't see any configuration in the GBM tar ball
so I assume that there is some standard packaging or configuration that
R has when developing packages (have not fully read through those docs
yet.)

Any thoughts or pointers?

Thanks in advance.

Anthony


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On 16-09-2012, at 20:47, Eberle, Anthony wrote:
> I have a question about how one can modify or override the compilers
> that R uses for package installations?  Or if perhaps this configuration
> is in some editable file somewhere.
> 
> Initially I built the version of R 2.15.1 on Solaris SPARC (virtual T4),
> but found out the build was done as 32 bit.  After some research, I
> found that the pre-compiled GCC version I had only allowed for 32 bit.
> I wanted 64 bit.  Therefore I ended up download the SunStudio compilers
> (12.1 version) and was able to export the compiler commands (per the R
> manual) and get a 64 bit version running.  The problem I have now is
> that I am trying to install the GBM package from CRAN (and from source
> as well.)  What I find is that something keeps trying to run
"c++"
> during compilation.  Since I only have the SUN compiler the file is
> named "CC" not "c++".  How do I override this?
> 
> I've tried the following with no success:
> 1. EXPORT CXX to point to my CC compiler (eg export
> CXX='/opt/SUNWspro/bin/CC')
> 2. Create an alias to c++ (eg alias c++='/opt/SUNWspro/bin/CC')
> 3. I even tried to create a symlink for g++: ln -s /opt/SUNWspro/bin/CC
> c++
Assuming you mean the gbm package. I had a look in the src directory of that
package.
There are .cpp files, which are C++ source files so it's not surprising that
a C++ compiler is required.
That's why R wants to use c++.

Berend

On 16 September 2012 at 13:47, Eberle, Anthony wrote:
| I have a question about how one can modify or override the compilers
| that R uses for package installations?  Or if perhaps this configuration
| is in some editable file somewhere.

You have several choices:

  a) system-wide:  $R_HOME/etc/Makeconf    

     (which we provide as a convenience link /etc/R/Makeconf on Debian/Ubuntu)

  b) per-user:     ~/.R/Makevars

     (which is my preferred personal choice to set gcc option, select clang,
...)

  c) per-package   src/Makevars


I like b) a lot to add/remove language-options such as -std=c++0x or -pedantic,
or to select clang / clang++ instead of gcc / g++, ...

Greetings to Northbrook,  Dirk  
  
-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com