[R] Compiling R Packages

[Erin Hodgess]

Which version of R are you using, please?

I had that problem with some earlier versions of R.



On Thu, Oct 30, 2008 at 3:59 PM, Cahill, Joshua
<Joshua.Cahill at sdstate.edu> wrote:
> I am working on a SLES 10 cluster with R available on it.  To better use my resources, I want to use Rmpi, but I am having a difficult time installing it.  I have set the $R_LIBS variable correctly.
>
> The MPI libraries are available through the PGI compiler, but this R instance was compiled with GCC.
>
> The Rmpi package can be compiled and installed with
>
> %R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args="CC=pgcc --with-mpi=/shared/pgi725/linux86-64/7.2/mpi/mpich"
>
> But when entering R and loading the library, I get
> %R
>> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so':
>  /home/<username>/.Rlib/Rmpi/libs/Rmpi.so: undefined symbol: __pgdbg_stub
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext,  :
>  dynamic/shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so' was not loaded
>>
>
> The undefined symbol is for the PGI debugger.
>
> It doesn't matter if the $CC variable is gcc, pgcc, or mpicc, and all three do show up in the make output during the configure process.
>
> Thanks for your help,
> Joshua
>
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-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com