[R] Rmpi on Linux x86_64 GNU/Linux

[Brian O'Gorman]

I'm having trouble with R CMD INSTALL Rmpi_0.5-5.tar.gz 
--configure-args=~/lam

lam is is installed locally.
lamboot  -d (or lamboot-d and also recon) works. make -k check from the 
lamtest suite passes all tests.
Is this is problem with the -fPIC compiler as in the message? Should it 
be modified in the Makefile?
Any help or comments are appreciated, thanks.


* Installing to library 
'/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6'
* Installing *source* package 'Rmpi' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Try to find mpi.h ...
Found in /import/home/u1/uaf/ogorman/lam/include
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... yes
Try to find liblam.so ...
checking for main in -llam... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include 
-I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include 
-DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c conversion.c 
-o conversion.o
gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include 
-I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include 
-DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c internal.c 
-o internal.o
gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include 
-I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include 
-DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c RegQuery.c 
-o RegQuery.o
gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include 
-I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include 
-DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o 
internal.o RegQuery.o Rmpi.o -L/import/home/u1/uaf/ogorman/lam/lib -lmpi 
-llam -lutil -lpthread -fPIC  
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: 
/import/home/u1/uaf/ogorman/lam/lib/libmpi.a(abort.o): relocation 
R_X86_64_32 can not be used when making a shared object; recompile with 
-fPIC
/import/home/u1/uaf/ogorman/lam/lib/libmpi.a: could not read symbols: 
Bad value
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
chmod: cannot access 
`/import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi/libs/*': 
No such file or directory
ERROR: compilation failed for package 'Rmpi'
** Removing 
'/import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi'

-- 
"The struggle for today, is not altogether for today - it is for a vast future also."
	-- Abraham Linclon, December 3, 1861