Hi Brian -- Prof. Ripley's reply to an earlier question
http://tolstoy.newcastle.edu.au/R/e2/help/07/08/24306.html points to the need for mpi to be compiled as a shared library. Hope that helps, Martin "Brian O'Gorman" <Brian.O'[EMAIL PROTECTED]> writes: > 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 > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.