Hello, I am having difficulty trying to install the xcms package for R 64-bit, on a machine running Red Hat Enterprise Linux Server release 5.4. The 32-bit version of R is also installed on there. Here is what I have done so far: The package has a dependency, netcdf-4.0.1. I've built this with the -fPIC flag so that it would be compatible with 64-bit version. So far so good. Then I try: R CMD INSTALL xcms and get the following: [emathe@helix MySoftware]$ R CMD INSTALL xcms * Installing to library '/home/emathe/R/i686-pc-linux-gnu-library/2.9' * Installing *source* package 'xcms' ... ** libs gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzROI.c -o mzROI.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp.c -o ramp.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c rampR.c -o rampR.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c util.c -o util.o gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c xcms.c -o xcms.o gcc -std=gnu99 -shared -L/usr/local/lib -o xcms.so base64.o mzROI.o netCDF.o ramp.o rampR.o util.o xcms.o -L/home/emathe/MySoftware/netcdf-4.0.1/lib -L/sw/lib -lnetcdf -lz -L/usr/local/R-2.9.1/lib/R/lib -lR /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libnetcdf.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [xcms.so] Error 1 ERROR: compilation failed for package 'xcms' * Removing '/home/emathe/R/i686-pc-linux-gnu-library/2.9/xcms' * Restoring previous '/home/emathe/R/i686-pc-linux-gnu- library/2.9/xcms' So I go into the xcms src and modify the MakeVars as you see below to reflect that I want to use R64: PKG_LIBS= -L/home/emathe/MySoftware/netcdf-4.0.1/lib -L/usr/lib64 -L/sw/lib -lnetcdf -lz PKG_CPPFLAGS= -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE But that doesn't work, I still get the same error. So then, I try to run the gcc's by hand, modifying the code as such: gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzROI.c -o mzROI.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp.c -o ramp.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c rampR.c -o rampR.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c util.c -o util.o gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c xcms.c -o xcms.o And that works just fine. But, the package is still not installed and I don't know what to do next. Can you help? Thanks, Ewy Ewy Mathé, Ph. D. Bioinformatics Staff Scientist, Laboratory of Human Carcinogenesis National Cancer Institute, NIH 37 Convent Drive Building 37, Room 3068 Bethesda, MD 20892-4255 Tel: 301-496-5835 Fax: 301-496-0497 [[alternative HTML version deleted]]

Ewy, I would try and recompile netCDF with the --enable-shared option on. I found that when I compile in 64 bit it does the trick. http://groups.google.com/group/xcms/browse_thread/thread/a323db68e2f0c 9e4/5abdb6ebe449ac6b?lnk=gst&q=configure+paul+benton#5abdb6ebe449ac6b Also xcms has it's own mailing list which you can find more about at: http://metlin.scripps.edu/download/ Hope it helps and let me know how it goes. Cheers, Paul H. Paul Benton Graduate Student Biomolecular Medicine Imperial College London South Kensington hpaul.benton08 at imperial.ac.uk On 8 Dec 2009, at 23:14, Mathe, Ewy (NIH/NCI) [E] wrote: > Hello, > > I am having difficulty trying to install the xcms package for R 64-bit, on a machine running Red Hat Enterprise Linux Server release 5.4. The 32-bit version of R is also installed on there. > > Here is what I have done so far: > > The package has a dependency, netcdf-4.0.1. I've built this with the -fPIC flag so that it would be compatible with 64-bit version. So far so good. > Then I try: > R CMD INSTALL xcms and get the following: > > [emathe at helix MySoftware]$ R CMD INSTALL xcms > * Installing to library '/home/emathe/R/i686-pc-linux-gnu- library/2.9' > * Installing *source* package 'xcms' ... > ** libs > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzROI.c -o mzROI.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp.c -o ramp.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c rampR.c -o rampR.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c util.c -o util.o > gcc -std=gnu99 -I/usr/local/R-2.9.1/lib/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c xcms.c -o xcms.o > gcc -std=gnu99 -shared -L/usr/local/lib -o xcms.so base64.o mzROI.o netCDF.o ramp.o rampR.o util.o xcms.o -L/home/emathe/MySoftware/netcdf-4.0.1/lib -L/sw/lib -lnetcdf -lz -L/usr/local/R-2.9.1/lib/R/lib -lR > /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC > /usr/local/lib/libnetcdf.a: could not read symbols: Bad value > collect2: ld returned 1 exit status > make: *** [xcms.so] Error 1 > ERROR: compilation failed for package 'xcms' > * Removing '/home/emathe/R/i686-pc-linux-gnu-library/2.9/xcms' > * Restoring previous '/home/emathe/R/i686-pc-linux-gnu- library/2.9/xcms' > > So I go into the xcms src and modify the MakeVars as you see below to reflect that I want to use R64: > PKG_LIBS= -L/home/emathe/MySoftware/netcdf-4.0.1/lib -L/usr/lib64 -L/sw/lib -lnetcdf -lz > PKG_CPPFLAGS= -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE > > But that doesn't work, I still get the same error. > So then, I try to run the gcc's by hand, modifying the code as such: > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzROI.c -o mzROI.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp.c -o ramp.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c rampR.c -o rampR.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c util.c -o util.o > gcc -std=gnu99 -I/usr/local/R-2.9.1-64/lib64/R/include -I/sw/include -I/home/emathe/MySoftware/netcdf-4.0.1/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c xcms.c -o xcms.o > > And that works just fine. But, the package is still not installed and I don't know what to do next. > > Can you help? > > Thanks, > Ewy > > > Ewy Math?, Ph. D. > Bioinformatics Staff Scientist, Laboratory of Human Carcinogenesis > National Cancer Institute, NIH > 37 Convent Drive > Building 37, Room 3068 > Bethesda, MD 20892-4255 > Tel: 301-496-5835 > Fax: 301-496-0497 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor