[BioC] installing xcms package for R 64-bit

[Benton, Paul]

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/a323db68e2f0c9e4/5abdb6ebe449ac6b?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 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
> 
> 
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