[R] NetCDF within R: installation assistance

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Dec 23 22:53:28 CET 2008 

On Tue, 23 Dec 2008, Ken Schmidt wrote:

> Greetings.  I am attempting to add NetCDF libraries within R, and have 
> failed.  We have R version 2.8, and are running on a 64-bit Redhat Linux 
> 2.6.18 kernel:
>
> Red Hat Enterprise Linux Client release 5.2 (Tikanga)
> Linux halfmoon.ncdc.noaa.gov 2.6.18-92.1.22.el5 #1 SMP Fri Dec 5 09:28:22 EST 
> 2008 x86_64 x86_64 x86_64 GNU/Linux
>
> I have run the installation instructions found at 
> "http://www.image.ucar.edu/Software/Netcdf/", but not successfully.  I'm 
> wondering if you can give some advice that will change our outcome?
>
> We've run "R CMD INSTALL 
> --configure-args="-with-netcdf_incdir=/usr/local/netcdf-3.6.1/include 
> -with-netcdf_libdir=/usr/local/netcdf-3.6.1/lib" ncdf_1.6.tar.gz" against 
> NetCDF 3.6.1, 3.6.2, and 4.0 all with the same results.
> I think our being on a 64-bit Linux has to do with the failure.  Can you 
> confirm this?

No, it works successfully, as the CRAN check logs will confirm at
http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64/RNetCDF-00check.html

You need a PIC library on x86_64 Linux: it is normal for use dynamic 
libraries (which are PIC), and that is the problem you need to address 
(with your RHEL support, not here).


> Outputs are below from the 64-bit system "halfmoon":
>
> [root at halfmoon local]# R --version
> R version 2.8.0 (2008-10-20)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under the terms of the
> GNU General Public License version 2.
> For more information about these matters see
> http://www.gnu.org/licenses/.
>
>
> Here is my output:
>
> [root at halfmoon local]# R CMD INSTALL 
> --configure-args="-with-netcdf_incdir=/usr/local/netcdf-3.6.1/include 
> -with-netcdf_libdir=/usr/local/netcdf-3.6.1/lib" ncdf_1.6.tar.gz
> * Installing to library '/usr/local/lib64/R/library'
> * Installing *source* package 'ncdf' ...
> checking for gcc... gcc -std=gnu99
> 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 -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking /usr/local/netcdf-3.6.1/include/netcdf.h usability... yes
> checking /usr/local/netcdf-3.6.1/include/netcdf.h presence... yes
> checking for /usr/local/netcdf-3.6.1/include/netcdf.h... yes
> Using user-specified netCDF include dir=/usr/local/netcdf-3.6.1/include
> Found netcdf.h in: /usr/local/netcdf-3.6.1/include
> checking for /usr/local/netcdf-3.6.1/lib/libnetcdf.a... yes
> Using user-specified netCDF library dir=/usr/local/netcdf-3.6.1/lib
> Found netcdf library file libnetcdf.a in directory 
> /usr/local/netcdf-3.6.1/lib
> configure: creating ./config.status
> config.status: creating R/load.R
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/netcdf-3.6.1/include 
> -I/usr/local/include    -fpic  -g -O2 -c ncdf2.c -o ncdf2.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/netcdf-3.6.1/include 
> -I/usr/local/include    -fpic  -g -O2 -c ncdf3.c -o ncdf3.o
> ncdf3.c: In function 'R_nc_get_vara_charvarid':
> ncdf3.c:221: warning: assignment discards qualifiers from pointer target type
> ncdf3.c: In function 'R_nc_get_vara_numvarid':
> ncdf3.c:267: warning: assignment discards qualifiers from pointer target type
> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/netcdf-3.6.1/include 
> -I/usr/local/include    -fpic  -g -O2 -c ncdf.c -o ncdf.o
> ncdf.c: In function 'R_nc_ttc_to_nctype':
> ncdf.c:424: warning: implicit declaration of function 'exit'
> ncdf.c:424: warning: incompatible implicit declaration of built-in function 
> 'exit'
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf2.o ncdf3.o ncdf.o 
> -L/usr/local/netcdf-3.6.1/lib -lnetcdf
> /usr/bin/ld: /usr/local/netcdf-3.6.1/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/netcdf-3.6.1/lib/libnetcdf.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make: *** [ncdf.so] Error 1
> chmod: cannot access `/usr/local/lib64/R/library/ncdf/libs/*': No such file 
> or directory
> ERROR: compilation failed for package 'ncdf'
> ** Removing '/usr/local/lib64/R/library/ncdf'
>
> Thanks in advance,
>
> Ken Schmidt
> National Climatic Data Center
> Asheville, NC 28801
>
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>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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