[R] Receive "unable to load shared object RNetCDF.o" during R INSTALL of RNetCDF

[Prof Brian Ripley]

The problem appears to be udunits2, which RNetCDF uses and ncdf does 
not.  Specifically

>> --with-udunits-lib='/soft/local/udunits-2.1.23/lib'"

is that path in the ld.so cache or in LD_LIBRARY_PATH?  If not, it 
will not be found by dlload.

On Tue, 6 Sep 2011, Paul Hiemstra wrote:

> Hi,
>
> You could try installing the ncdf package. This installed for my without
> any problems when RNetCDF failed. I suspect ncdf has very similar
> functionality, but i've only worked with ncdf.
>
> install.packages("ncdf")
>
> should do the trick...
>
> cheers,
> Paul
>
> On 09/05/2011 08:56 PM, David Brown wrote:
>> On a Red Hat Linux cluster I am seeing the following after multiple
>> other packages were successfully installed. The error seems to suggest
>> that RNetCDF.o was not copied to the appropriate lib folder. The admin
>> user performing the install has the required privileges to perform the
>> install. Words of wisdom are greatly appreciated:
>>
>> R CMD INSTALL --configure-args="--with-netcdf-include='/soft/local/netcdf/netcdf-3.6.2/include/'
>> --with-netcdf-lib='/soft/local/netcdf/netcdf-3.6.2/libso'
>> --with-udunits-include='/soft/local/udunits-2.1.23/include'
>> --with-udunits-lib='/soft/local/udunits-2.1.23/lib'"
>> RNetCDF_1.5.2-2.tar.gz
>>
>> * installing to library ‘/soft/local/r/R-2.13.1/lib64/R/library’
>> * installing *source* package ‘RNetCDF’ ...
>> 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 ISO C89... none needed
>> checking for nc_open in -lnetcdf... yes
>> checking for utInit in -ludunits2... no
>> checking for utScan in -ludunits2... yes
>> checking how to run the C preprocessor... gcc -std=gnu99 -E
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for ANSI C header files... no
>> 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 netcdf.h usability... yes
>> checking netcdf.h presence... yes
>> checking for netcdf.h... yes
>> checking udunits.h usability... yes
>> checking udunits.h presence... yes
>> checking for udunits.h... yes
>> configure: creating ./config.status
>> config.status: creating R/load.R
>> config.status: creating src/Makevars
>> ** libs
>> gcc -std=gnu99 -I/soft/local/r/R-2.13.1/lib64/R/include
>> -I/soft/local/udunits-2.1.23/include
>> -I/soft/local/netcdf/netcdf-3.6.2/include/  -I/usr/local/include
>> -fpic  -g -O2 -c RNetCDF.c -o RNetCDF.o
>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o RNetCDF.so RNetCDF.o
>> -ludunits2 -lnetcdf -L/soft/local/udunits-2.1.23/lib
>> -L/soft/local/netcdf/netcdf-3.6.2/libso -lexpat
>> installing to /soft/local/r/R-2.13.1/lib64/R/library/RNetCDF/libs
>> ** R
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
>> '/soft/local/r/R-2.13.1/lib64/R/library/RNetCDF/libs/RNetCDF.so':
>>   libudunits2.so.0: cannot open shared object file: No such file or directory
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing ‘/soft/local/r/R-2.13.1/lib64/R/library/RNetCDF’
>> [swadm at boar01]/soft/local/temp%
>>
>> ______________________________________________
>> R-help at 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.
>
>
> -- 
> Paul Hiemstra, Ph.D.
> Global Climate Division
> Royal Netherlands Meteorological Institute (KNMI)
> Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
> P.O. Box 201 | 3730 AE | De Bilt
> tel: +31 30 2206 494
>
> http://intamap.geo.uu.nl/~paul
> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>
> ______________________________________________
> R-help at 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.
>

-- 
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