RNetCDF cannot open shared object file

Question

I am trying to install the RNetCDF package on my laptop (Ubuntu 12.04) with the command

install.packages('RNetCDF',lib='/home/my_computer/RSCRIPTS/R_LIB/',configure.args="--with-netcdf-include='/home/my_computer/bin/libs4cdo-0.0.10/netcdf-4.2/include/' --with-netcdf-lib='/home/my_computer/local/bin' --with-hdf5-lib='/home/my_computer/local/lib/' --with-udunits-include='/usr/local/lib/' --with-udunits-lib='/usr/local/lib/'",repos='http://star-www.st-andrews.ac.uk/cran/')

but the package won't install. See the message below:

trying URL 'http://star-www.st-andrews.ac.uk/cran/src/contrib/RNetCDF_1.6.1-2.tar.gz'
Content type 'application/x-gzip' length 70301 bytes (68 Kb)
opened URL
==================================================
downloaded 68 Kb

* installing *source* package ‘RNetCDF’ ...
** package ‘RNetCDF’ successfully unpacked and MD5 sums checked
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... 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 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/usr/share/R/include -I/usr/local/lib/ -I/home/bauduinm/bin/libs4cdo-0.0.10/netcdf-4.2/include/      -fpic  -O3 -pipe  -g -c RNetCDF.c -o RNetCDF.o
gcc -std=gnu99 -shared -o RNetCDF.so RNetCDF.o -ludunits2 -lnetcdf -L/home/my_computer/local/lib/ -L/usr/local/lib/ -L/home/my_computer/local/bin -lexpat -L/usr/lib/R/lib -lR
installing to /home/my_computer/RSCRIPTS/R_LIB/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 '/home/my_computer/RSCRIPTS/R_LIB/RNetCDF  /libs/RNetCDF.so':
libexpat.so.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed  
* removing ‘/home/my_computer/RSCRIPTS/R_LIB/RNetCDF’

The downloaded packages are in
‘/tmp/Rtmpl5MniY/downloaded_packages’
Warning message:
In install.packages("RNetCDF", lib = "/home/my_computer/RSCRIPTS/R_LIB/",  :
    installation of package ‘RNetCDF’ had non-zero exit status

When I try with

sudo R CMD INSTALL --libary='/home/my_computer/RSCRIPTS/R_LIB/' --configure-args="--with-netcdf-include='/home/my_computer/bin/libs4cdo-0.0.10/netcdf-4.2/include/' --with-netcdf-lib='/home/my_computer/local/lib/' --with-hdf5-lib='/home/my_computer/local/lib/' --with-udunits-include=/usr/local/lib/ --with-udunits-lib=/usr/local/lib/" /home/my_computer/Downloads/RNetCDF_1.6.1-2.tar.gz

the error message is replaced with

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
unable to load shared object '/usr/local/lib/R/site-library/RNetCDF/libs/RNetCDF.so':
  libnetcdf.so.7: cannot open shared object file: No such file or directory

libnetcdf.so.7 is definitely in /home/my_computer/local/lib/ which is also my LD_LIBRARY_PATH. Admittedly, the libexpat.so.0, which is one of the files in the first error message (with install.packages), is situated in intel related folders which don't look like they have anything to do with netcdf libraries.

Could anyone enlighten me?

Thanks.

Edit: Well, I'll never know what happened because when I tried again 3 days later with the exact same install.packages command line the package installed without any problems whatsoever... So my only advice to someone who may have the same problem is to log out of R and start again, just in case some previous mistakes in the session remained in the log.

Answer 1

Try adding --no-test-load to R CMD INSTALL this will avoid the error during the install.

Then check if you can load the package in a normal R session (with library(RNetCDF)). If this fails due to the 'unable to load shared object' error:

1. check if R uses your $LD_LIBRARY_PATH with Sys.getenv("LD_LIBRARY_PATH")
2. look the output of ldd /usr/local/lib/R/site-library/RNetCDF/libs/RNetCDF.so and see whether the libnetcdf.so.7 is resolved to path that is included in R's LD_LIBRARY_PATH

BTW, I had no problems installing RNetCDF using the libnetcdf that comes with Ubuntu (apt-get install libnetcdf-dev [version 4.1.1]); unless you definitely need version 4.2 of libnetcdf you might want to try this.