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Hello from mpls, and, I am seeking guidence on "unable to load shared object RNetCDF.o"

From: Dave B.
Sent on: Monday, September 5, 2011 10:49 PM
I have tried the 'official' list at the following link:

   "http://tolstoy.newcastle.edu.au/R/e15/help/11/09/index.html"

I followed up with the list owner with a request to remove a username I inadvertently included in my post and received a response from someone who seemed to be easily agitated. Long story short I have yet to see my post.

I am contacting you (in part) because I was recently in the area for the 'SF.com' conference. People here brag about how good Minneapolis is, but such people clearly have never been to San Francisco. I realize my post is likely an abuse of this list. But my recent visit reminded me of how nice people are out there (e.g. Gabriel the trumpet player). Should I make it to next year's conference I will buy the 13 list organizers a beer. This not a bribe, just an effort to show you that I am a nice person too. Here is my post:

On a Red Hat Linux cluster I am seeing the following error 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[masked]/include'
--with-udunits-lib='/soft/local/udunits[masked]/lib'"
RNetCDF_[masked].tar.gz

* installing to library ‘/soft/local/r/R[masked]/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[masked]/lib64/R/include
-I/soft/local/udunits[masked]/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[masked]/lib
-L/soft/local/netcdf/netcdf-3.6.2/libso -lexpat
installing to /soft/local/r/R[masked]/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[masked]/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[masked]/lib64/R/library/RNetCDF’

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