David Brown
2011-Sep-05 20:56 UTC
[R] Receive "unable to load shared object RNetCDF.o" during R INSTALL of RNetCDF
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%
Paul Hiemstra
2011-Sep-06 11:26 UTC
[R] Receive "unable to load shared object RNetCDF.o" during R INSTALL of RNetCDF
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%
>
> ______________________________________________
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> PLEASE do read the posting guide
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> 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
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