thr3ads.net - R help - [R] Receive "unable to load shared object RNetCDF.o" during R INSTALL of RNetCDF [Sep 2011]

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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

head link

[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%
>
> ______________________________________________
> 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

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