[R] ncdf4 installation problem: undefined symbol [SEC=UNCLASSIFIED]

[Andrew Harley]

Hello,
 
I'm trying to install ncdf4 on RHEL 5.8, R version 2.15.1.

Previously installed is netcdf 3.6.2 from Red Hat, so I've compiled and installed netcdf 4.2.1.1 (with hdf5 and zlib as per install instructions, and also set --enable-netcdf4 option) into /usr/local.

When attempting to install ncdf4 it is failing with:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/ncdf4/libs/ncdf4.so':
  /usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate
Error: loading failed
Execution halted

I'm guessing I'm missing somewhere that I need to specify the path, but the configure script picks up version netcdf 4.2.1.1 and explicitly setting LD_LIBRARY_PATH to /usr/local/lib doesn't help either. Can anyone please help with where I should be looking? Full command output below:

$ R CMD INSTALL ncdf4_1.6.1.tar.gz 
* installing to library '/usr/lib64/R/library'
* installing *source* package 'ncdf4' ...
** package 'ncdf4' successfully unpacked and MD5 sums checked
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:

This netCDF 4.2.1.1 has been built with the following features: 

  --cc        -> gcc
  --cflags    ->  -I/usr/local/include -I/usr/local/include
  --libs      -> -L/usr/local/lib -lnetcdf

  --has-c++   -> no
  --cxx       -> 
  --has-c++4  -> no
  --cxx4      -> 

  --fc        -> 
  --fflags    -> 
  --flibs     -> 
  --has-f90   -> no

  --has-dap   -> no
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no
  --has-szlib -> 

  --prefix    -> /usr/local
  --includedir-> /usr/local/include
  --version   -> netCDF 4.2.1.1

---
netcdf.m4: about to set rpath, here is source string: >-L/usr/local/lib -lnetcdf<
netcdf.m4: final rpath:   -Wl,-rpath,/usr/local/lib
Netcdf library version: netCDF 4.2.1.1
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: gcc
configure: creating ./config.status
config.status: creating R/load.R
config.status: creating src/Makevars
 
**********************  Results of ncdf4 package configure *******************
 
netCDF v4 CPP flags 	= -I/usr/local/include -I/usr/local/include
netCDF v4 LD flags  	=   -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf
netCDF v4 runtime path 	=   -Wl,-rpath,/usr/local/lib
 
******************************************************************************

** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c ncdf.c -o ncdf.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c ncdf2.c -o ncdf2.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c ncdf3.c -o ncdf3.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c src_ncdf4.c -o src_ncdf4.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/ncdf4/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ncdf4'
    finding HTML links ... done
    ancdf4                                  html  
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:58: missing file link 'ncvar_put'
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:76: missing file link 'ncvar_put'
    ancvar_put                              html  
    nc_close                                html  
    nc_create                               html  
    nc_enddef                               html  
    nc_open                                 html  
    nc_redef                                html  
    nc_sync                                 html  
    nc_version                              html  
    ncatt_get                               html  
    ncatt_put                               html  
    ncdf4-internal                          html  
    ncdim_def                               html  
    ncvar_add                               html  
    ncvar_change_missval                    html  
    ncvar_def                               html  
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:67: missing file link 'ncvar_put'
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:100: missing file link 'ncvar_put'
    ncvar_get                               html  
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_get.Rd:77: missing file link 'ncvar_put'
    ncvar_rename                            html  
    print.ncdf4                             html  
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib64/R/library/ncdf4/libs/ncdf4.so':
  /usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/lib64/R/library/ncdf4'

Thanks,

Andrew Harley
Linux Systems Administrator
Climate and Water Division (ICT Operations)
Bureau of Meteorology, Australia
03 9616 8441
http://www.bom.gov.au/water/