Hi Tobey,
I'm running R on Mac OS X, installed netcdf from Homebrew, and I run into
the same problem when installing ncdf from source. I see one obvious error
in the configure step (my guess is you are having a similar error, but
without your configure output we can't know):
netcdf.m4: about to set rpath, here is source string:
>-L/usr/local/Cellar/netcdf/4.3.0/lib -lnetcdf<
expr: syntax error
netcdf.m4: final rpath: -Wl,-rpath,
So, for me, $NETCDF_LDFLAGS == -L/usr/local/Cellar/netcdf/4.3.0/lib
-lnetcdf. This is the part that fails in the configure step:
for word in $NETCDF_LDFLAGS; do
if test `expr $word : -L/` -eq 3; then
slibdir=`expr substr $word 3 9999`
NETCDF_RPATH="$NETCDF_RPATH -Wl,-rpath,$slibdir"
fi
done
So, something is wrong with how `expr` is being called, it seems. You
should forward this to the maintainer. Perhaps `expr` is being used in a
non-portable way.
-Kevin
On Wed, Nov 20, 2013 at 12:49 PM, Tobey Carman <[email protected]>wrote:
> Hi -
> I am not sure if this is the right place for this question. I am fairly new
> to R and still figuring out how to best manage packages. If this is not the
> best venue for this question, please direct me elsewhere.
>
> I am trying to install the ncdf4 R package using:
>
> > install.packages('ncdf4')
>
> This command, downloads the package, finds nc-config, appears to collect
> all the correct settings, and appears to compile ncdf4 with no errors. But
> after compiling, and running a few tests, the command fails during a test
> to load the just-compiled ncdf4 libraries:
>
> > install.packages('ncdf4')
> ...
> skipping lots of output for downloading, nc-config, configuring, compiling,
> testing...
> ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
>
> '/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so':
>
>
> dlopen(/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so,
> 6): Symbol not found: _nc_close
> Referenced from:
>
> /usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so
> Expected in: flat namespace
> in
>
> /usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
>
> /usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4
> Warning in install.packages :
> installation of package ncdf4 had non-zero exit status
> >
>
> I am on a Mac, 10.8.2. I am using Homebrew to manage my packages. I have
> the main netcdf library, 4.2.1.1, that is installed via Homebrew and has
> been working fine in several other applications. Likewise I am using a
> Homebrew version of R.
>
> I am not sure how to keep trouble shooting this. I can provide more output
> if necessary.
> Thanks,
>
> Tobey Carman
>
> Spatial Ecology Lab,
> University of Alaska Fairbanks
>
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>
>
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