Hi Kevin -
You are right, I do have the same syntax error and same final rpath, with
the only difference that I have netcdf 4.2.1.1
I had seen that yesterday, but forgot about it
I have now tried install.packages('ncdf4') with R 3.0.0 and R 3.0.2, with
identical results (except r3.0.0 uses cc, while r3.0.2 uses clang)
Thanks
Tobey


On Wed, Nov 20, 2013 at 12:29 PM, Kevin Ushey <kevinushey@gmail.com> wrote:

> 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 <tobeycarman@gmail.com>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
>>
>>         [[alternative HTML version deleted]]
>>
>>
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>> R-SIG-Mac@r-project.org
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>>
>>
>

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