Re: [netcdfgroup] how to link netcdf4 to R package ncdf4

• To: "David W. Pierce" <dpierce@xxxxxxxx>
• Subject: Re: [netcdfgroup] how to link netcdf4 to R package ncdf4
• From: Emanuele Cordano <emanuele.cordano@xxxxxxxxx>
• Date: Fri, 9 May 2014 16:29:10 +0200

Thank you David, 

I work with Snow Leopard 

I got the following: 

vara:~ ecor$ nc-config --all

This netCDF 4.3.2 has been built with the following features: 

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

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

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

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

  --prefix    -> /Users/ecor/local
  --includedir-> /Users/ecor/local/include
  --version   -> netCDF 4.3.2



vara:~ ecor$ 

On May 9, 2014, at 4:14 PM, David W. Pierce wrote:

> Hi Emanuele
> 
> Barring bugs, it should not be possible to install ncdf4 correctly without it 
> knowing where the libraries are. I think it's more likely that the netcdf  
> library was not compiled with netcdf version 4 support enabled. When you do 
> "nc-config --all" from your command line, what does it report?
> 
> Also, am I right in assuming that this is a typo: "netcdf-4 and hfd4 
> library"? You need the hdf5 library for modern (version 4) functionality, not 
> the hdf4 library.
> 

Sorry for typo,   I wanted to say "hdf5"

Thank you 

Emanuele

> Regards,
> 
> --Dave
> 
> On May 9, 2014 4:32 AM, "Emanuele Cordano" <emanuele.cordano@xxxxxxxxx> wrote:
> Dear all, 
> 
> I'm using the netcdf-4 libraries from R. 
> I installed ncdf4 package 
> (http://cran.r-project.org/web/packages/ncdf4/index.html) and also the 
> netcf-4 land hfd4 library as written on 
> http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_default.
> 
> I launched an R script where a netCDF archive with weather data should be 
> created but I obtain the following error:
> ....
> "Calling R_nc4_create for file  
> /Users/ecor/Documents/workspace_new/activity_misc/RSUBDAILYCLIM/inst/trentino/data"
> Error in R_nc4_create: NetCDF: Can't add HDF5 file metadata (creation mode 
> was 4096)
> Error in nc_create(ncpath, nclist, force_v4 = TRUE, verbose = TRUE) : 
>   Error in nc_create!
> In addition: There were 16 warnings (use warnings() to see them)
> 
> It looks like ncdf4 does not find the netcdf-4 and hdf5 libraries. 
> How can I link these libraries to the R ncdf4 package? 
> Actually I have not found yet  any instruction about this on the web. 
> 
> Thank you 
> Regards
> 
> Emanuele Cordano
> 
> 
> 
> 
> 
> Emanuele Cordano
> Environmental Engineer / Ingegnere per l' Ambiente e il territorio nr. 3587 
> (Albo A - Provincia di Trento)
> Fondazione Edmund Mach
> CRI - Reasearch and Innovation Center
> Agro-Eco-System Dynamic Platform
> Via Mach 1
> 38017 San Michele All'Adige (Italy)
> phone +39 0461 615397
> email: emanuele.cordano@xxxxxxxx ,emanuele.cordano@xxxxxxxxx
> 
> 
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• References:
  • [netcdfgroup] how to link netcdf4 to R package ncdf4
    • From: Emanuele Cordano
  • Re: [netcdfgroup] how to link netcdf4 to R package ncdf4
    • From: David W. Pierce