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: Sun, 11 May 2014 19:25:58 +0200

Thank you Dave,

in my script I imported a dataset and I create the netcdf variable and 
dimensins and I would like to create a netCDF-4 file with nc_create(). 
I set force_v4=FALSE, and now it works. Previously it was force_v4=TRUE. 

Thank you for the suggestions. 

Regards, 

Emanuele


 
On May 9, 2014, at 4:39 PM, David W. Pierce wrote:

> It's possible it's simply an error in ncdf4. I don't know how many people 
> specify force_v4=TRUE, that may not be a well-tested branch of the code. Can 
> you send me a minimal R script and/or necessary data that reproduces this?
> 
> Regards,
> 
> --Dave
> 
> 
> 
> On Fri, May 9, 2014 at 7:14 AM, David W. Pierce <dpierce@xxxxxxxx> 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.
> 
> 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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> 
> 
> -- 
> David W. Pierce
> Division of Climate, Atmospheric Science, and Physical Oceanography
> Scripps Institution of Oceanography, La Jolla, California, USA
> (858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce@xxxxxxxx

• 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
  • Re: [netcdfgroup] how to link netcdf4 to R package ncdf4
    • From: David W. Pierce