[R-sig-Geo] NetCDF: Unknown file format?

[Michael Sumner]

Hello,

On Thu, 30 Jul 2015 at 01:54 Ziyu Ma <paul.ziyu.ma at gmail.com> wrote:

> Dear all,
>
> I just found out the "raster" package actually handles NetCDF4 very nicely:
> for example, NetCDF4 files can be converted to a raster simply by:
>
> raster("FileName.nc", varname="SingleVariableToExtractInTheNetCDF4File")
>
>
That is great - but raster (last time I looked) relies on ncdf or ncdf4
being available for this format.
Is this now on Linux rather than Windows?  Can you please include the
output of sessionInfo()? (which lists the R build and package versions)

FWIW, if you didn't have either ncdf or ncdf4 it would pass to the GDAL
logic (via rgdal) and you might get success (but not on the
Windows-CRAN-rgdal, which doesn't include NetCDF - another wrinkle in this
adventure).

Cheers, Mike.


I think it might be useful information to everybody so I repost it here.
>
> Cheers,
> Ma
>
> Ziyu Ma
> PhD Student
> Ecoinformatics & Biodiversity,
> Department of Bioscience, Aarhus University
> Ny Munkegade 114, DK-8000 Aarhus C, Denmark
>
>
> On Wed, Jul 29, 2015 at 3:22 PM, Ziyu Ma <paul.ziyu.ma at gmail.com> wrote:
>
>> Thank you Mike,
>>
>> I see that there's probably no fast solution for this. And yes, there are
>> lots of data. I will learn to work with it in Linux then.
>>
>> Cheers
>> Ma
>>
>> Ziyu Ma
>> PhD Student
>> Ecoinformatics & Biodiversity,
>> Department of Bioscience, Aarhus University
>> Ny Munkegade 114, DK-8000 Aarhus C, Denmark
>>
>>
>> On Wed, Jul 29, 2015 at 2:27 PM, Michael Sumner <mdsumner at gmail.com>
>> wrote:
>>
>>>  Essentially this is probably that NetCDF4 (version 4 of the external
>>> library) is required, but that neither ncdf or RNetCDF have been built with
>>> that. The ncdf4 package is the only one that *requires* this, and CRAN
>>> supports NetCDF-3 for Windows via ncdf and RNETCDF and doesn't support
>>> ncdf4 for Windows.
>>>
>>> (There are many features in the NetCDF format, and there are many
>>> features not supported by any of these packages whether version 4 or not.)
>>>
>>> You can get a build of ncdf4 for Windows here:
>>>
>>> http://cirrus.ucsd.edu/~pierce/ncdf/
>>>
>>> but you're on your own in terms of what version of R that will work in,
>>> if at all, etc.
>>>
>>> You can  build one of the three packages yourself against NetCDF4
>>> proper, and that is my preference - it's easiest on Linux, but it's not
>>> exactly "easy" if you are used to windows and the CRAN support for binary
>>> packages.
>>>
>>> If this is confusing that's just how it is - there are three R packages
>>> for NetCDF, none of them support everything in NetCDF and what works best
>>> depends on what you have available. If you have to do this a lot I
>>> recommend learning to work in Linux.
>>>
>>> Cheers, Mike.
>>>
>>> On Wed, 29 Jul 2015 at 21:45 Ziyu Ma <paul.ziyu.ma at gmail.com> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I tried to use R to open NetCDF file from the ESA's  soil moisture
>>>> database:
>>>> http://www.esa-soilmoisture-cci.org/node/145
>>>>
>>>> I have tried to use the R packages "ncdf" or "RNetCDF", but whenever I
>>>> tried to open the file, I have this same error message:
>>>>
>>>> "Error in R_nc_open: NetCDF: Unknown file format"
>>>>
>>>> I'm confused since I think both packages where designed to handle this
>>>> file
>>>> format. Is there some other dependent softwares/packages missing on my
>>>> computer? I'm running Windows 7 64 bit and R 3.2.0 64 bit.
>>>>
>>>> The soil moisture database recommends the "ncdf4" package, but the
>>>> Windows
>>>> version of it is no longer available.
>>>>
>>>> Thank you very much.
>>>>
>>>> Cheers,
>>>> Ma
>>>>
>>>> Ziyu Ma
>>>> PhD Student
>>>> Ecoinformatics & Biodiversity,
>>>> Department of Bioscience, Aarhus University
>>>> Ny Munkegade 114, DK-8000 Aarhus C, Denmark
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>
>>
>

	[[alternative HTML version deleted]]