opendap accessibility on Windows

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opendap accessibility on Windows

Christina Hernandez
Hello,

I am working on a project where we are accessing large data files via opendap. Myself and two of the higher-ups on the project are working on Windows machines, and we have been unable to access remote files using the ncdf4 package. We have followed the package author's notes for installation on a Windows machine, and we have successfully installed the netcdf-4 libraries and the ncdf4 R package. However, the program still works only on local files. It is not an issue with connectivity of my machine since I am able to remotely access these same data files using Matlab.
I then attempted to follow the package author's notes on cross-compiling in a Linux environment, I was using a Ubuntu Virtual Box. These notes are available here: http://cirrus.ucsd.edu/~pierce/ncdf/how_to_build_on_windows.html
However, I do not really know what I'm doing and I was unable to successfully cross-compile the dependencies. Has anyone dealt with this on a Windows machine? Is there a different way to access remote files through R? \We have considered writing a Python script that can be run from within an R program, so that users that are only familiar with R can still access remote files without downloading a lot of large files.
Any advice is appreciated.


Christina Hernandez
Research Assistant
Ecosystem Modeling Lab
Gulf of Maine Research Institute
[hidden email]


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Re: opendap accessibility on Windows

Roy Mendelssohn - NOAA Federal
Hi Christina:

My memory is that Pierce had problems getting the netcdf4 library to work with OpeNDAP included on Windows.  OPeNDAP does work with ncdf4 on a Mac or a Linux box.

So one option is to run on a Linux VM on Windows.  There may be more direct options, depending on what datasets you are trying to access. Can you send me the URLs you are trying to access?

Thanks,

-Roy



> On Jul 6, 2015, at 5:08 AM, Christina Hernandez <[hidden email]> wrote:
>
> Hello,
>
> I am working on a project where we are accessing large data files via opendap. Myself and two of the higher-ups on the project are working on Windows machines, and we have been unable to access remote files using the ncdf4 package. We have followed the package author's notes for installation on a Windows machine, and we have successfully installed the netcdf-4 libraries and the ncdf4 R package. However, the program still works only on local files. It is not an issue with connectivity of my machine since I am able to remotely access these same data files using Matlab.
> I then attempted to follow the package author's notes on cross-compiling in a Linux environment, I was using a Ubuntu Virtual Box. These notes are available here: http://cirrus.ucsd.edu/~pierce/ncdf/how_to_build_on_windows.html
> However, I do not really know what I'm doing and I was unable to successfully cross-compile the dependencies. Has anyone dealt with this on a Windows machine? Is there a different way to access remote files through R? \We have considered writing a Python script that can be run from within an R program, so that users that are only familiar with R can still access remote files without downloading a lot of large files.
> Any advice is appreciated.
>
>
> Christina Hernandez
> Research Assistant
> Ecosystem Modeling Lab
> Gulf of Maine Research Institute
> [hidden email]
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
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______________________________________________
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Re: opendap accessibility on Windows

Michael Sumner-2
In reply to this post by Christina Hernandez
On Tue, 7 Jul 2015 at 01:38 Christina Hernandez <[hidden email]> wrote:

> Hello,
>
> I am working on a project where we are accessing large data files via
> opendap. Myself and two of the higher-ups on the project are working on
> Windows machines, and we have been unable to access remote files using the
> ncdf4 package. We have followed the package author's notes for installation
> on a Windows machine, and we have successfully installed the netcdf-4
> libraries and the ncdf4 R package.


I've done this on Windows by using Unidata's DLLs that they provide for
download and including them in the build process for ncdf4:

http://www.unidata.ucar.edu/software/netcdf/docs/winbin.html

But this leaves you several branches out with an unsupported package build
(by CRAN) and with Microsoft compiled opendap files.

Please note that you don't need ncdf4 for NetCDF4 faciilties, RNetCDF (and
ncdf) can be built with that version and many features (including remote
file access) work fine.

I would aim for working on Linux, it's much more straightforward to
build/get these tools there. It would be excellent if CRAN's win builder
had these standard libraries, and others like HDF4/5,  but I don't know if
that is possible.

cheers, Mike.

However, the program still works only on local files. It is not an issue

> with connectivity of my machine since I am able to remotely access these
> same data files using Matlab.
> I then attempted to follow the package author's notes on cross-compiling
> in a Linux environment, I was using a Ubuntu Virtual Box. These notes are
> available here:
> http://cirrus.ucsd.edu/~pierce/ncdf/how_to_build_on_windows.html
> However, I do not really know what I'm doing and I was unable to
> successfully cross-compile the dependencies. Has anyone dealt with this on
> a Windows machine? Is there a different way to access remote files through
> R? \We have considered writing a Python script that can be run from within
> an R program, so that users that are only familiar with R can still access
> remote files without downloading a lot of large files.
> Any advice is appreciated.
>
>
> Christina Hernandez
> Research Assistant
> Ecosystem Modeling Lab
> Gulf of Maine Research Institute
> [hidden email]
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.