Open rsieg opened 4 years ago
lebensterben
commented
4 years ago NetCDF has extensive documentation but it's really confusing on what exact utilities you need to install the R ncdf4 package.
It seems that the C library is what other language interfaces depend on. https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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rsieg
commented
4 years ago Probably. I don't know enough to be sure, though. I have asked the ncdf4 package creator/maintainer for advice.
Thanks
On 1/30/20 7:04 PM, Lucius Hu wrote:
NetCDF has extensive documentation but it's really confusing on what exact utilities you need to install the R ncdf4 package.
It seems that the C library is what other language interfaces depend on. https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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rsieg
commented
4 years ago I checked with the creator of R's ncdf4 package. He confirms that C is the way to go.
On Thu, Jan 30, 2020, 19:04 Lucius Hu notifications@github.com wrote:
NetCDF has extensive documentation but it's really confusing on what exact utilities you need to install the R ncdf4 package.
It seems that the C library is what other language interfaces depend on.
https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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rsieg
commented
4 years ago swupd now lists NetCDF as part of the R-extras package. It is not listed under R-extras in bundles.html. Whom to believe?
On 1/30/20 7:04 PM, Lucius Hu wrote:
NetCDF has extensive documentation but it's really confusing on what exact utilities you need to install the R ncdf4 package.
It seems that the C library is what other language interfaces depend on. https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
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lebensterben
commented
4 years ago Just install R-extras bundle and check whether it's indeed installed.
rsieg
commented
4 years ago "find" does not indicate the presence of anything netcdf or ncdf in R bundles. ncdf occurs in Python. Trying to install R's ncdf4 package in R-studio fails. ncdf4 requires NetCDF's nc-config.
Installation of the ncdf4 package in CL R-studio on another computer on which I installed NetCDF4 from source succeeds. Even though the NetCDF4 install did not pass many of its tests, the important (from R's standpoint) nc-config file is present.
On 2/5/20 7:31 PM, Lucius Hu wrote:
Just install R-extras bundle and check whether it's indeed installed.
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fenrus75
commented
4 years ago I've tried to add these to R-extras fwiw.... surprised it's not working?
On Sat, Feb 8, 2020 at 10:34 AM rsieg notifications@github.com wrote:
"find" does not indicate the presence of anything netcdf or ncdf in R bundles. ncdf occurs in Python. Trying to install R's ncdf4 package in R-studio fails. ncdf4 requires NetCDF's nc-config.
Installation of the ncdf4 package in CL R-studio on another computer on which I installed NetCDF4 from source succeeds. Even though the NetCDF4 install did not pass many of its tests, the important (from R's standpoint) nc-config file is present.
On 2/5/20 7:31 PM, Lucius Hu wrote:
Just install R-extras bundle and check whether it's indeed installed.
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rsieg
commented
4 years ago Trying certainly is appreciated. Does the question indicate it loads OK into R-studio for you?
If not, might it be simpler to create a bundle of NetCDF and HDF5? These are used by programs in quite a few languages.
On 2/8/20 11:04 AM, Arjan van de Ven wrote:
I've tried to add these to R-extras fwiw.... surprised it's not working?
On Sat, Feb 8, 2020 at 10:34 AM rsieg notifications@github.com wrote:
"find" does not indicate the presence of anything netcdf or ncdf in R bundles. ncdf occurs in Python. Trying to install R's ncdf4 package in R-studio fails. ncdf4 requires NetCDF's nc-config.
Installation of the ncdf4 package in CL R-studio on another computer on which I installed NetCDF4 from source succeeds. Even though the NetCDF4 install did not pass many of its tests, the important (from R's standpoint) nc-config file is present.
On 2/5/20 7:31 PM, Lucius Hu wrote:
Just install R-extras bundle and check whether it's indeed installed.
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rsieg
commented
4 years ago I did a proper install from source today of HDF5 and NetCDF. Then, I was able to install the R package ncdf4 again, and everything seems to work from R studio. Just so you know one or two variables are eliminated.
On Sat, Feb 8, 2020, 16:30 Bob Siegfried robtsiegfried@gmail.com wrote:
Trying certainly is appreciated. Does the question indicate it loads OK into R-studio for you?
If not, might it be simpler to create a bundle of NetCDF and HDF5? These are used by programs in quite a few languages.
On 2/8/20 11:04 AM, Arjan van de Ven wrote:
I've tried to add these to R-extras fwiw.... surprised it's not working?
On Sat, Feb 8, 2020 at 10:34 AM rsieg notifications@github.com notifications@github.com wrote:
"find" does not indicate the presence of anything netcdf or ncdf in R bundles. ncdf occurs in Python. Trying to install R's ncdf4 package in R-studio fails. ncdf4 requires NetCDF's nc-config.
Installation of the ncdf4 package in CL R-studio on another computer on which I installed NetCDF4 from source succeeds. Even though the NetCDF4 install did not pass many of its tests, the important (from R's standpoint) nc-config file is present.
On 2/5/20 7:31 PM, Lucius Hu wrote:
Just install R-extras bundle and check whether it's indeed installed.
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lebensterben
commented
4 years ago @rsieg
I failed to install ncdf4 in R with error
ERROR: configuration failed for package ‘ncdf4’
* removing ‘/home/lucius/R/x86_64-generic-linux-gnu-library/3.6/ncdf4’This might result from missing nc-config script that comes with netcdf 4 distribution.
But I'm able to load ncdf4 library in R with library(ncdf4), which is provided in R-extras bundle. Can you check whether this library works?
rsieg
commented
4 years ago R's ncdf4 library works with installation of the R-extras package. Tested with sresa1b_ncar_ccsm3-example.nc https://www.unidata.ucar.edu/software/netcdf/examples/sresa1b_ncar_ccsm3-example.nc from https://www.unidata.ucar.edu/software/netcdf/examples/files.html
On 2/10/20 7:26 PM, Lucius Hu wrote:
@rsieg https://github.com/rsieg
I failed to install |ncdf4| in R with error
|ERROR: configuration failed for package ‘ncdf4’ * removing ‘/home/lucius/R/x86_64-generic-linux-gnu-library/3.6/ncdf4’ |
This might result from missing |nc-config| script that comes with |netcdf 4| distribution.
But I'm able to load |ncdf4| library in R with |library(ncdf4)|, which is provided in |R-extras| bundle. Can you check whether this library works?
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NetCDF utilities are required to install the R package ncdf4. Swupd search returns "Bundle with the best search result: python-extras", but a search of python-extras does not show that to be the case, nor, having python-extras installed, can I find netcdf in my file system. I would like to request the NetCDF libraries be made available.