Error while running matching_surface.csh

AMET
#1

The following error was received while running the matching_surface.csh file. Can you please help in resolving this.

Error: Required Package ncdf4 was not loaded
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘ncdf4’
Execution halted
Date/Time END

Thanks and regards.

#2

It appears the R package ncdf4 is not on your system. This is the R package that allows AMET to read NetCDF model output.

The install document has a list of these requirements.

This is a screen shot of the matching surface script. Here are the three dependencies of that script. The analysis scripts have a few additional plotting related R packages.

image002.jpg
image002.jpg814×142 25.8 KB

#3

Thank you sir for the reply. I have installed the RMySQL and date but am unable to install ncdf4. I get the following error.

If you installed the netcdf library (and nc-config) in a standard location, nc-config
should be found automatically. Otherwise, you can specify the full path and name of
the nc-config script by passing the --with-nc-config=/full/path/nc-config argument
flag to the configure script. For example:

./configure --with-nc-config=/sw/dist/netcdf4/bin/nc-config

Special note for R users:

To pass the configure flag to R, use something like this:

R CMD INSTALL --configure-args="–with-nc-config=/home/joe/bin/nc-config" ncdf4

where you should replace /home/joe/bin etc. with the location where you have
installed the nc-config script that came with the netcdf 4 distribution.

ERROR: configuration failed for package ‘ncdf4’

  • removing ‘/usr/lib64/R/library/ncdf4’

The downloaded source packages are in
‘/tmp/RtmpiEjw0N/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making ‘packages.html’ … done
Warning message:
In install.packages(c(“ncdf4”)) :
installation of package ‘ncdf4’ had non-zero exit status

My netcdf installations are present in my home location. How do I link the nc-config. I have tried configuring through R CMD INSTALL command too. But it doesnt work.
Kindly advice.

Thanks and regards.

#4

Sir,
Can ncdf be used instead of ncdf4 . I have installed netcdf without hdf5 due to which ncdf4 is not getting installed in R. What are the options?

Thanks and regards.

#5

Please attempt to install netcdf C and Fortran libraries according to the following instructions: https://github.com/USEPA/CMAQ/blob/master/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_build_library_gcc.md

#6

Thank you sir. The problem is resolved. I reinstalled netcdf with HDF5 support.