Better debugging for model2netcdf.ED2

[Aariq]

Description

1. wraps ncdf4::ncvar_put() so that the variable name is printed before any warnings it gives
2. changes behavior of an on.exit() to remove warnings about closing nc connection multiple times

(I also snuck in removing an incorrect usage of ...)

Motivation and Context

Currently model2netcdf.ED2() prints a lot of warnings of the form

"ncvar_put: warning: you asked to write xxx values, but the passed data array has yyy entries!"

These warnings are uninformative in this context because the variable name is not printed anywhere.

Before

> model2netcdf.ED2("completed_runs/MANDIFORE-PNW-4538/outdir/out/ENS-00001-1000020684/", settings = settings)
2022-12-19 21:40:29 INFO   [model2netcdf.ED2] : 
   ----- Processing year: 2002 
2022-12-19 21:40:29 INFO   [read_E_files] : 
   *** Reading -E- file *** 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
2022-12-19 21:40:38 INFO   [model2netcdf.ED2] : 
   *** Writing netCDF file *** 
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
[1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!"
2022-12-19 21:40:38 INFO   [model2netcdf.ED2] : 
   ----- Processing year: 2003 
2022-12-19 21:40:38 INFO   [read_E_files] : 
   *** Reading -E- file *** 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
2022-12-19 21:40:46 INFO   [model2netcdf.ED2] : 
   *** Writing netCDF file *** 

After

model2netcdf.ED2("completed_runs/MANDIFORE-PNW-4538/outdir/out/ENS-00001-1000020684/", settings = settings)
2022-12-19 21:47:34 INFO   [model2netcdf.ED2] : 
   ----- Processing year: 2002 
2022-12-19 21:47:34 INFO   [read_E_files] : 
   *** Reading -E- file *** 
2022-12-19 21:47:43 INFO   [model2netcdf.ED2] : 
   *** Writing netCDF file *** 
With 'AGB_PFT': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With 'BSEEDS': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With 'DBH': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With 'DDBH': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With var 'NPP_PFT': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With 'TRANSP_PFT': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
With 'DENS': [1] "ncvar_put: warning: you asked to write 22 values, but the passed data array has 24 entries!" 
2022-12-19 21:47:43 INFO   [model2netcdf.ED2] : 
   ----- Processing year: 2003 
2022-12-19 21:47:43 INFO   [read_E_files] : 
   *** Reading -E- file *** 
2022-12-19 21:47:50 INFO   [model2netcdf.ED2] : 
   *** Writing netCDF file *** 

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.