[netcdfgroup] [ncdf4] error converting GEIA data to netCDF

• To: netcdfgroup@xxxxxxxxxxxxxxxx, r-help@xxxxxxxxxxxxx,
• Subject: [netcdfgroup] [ncdf4] error converting GEIA data to netCDF
• From: Tom Roche <Tom_Roche@xxxxxxxxx>,
• Date: Mon, 27 Aug 2012 23:31:23 -0400

summary: I can successfully ncvar_put(...) data to a file, but when I
try to ncvar_get(...) the same data, I get

> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset 
> else addOffset = 0 : 
>   argument is of length zero

How to fix or debug?

details:

R code @

https://github.com/TomRoche/GEIA_to_NetCDF

successfully (if crudely) uses R packages={ncdf4, maps, fields} to

+ extract data from a GEIA-distributed datafile

https://github.com/downloads/TomRoche/GEIA_to_netCDF/N2OOC90Y.1A

+ display the data (mostly successfully--the map's legend has problems
  which I'll attack later)

https://github.com/downloads/TomRoche/GEIA_to_netCDF/output.1.png

+ create a netCDF file using the data read from the GEIA file. (At
  least, after nc_sync(netcdf.file), the file `ncdump -h`s properly.)

However, I can only *put* the data to the netCDF file:

> ncvar_put(
> + nc=netcdf.file,
> + varid=emis.var,
> + vals=t(global.emis.mx),
> + start=c(1, 1, 1),
> + count=c(-1,-1, 1)) # -1 -> all data

When I try to *pull* the data *from* the netCDF I created,

> > target.data <- ncvar_get(
> +   nc=netcdf.file,
> +   varid=emis.var,
> +   # read all the data
> +   start=rep(1, emis.var$ndims),
> + #  count=rep(-1, emis.var$ndims))

I get

> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset 
> else addOffset = 0 : 
>   argument is of length zero

And I get the same error if I try the minor variation(s)

> target.data <- ncvar_get(
+   nc=netcdf.file,
+ #  varid=emis.var,
+   varid=emis.var.name,
+   # read all the data
+   start=rep(1, emis.var$ndims),
+   count=c(-1, -1, 1))

But the data itself appears to be OK--at least, it virtualizes
properly (above). So I'm thinking I must just be missing something
simple, and hoping Someone Out There with fresh eyeballs can point to
my error(s).

(And, in case you're wondering:

- I'm not just ncvar_put'ing the data for the exercise: I want the
  GEIA data in netCDF format for subsequent use.

- I tried to find the GEIA data distributed in netCDF format, and
  asked around, but have gotten no responses.

) TIA, Tom Roche <Tom_Roche@xxxxxxxxx>

• Follow-Ups:
  • Re: [netcdfgroup] [ncdf4] error converting GEIA data to netCDF
    • From: Roy Mendelssohn
  • Re: [netcdfgroup] [ncdf4] error converting GEIA data to netCDF
    • From: Roy Mendelssohn