[R-sig-Geo] Problem with raster package and netcdf file

[Julian Burgos]

Dear list,

I am having some troubles opening accessing a raster in the netCDF format.
 The file is bathimetric data from GEBCO:
http://www.gebco.net/data_and_products/gridded_bathymetry_data/

If I use the ncdf4 package to open and access the data, I have no issues:

library(ncdf4)
> d <- nc_open("gebco_08_-82_37_63_80.nc")
> z <- as.vector(ncvar_get(d,varid="z"))
> head(z)
[1]  19  40  61  83 106 128


But if I try to use the raster package to access the file and create a
raster object, I get the following error:

bat <- raster(file="gebco_08_-82_37_63_80",varname="z")
Error in .varName(nc, varname, warn = warn) :
  varname: z does not exist in the file. Select one from:

... and no varnames are listed.


If I do not define a variable name and let the raster package choose it, I
get this:

> bat <- raster(file="gebco_08_-82_37_63_80",varname="z")
Error in .varName(nc, varname, warn = warn) :

The description of the netCDF file is as following:

> d
[1] "File gebco_08_-82_37_63_80.nc (NC_FORMAT_CLASSIC):"
[1] ""
[1] "     6 variables:"
[1] "        double x_range[side]   "
[1] "            units: user_x_unit"
[1] "        double y_range[side]   "
[1] "            units: user_y_unit"
[1] "        short z_range[side]   "
[1] "            units: user_z_unit"
[1] "        double spacing[side]   "
[1] "        int dimension[side]   "
[1] "        short z[xysize]   "
[1] "            scale_factor: 1"
[1] "            add_offset: 0"
[1] "            node_offset: 1"
[1] ""
[1] "     2 dimensions:"
[1] "        side  Size:2"
[1] "        xysize  Size:89784000"
[1] ""
[1] "    2 global attributes:"
[1] "        title: GEBCO_08 Grid"
[1] "        source: 20100927"

I am using R 15.2 on Linux (Fedora), raster 2.1-8, and ncdf4 version
ncdf4_1.6.1_20120411.
Any help will be welcomed!

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian at hafro.is