[R-sig-Geo] [raster] problem with large netCDF file

[Tom Roche]

I'm trying to create an extents object from a large netCDF file on a
linux cluster running RHEL 5.4. I'd try to make the file publicly
available, but

$ ls -alh ./METCRO3D_080101
-r--r--r-- 1 me mygroup 5.3G Jan  8 11:32 ./METCRO3D_080101

# extension used below
$ ln -s ./METCRO3D_080101 ./METCRO3D_080101.nc

# note netCDF-ness of file, and existence of datavar=ZF
$ ncdump -v ZF ./METCRO3D_080101 | head
netcdf METCRO3D_080101 {
dimensions:
        TSTEP = UNLIMITED ; // (25 currently)
        DATE-TIME = 2 ;
        LAY = 24 ;
        VAR = 17 ;
        ROW = 299 ;
        COL = 459 ;
variables:
        int TFLAG(TSTEP, VAR, DATE-TIME) ;
$ ncdump -v ZF ./METCRO3D_080101 | tail
    19116.16, 19112.75, 19128.86, 19171.77, 19206.04, 19224.66, 19247.3, 
    19293.71, 19343.23, 19370.01, 19386.64, 19389.33, 19391.63, 19417.19, 
    19442.12, 19456.19, 19471.03, 19481.76, 19485.71, 19492.51, 19501.67, 
    19511.11, 19499.88, 19470.57, 19464.8,  19466.73, 19467.94, 19481.03, 
    19502.62, 19534.05, 19562.75, 19607.45, 19659.45, 19687.44, 19706.39, 
    19735.43, 19790.02, 19842.22, 19862.31, 19867.04, 19871.75, 19876.44, 
    19881.59, 19882.53, 19838.23, 19772.65, 19724.43, 19754.49, 19824.58, 
    19852.86, 19897.51, 19921.67, 19909.53, 19925.96, 19937.74, 19940.95, 
    19944.61, 19948.7,  19953.03, 19957.13 ;
}

$ R
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

...

> library(raster)
Loading required package: sp
raster 2.0-41 (21-December-2012)
> system('ls -alh ./METCRO3D_080101')
-r--r--r-- 1 me mygroup 5.3G Jan  8 11:32 ./METCRO3D_080101
> system('ls -alh ./METCRO3D_080101.nc')
lrwxrwxrwx 1 me mygroup 17 Feb 10 13:46 ./METCRO3D_080101.nc -> ./METCRO3D_080101
> raster('./METCRO3D_080101', varname='ZF')
rgdal: version: 0.8-4, (SVN revision 431)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.7.3, released 2010/11/10
Path to GDAL shared files: /usr/local/share/gdal
GDAL does not use iconv for recoding strings.
Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
Path to PROJ.4 shared files: (autodetected)
Error in .local(.Object, ...) : 
  `/home/rtd/code/regridding/MOZART_global_to_AQMEII-NA/METCRO3D_080101' not recognised as a supported file format.


Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create a RasterLayer object from this file.

# Thinking that `raster` might want a supported extension to convince
# it of the file's netCDF-ness, I tried

> raster('./METCRO3D_080101.nc', varname='ZF')
Error in .local(.Object, ...) : 
  `.../METCRO3D_080101' not recognised as a supported file format.


Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create a RasterLayer object from this file.

But plainly `ncdump` thinks METCRO3D_080101 *is* netCDF.
Can I convince `raster`? Either way, how to proceed?

Your assistance is appreciated, Tom Roche <Tom_Roche at pobox.com>