NetCDF Information

• NetCDF Wikipedia entry
• NetCDF Source, UniData
• NetCDF v. 4.1.1 code
• Installation instructions
• FAQ
• NetCDF-4 FTP site (for HDF5 and zlib compression library) (see Shared Library Information)
• GSP's guide to NetCDF format data and R/ncdf
• R/ncdf4 (NetCDF v.4 and HDF5) and R/ncdf (NetCDF v. 3)
• local R example with R/qtl cross phenotypes

Local installation notes

• Linix install. Must be in this order, especially to use shared libraries.

  % cd /unsup/netcdf
  % tar -xvf zlib-1.2.3.tar.gz
  % cd zlib-1.2.3
  % ./configure --prefix=/unsup/netcdf
  % make check install CFLAGS=-fPIC
  
  % cd /unsup/netcdf
  % tar -xvf hdf5-1.8.4.tar.gz
  % cd hdf5-1.8.4
  % ./configure --with-zlib=/unsup/netcdf --prefix=/unsup/netcdf
  % make clean-recursive
  % make check install CFLAGS=-fPIC
  
  % cd /unsup/netcdf
  % tar -xvf netcdf-4.1.1.tar.gz
  % cd netcdf-4.1.1
  % ./configure --with-hdf5=/unsup/netcdf --with-zlib=/unsup/netcdf --prefix=/unsup/netcdf
  % make clean-recursive
  % make check install CFLAGS=-fPIC
  

• R package install.

  % R CMD INSTALL --configure-args="--with-netcdf_incdir=/unsup/netcdf/include --with-netcdf_libdir=/unsup/netcdf/lib --with-nc-config=/unsup/netcdf/bin/nc-config" ncdf4_1.0.tar.gz
  % cp /unsup/netcdf/lib/libhdf5_hl.so.6 ~/R/x86_64-unknown-linux-gnu-library/2.10/ncdf4/libs
  % setenv LD_LIBRARY_PATH /unsup/netcdf/lib 
  

• The "LD_LIBRARY_PATH" line should actually go in your .cshrc (or .cshrc.local) file. Now invoke R

  > library(ncdf4)
  

• If you want to use Yandell's version on AFS at UW, put the following in your .cshrc.local file:

  R_LIBS_USER="/u/y/a/yandell/R/x86_64-unknown-linux-gnu-library/2.10"