I have netcdf-c and netcdf-fortran built with nc4 support, but in different directories. With my variable NETCDF was initially set as the path to netcdf-fortran, the configuration of WRF returned a warning message:

NETCDF4 IO features are requested, but this installation of NetCDF
  /opt/netcdf_fortran/4_4_4/intel
DOES NOT support these IO features.

Please make sure NETCDF version is 4.1.3 or later and was built with
--enable-netcdf4

OR set NETCDF_classic variable
   bash/ksh : export NETCDF_classic=1
      echo  csh : setenv NETCDF_classic 1

Then re-run this configure script

!!! configure.wrf has been REMOVED !!!

What I did to resolve this is to make links for netcdf-c and netcdf-fortran, then put them together according to the /lib, /include, /bin structure, and update the variable NETCDF as the path to the new directory.