To build this package, you must have the netcdf library (>=4.1.3) installed as well as hdf5
and zlib. 
The configure script will check for nc-config and test to ensure the local library supports nc4,
and correspondingly, hdf5. If a configure script cannot be found, you can specify its location
via --with-nc-config. In the absence of nc-config, the configure script will search standard
locations for netcdf.h and for nc_open and nc_create within the library. The configure script
was adapted from the ncdf package (1.6) on CRAN.
 
This package requires that netcdf be linked against hdf5 and that hdf5 be linked against zlib.

These packages are not configured this way by default, so you need to do a custom build from 
source. Though binary packages are available for Mac, you cannot use them and you must follow
the procedures below.

Obtain the source tarballs. There may be newer versions available by the time you read this.

For both Mac and Linux:

mkdir -p ~/Downloads
cd ~/Downloads
curl -O http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz
curl -O ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.7.tar.gz
curl -O ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/zlib-1.2.5.tar.gz


For Linux
=========

Build zlib:

tar zxf zlib-1.2.5.tar.gz
cd zlib-1.2.5
./configure
sudo make install

Build hdf5:

cd ~/Downloads
tar zxf hdf5-1.8.7.tar.gz
cd hdf5-1.8.7
./configure --with-zlib=/usr/local --enable-shared --prefix=/usr/local
sudo make install


Create a file called:
/etc/ld.so.conf.d/hdf5.conf

which should only contain the following line (plus a newline):
/usr/local/lib

Now run this command:
sudo /sbin/ldconfig

Build netcdf:

cd ~/Downloads
tar zxf netcdf-4.1.3.tar.gz
cd netcdf-4.1.3
./configure --disable-dap --enable-shared --enable-netcdf4
sudo make install

Check your installation:
nc-config --has-nc4

and

nc-config --has-hdf5

should both return "yes".

cd /usr/local/lib64
sudo ln -s /usr/local/lib/libnetcdf* .

Check that you can build, check, and install the ncdfFlow package.

For Mac
=======

If you only want to build and run the package for a single architecture, the procedure
is pretty straightforward and similar to the one for Linux, except you don't need to do the
ldconfig stuff.

These instructions document the procedure for creating multi-arch libraries, which
is more complex. It's worth doing when you consider that different versions of Mac OS
have different notions of what is the default architecture for R, and sometimes
the GUI version and the command line version of R use different architectures
by default.

With many libraries, you can do a multi-arch install by simply pre-pending
CFLAGS="-arch i386 -arch x86_64 -arch ppc"
to your configure command. That's how zlib is built below.
Unfortunately, there are other cases where that doesn't work. 
In these cases, we must build the three architectures separately
and merge them with the 'lipo' tool, as documented below for
hdf5 and netcdf.

Assuming you have downloaded the sources as above:

Build zlib:

tar zxf zlib-1.2.5.tar.gz 
cd zlib-1.2.5
CFLAGS="-arch i386 -arch x86_64 -arch ppc" ./configure 
sudo make install

Build hdf5:

For some reason, omitting --prefix from the configure command
and expecting it to install to /usr/local, does not always work.
Hence we specify --prefix explicitly here.

cd ~/Downloads
tar zxf hdf5-1.8.7.tar.gz 
cd hdf5-1.8.7
mkdir universal
tar zxf ../hdf5-1.8.7.tar.gz 
mv hdf5-1.8.7/ i386
tar zxf ../hdf5-1.8.7.tar.gz 
mv hdf5-1.8.7/ x86_64
tar zxf ../hdf5-1.8.7.tar.gz 
mv hdf5-1.8.7/ ppc
cd i386
CXXFLAGS="-arch i386" FCFLAGS="-arch i386" LDFLAGS="-arch i386" FFLAGS="-arch i386" \
CFLAGS="-arch i386" ./configure --prefix=/usr/local --with-zlib=/usr/local --enable-shared \
--host=i386-apple-darwin
make

cd ../x86_64
CXXFLAGS="-arch x86_64" FCFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" FFLAGS="-arch x86_64" \
CFLAGS="-arch x86_64" ./configure --prefix=/usr/local --with-zlib=/usr/local --enable-shared \
--host=x86_64-apple-darwin
make
sudo make install # for headers; you will overwrite libs later

cd ../ppc
CXXFLAGS="-arch ppc" FCFLAGS="-arch ppc" LDFLAGS="-arch ppc" FFLAGS="-arch ppc" \
CFLAGS="-arch ppc" ./configure --prefix=/usr/local --with-zlib=/usr/local --enable-shared \
--host=ppc-apple-darwin
make

cd ../universal
lipo -create -output libhdf5.7.dylib ../i386/src/.libs/libhdf5.7.dylib \
 ../x86_64/src/.libs/libhdf5.7.dylib ../ppc/src/.libs/libhdf5.7.dylib
lipo -create -output libhdf5.a ../i386/src/.libs/libhdf5.a ../x86_64/src/.libs/libhdf5.a \
 ../ppc/src/.libs/libhdf5.a
lipo -create -output libhdf5_hl.7.dylib ../i386/hl/src/.libs/libhdf5_hl.7.dylib \
 ../x86_64/hl/src/.libs/libhdf5_hl.7.dylib ../ppc/hl/src/.libs/libhdf5_hl.7.dylib
lipo -create -output libhdf5_hl.a ../i386/hl/src/.libs/libhdf5_hl.a ../x86_64/hl/src/.libs/libhdf5_hl.a ../ppc/hl/src/.libs/libhdf5_hl.a

file libhdf5* # to verify that libs are multi-arch
sudo cp libhdf5* /usr/local/lib


Build netcdf:

cd ~/Downloads
tar zxf netcdf-4.1.3.tar.gz
cd netcdf-4.1.3
mkdir universal
tar zxf ../netcdf-4.1.3.tar.gz
mv netcdf-4.1.3 i386
tar zxf ../netcdf-4.1.3.tar.gz
mv netcdf-4.1.3 x86_64
tar zxf ../netcdf-4.1.3.tar.gz
mv netcdf-4.1.3 ppc

cd i386
CXXFLAGS="-arch i386" FCFLAGS="-arch i386" LDFLAGS="-arch i386" FFLAGS="-arch i386" \
CFLAGS="-arch i386" ./configure --host=i386-apple-darwin --disable-dap \
--enable-shared --enable-netcdf4
make

cd ../x86_64
CXXFLAGS="-arch x86_64" FCFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" FFLAGS="-arch x86_64" \
CFLAGS="-arch x86_64" ./configure --host=x86_64-apple-darwin --disable-dap \
--enable-shared --enable-netcdf4
make
sudo make install # for headers; you will overwrite libs later

cd ../ppc
CXXFLAGS="-arch ppc" FCFLAGS="-arch ppc" LDFLAGS="-arch ppc" FFLAGS="-arch ppc" \
CFLAGS="-arch ppc" ./configure --host=ppc-apple-darwin --disable-dap \
--enable-shared --enable-netcdf4
make

cd ../universal
lipo -create -output libnetcdf.7.dylib ../i386/liblib/.libs/libnetcdf.7.dylib \
 ../x86_64/liblib/.libs/libnetcdf.7.dylib ../ppc/liblib/.libs/libnetcdf.7.dylib
lipo -create -output libnetcdf.a ../i386/liblib/.libs/libnetcdf.a \
../x86_64/liblib/.libs/libnetcdf.a ../ppc/liblib/.libs/libnetcdf.a
lipo -create -output libnetcdf.dylib ../i386/liblib/.libs/libnetcdf.dylib \
 ../x86_64/liblib/.libs/libnetcdf.dylib ../ppc/liblib/.libs/libnetcdf.dylib
lipo -create -output libnetcdf_c++.4.dylib ../i386/cxx/.libs/libnetcdf_c++.4.dylib \
 ../x86_64/cxx/.libs/libnetcdf_c++.4.dylib ../ppc/cxx/.libs/libnetcdf_c++.4.dylib
lipo -create -output libnetcdf_c++.a ../i386/cxx/.libs/libnetcdf_c++.a \
 ../x86_64/cxx/.libs/libnetcdf_c++.a ../ppc/cxx/.libs/libnetcdf_c++.a
lipo -create -output libnetcdf_c++.dylib ../i386/cxx/.libs/libnetcdf_c++.dylib \
 ../x86_64/cxx/.libs/libnetcdf_c++.dylib ../ppc/cxx/.libs/libnetcdf_c++.dylib
lipo -create -output libnetcdff.5.dylib ../i386/fortran/.libs/libnetcdff.5.dylib \
 ../x86_64/fortran/.libs/libnetcdff.5.dylib ../ppc/fortran/.libs/libnetcdff.5.dylib
lipo -create -output libnetcdff.a ../i386/fortran/.libs/libnetcdff.a \
 ../x86_64/fortran/.libs/libnetcdff.a ../ppc/fortran/.libs/libnetcdff.a
lipo -create -output libnetcdff.dylib ../i386/fortran/.libs/libnetcdff.dylib \
 ../x86_64/fortran/.libs/libnetcdff.dylib ../ppc/fortran/.libs/libnetcdff.dylib
file libnetcdf* # to verify that all libraries are multi-arch
sudo cp libnetcdf* /usr/local/lib

Check your installation:
nc-config --has-nc4

and

nc-config --has-hdf5

should both return "yes".


Now verify that you can build, check and install the ncdfFlow package.