If you try to cross-compile a library such as fftw3 on a your 64 bit linux, the configure will most certainly fail !
This is because the compiler needs two libraries that are preinstalled in 64bits but it needs them with a 32bit compatibility to run on Android.
So all you need to do is :
</>sudo apt-get install lib32stdc++6
</>sudo apt-get install lib32z1-dev
And BOOM your configure will run succesfully, and most probably the subsequent call to make and make install will too.