The solution is to add 'sage_fortran' to the beginning of the list of fortran compilers on the cygwin line in src/numpy/distutils/fcompiler/init.py
CC: @williamstein
Component: porting: Cygwin
Author: Mike Hansen
Reviewer: Peter Jeremy, William Stein
Merged: sage-4.4.1.alpha2
Issue created by migration from https://trac.sagemath.org/ticket/7321