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I forgot about this question, but just as a quick follow-up Jesus and I met last week at the University of Essex and I walked him through building Sage on Windows/Cygwin using the instructions at: https://trac.sagemath.org/wiki/Cygwin64Port

As we noted at the time, one bit of information currently missing from those instructions is to set:

export FFLAS_FFPACK_CONFIGURE=--disable-openmp

This is just to work around a slight defect in the build system that should get fixed at some point...