This happens at least in the following situation: Sage 9.1.beta9 on OS X, using the system's rather than Sage's Python, no pkg-config installed.
CC: @jhpalmieri @dimpase @orlitzky
Component: build: configure
Author: Matthias Koeppe
Branch: 0ac76c3
Reviewer: Dima Pasechnik
Issue created by migration from https://trac.sagemath.org/ticket/29448