I've run into this a couple times lately so it's worth noting for others. aclocal only searches /usr/share/aclocal by default. This poses a problem because our pkg-config is in /usr/local, but there's an easy fix. Create a new file named /usr/share/aclocal/dirlist with a line for each additional directory you want to search. In our case just /usr/local/share/aclocal. Presto, now autoconf can find pkg-config's macros.