Hey Mike!
Yep, we’re about to update the instructions to deal with this. You can be one of the first to try it out…
So first thing:
$ port install pkgconfig
and try again. If that fails, try:
$ EIGEN_CFLAGS="-isystem /opt/local/include/eigen3" ./configure
(Eigen3 installs in a different location from homebrew). If that still fails, you may be running into the same issues as @Adriano_BERNINI in this post. I sincerely hope you’re not, since this will probably take a while to figure out… In any case, if you can’t get it to work, please post the content of your configure.log file (within [code] … [/code] tags if possible, makes things much easier to read), otherwise we won’t be able to figure out what’s going on…