First, you'll need to install either Xcode or Make. There's another stack question that relates the process for installing make in OSX install make command without already having make (mac os 10.5)
At which point you'll simply put in to terminal:
make targetfile
http://mrbook.org/tutorials/make/ has some great background on how this works. Make is simply for compiling big multifile programs.
IIRC Pure Data is kind of tricky to compile in the first place, so you'll want to keep instructions for compilation handy - the Pure Data mailing list often has users confused by this process.