First you need to install either Xcode or Make. There's another question on the stack that binds the make installation process on OSX install make command without make already done (mac os 10.5)
At this point, you simply add the terminal:
make targetfile
http://mrbook.org/tutorials/make/ provides some excellent information on how this works. Make is just for compiling large multidisciplinary programs.
IIRC Pure Data is quite difficult to compile in the first place, so you want to save instructions for compilation - the Pure Data mailing list often causes user confusion with this process.
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