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How can I install headerdoc on a UNIX system, Debian, when I hit make, it complains cc1: error: unrecognized command line option "-flat_namespace" when I remove that option from Makefile it won't compile.

A: 

You might want to consider doxygen, instead. It's portable. This thing appears to support any system you like so long as it's MacOSX.

Oddly, the MacOSX gcc doesn't have a -flat-namespace compiler option in the doc, but it is there. There is some evidence that it is related to linking. Perhaps you could edit your question to post what happens when you leave it out?

bmargulies