The written pkgconfig *.pc files do not honor --libdir and --incdir given to configure. Here's a patch that fixes those. Dunno if libdir should point to $libdir or $shlibdir, I opted for the former.
Honor --libdir and --incdir in *.pc
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Honor --libdir and --incdir in *.pc
This Sourceforge bug tracker here has been abandoned many years ago.
Our new tracker can be found through http://www.ffmpeg.org/bugreports.html