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Interesting ! But I think I've found a simpler -temporary- solution ;-) :
mv /usr/lib/pkgconfig/x11.pc /usr/lib/pkgconfig/x11.pc.old
compile...
mv /usr/lib/pkgconfig/x11.pc.old /usr/lib/pkgconfig/x11.pc

Explanation : gtk+-3.0 depends here on x11. It's not really used with win32, but if you are on linux, and you happen to have X11 development files installed (libx11-dev on Debian/Ubuntu), you're likely to have x11.pc somewhere.

Vala sees an "x11" dep, and tells pkg-config to try to find the corresponding "x11.pc". It it doesn't find it, work fine though. If it does... it uses it, and screws up !

A permanent solution would be yours, or simpler :
In gtk+-3.0.deps, replace "x11" with "x11lin", and copy "x11.vapi" as "x11lin.vapi". It won't try to use the .pc anymore.

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