libayatana-appindicator fails to cross build from source, because it
uses the build architecture vapigen. Since the library search path is
architecture-dependent, vapigen fails location dependencies as a result.
A triplet-prefixed vapigen should be used. The best way of discovering
the correct vapigen is detecting it from the vapigen.pc file. I'm
attaching a patch for your convenience. Please consider applying it and
forwarding it upstream.

Helmut