Autoconf reports actually installed packages as missing on 64 bit systems. X11 is an example. the issue is that the .pc files for these packages are being installed in /usr/lib/x86_64-linux-gnu/pkgconfig and autoconf is only looking in /usr/lib/pkgconfig/ for them. Simply creating symlinks from the x86_64-linux-gnu/pkgconfig dir into the /usr/lib/pkgconfig dir solves this problem
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