This typically works:
# ./configure --prefix=/usr/custom/ CFLAGS="-I/usr/local/include/" LDFLAGS="-L/usr/local/lib/"
I would recommend setting prefix to something other than /usr/ or /usr/local/, so you'll keep your base and package dirs clean ... But that's not a requirment and totally up to you.
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UNIX was not designed to stop you from doing stupid things, because that would also stop you from doing clever things.
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