I added autoconf-2.66 to Haiku (http://dev.haiku-os.org/changeset/37438) but we then found that it wasn't able to build pkgconfig due to a suspected regression in AC_CHECK_SIZEOF: http://ports.haiku-files.org/ticket/376 I have rolled it back to 2.65 for now, until it's fixed again. Also another developer has noted that AX_CHECK_GL is using -lm, Haiku has the math lib build so it doesn't need -lm, so perhaps an AC_CHECKLIB is needed there.
-scottmc (HaikuPorts)