autotools syntax error with ax_check_compile_flag
autoreconf isn't magic (though I encounter package maintainers who obviously believe this). When you ran autoreconf, it failed to find the AX_CHECK_COMPILE_FLAG macro, and produced a corrupt configure script. Usually that produces an error/diagnostic message at the same time.
'AX_CHECK_COMPILE_FLAG` comes from the autoconf archive project, and Debian has a package which provides this, named autoconf-archive. Likely, you forgot to install it:
sudo apt-get install autoconf-archive