I've fixed these bugs in my fork. They seems to be harmless and doesn't affect project build much.
You can just do what autogen suggests.
1. Rename configure.in to configure.ac
2. Add ACLOCAL_AMFLAGS = -I m4 to Makefile.am
3. Add AC_CONFIG_MACRO_DIR([m4]) to configure.ac

I think that's all I've done.