The latest version of autopoint (0.18.3.1) defaults to / (root) if the macro directory is not specified in either the configure.ac file or the Makefile.am file. Not setting these values may also cause issues with aclocal. For more information, please see the Gentoo lxtask bug.
The solution is to add AC_CONFIG_MACRO_DIR([m4]) to configure.ac and to add ACLOCAL_AMFLAGS= -I m4 to Makefile.am. I've attached a patch that adds these values.
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