automake’s behavior seems to have changed between 1.15.1 and 1.16.1:

1.15.1:

all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) $(HEADERS) config.h

1.16.1:

all-am: Makefile $(PROGRAMS) $(LTLIBRARIES) $(HEADERS) config.h

This causes an automake file which builds a library and a program that uses that library to fail.

An example can be seen here - https://github.com/codebrainz/morse/issues/1#issuecomment-429200053.