Thanks, but the problem is not there.
You've doubly defined your target, once at line 35275 and once at line 61202 in your Makefile. Remove one and the warnings will go away.
It's automake that creates the Makefile! My Makefile.am contains only bla_SOURCES=file1.cpp file2.cxx And then automake doubly defines the target. Thus the question how to tell automake not to doubly define that.
Thanks. -jec