Given a Makefile.am with myprog_LDADD = -pthread
automake will correctly output this warning Makefile.am:17: error: linker flags such as '-pthread' belong in 'myprog_LDFLAGS' It would be nice to also have automake report -l flags in LDFLAGS that actually belong into LIBADD/LDADD: myprog_LDFLAGS = -ldl is currently silently allowed, but is known to cause problems: http://stackoverflow.com/questions/13610572/correcting-the-gcc-command-line-ordering-using-automake