Conditionals should enclose complete statements like variables or rules definitions. Automake cannot deal with conditionals used inside a variable definition, for instance, and is not even able to diagnose this situation. The following example would not work:
# This syntax is not understood by Automake AM_CPPFLAGS = \ -DFEATURE_A \ if WANT_DEBUG -DDEBUG \ endif -DFEATURE_B
However the intended definition of AM_CPPFLAGS can be achieved
with
if WANT_DEBUG DEBUGFLAGS = -DDEBUG endif AM_CPPFLAGS = -DFEATURE_A $(DEBUGFLAGS) -DFEATURE_B
or
AM_CPPFLAGS = -DFEATURE_A if WANT_DEBUG AM_CPPFLAGS += -DDEBUG endif AM_CPPFLAGS += -DFEATURE_B
More details and examples of conditionals are described alongside various Automake features in this manual (see Conditional Subdirectories, see Conditional compilation of sources, see Conditional compilation of programs, see Building Libtool Libraries Conditionally, see Libtool Libraries with Conditional Sources).