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The Autoconfig manual states that comment lines can start with either dnl or #.

Is there any difference between them, any reason to use one rather than the other in any circumstance? Or is it purely a matter of taste?

+2  A: 

dnl is an m4 macro that discards all input that follows it on the same line (including the newline). # doesn't mean anything in m4, so it ends up in the target (Makefile?), in which it acts as a comment.

So the key difference is that dnl is a comment in the original source, whereas # becomes a comment in the generated file.

Marcelo Cantos
Erm... not quite, it seems to me after some tests. 1) I was referring to configure.in (and its target configure). 2) '#' comments in configure.in do not appear in configure. 3) '#' comments in Makefile.am *do* appear in the Makefile. 4) 'dnl' lines in Makefile.am *do* appear in the Makefile. 5) '##' comments in Makefile.am, on the other hand, do *not* appear in the Makefile.
DevSolar
This is a good example of why the name 'configure.in' was deprecated in favor of 'configure.ac'. autoconf treats configure.ac differently that typical *.in input files. configure.ac is parsed by m4, but Makefile.am is not, nor are the input files used by configure to generate targets. So dnl is only a comment in configure.ac or in m4 macros defined in aclocal.m4, acinclude.m4, or elsewhere.
William Pursell
+2  A: 

In configure.ac, lines commented with '#' that occur after AC_INIT will appear in the resulting configure script. dnl comments will not. One purpose of dnl is to discard unwanted newlines in an effort to make the configure script readable. Also, it is appropriate to use dnl comments to document an m4 macro; those comments make no sense in the configure script, since the m4 macro does not appear there, only its expansion.

Comments in Makefile.am are treated differently. Makefile.am is not processed by m4, but by automake, where the convention is to discard lines which begin with ## preceded only by whitespace. (Although ### comments carry through to the Makefile.in) Since Makefile.am is not processed by m4, 'dnl' does not introduce a comment.

William Pursell