The definition of AM_INIT_AUTOMAKE does not end in a newline character, which can cause tricky-to-track errors if the call is followed by an M4 comment. I believe this is new behavior because an old set of Autotools configuration files that used to work failed when I recently re-ran automake. I'm running Ubuntu Trusty Tahr (14.04 LTS) with the following Automake and Autoconf versions: $ automake --version | head -1 automake (GNU automake) 1.14.1 $ autoconf --version | head -1 autoconf (GNU Autoconf) 2.69 I've attached a minimal reproducer, a configure.ac file with only the following contents: AC_INIT([badness], [1.0], [pakin@lanl.gov], [badness]) AM_INIT_AUTOMAKE([1.14])dnl This comment causes configure to break. AC_CONFIG_FILES([Makefile]) AC_OUTPUT Here's how to produce the error: $ touch Makefile.am $ aclocal $ automake --add-missing --foreign configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' $ autoconf $ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes ./configure: line 3493: syntax error: unexpected end of file The error is caused by line 2313, which contains fiac_config_files="$ac_config_files Makefile" instead of fi ac_config_files="$ac_config_files Makefile" That is, bash is in fact complaining about a missing "fi". Removing the comment from configure.ac or moving it onto a line of its own works around the problem, but I think it would be nicer if init.m4 replaced the final "fi])" (right after the "Your 'rm' program is bad" message) with fi ]) Hopefully, that'll save someone else the effort of associating an "end of file" error with a comment appearing in the wrong place. Thanks for your time, -- Scott