why automake fails to generate Makefile.in - makefile

Question

Trying to use automake/autoconf (versions 1.10 and 2.61, respectively). Everything is working OK, except automake is not generating Makefile.in.
There are some warnings generated, but I don't think they're significant. However, the last line makes me think it's generating something it shouldn't and stopping there. There is a md5.cc and md5.c file in the project.
xanadu:fsd wwilliam$ automake --add-missing
configure.ac:46: warning: AC_COMPILE_IFELSE was called before AC_USE_SYSTEM_EXTENSIONS
/var/tmp/autoconf/autoconf-15~193/SRC/autoconf/lib/autoconf/specific.m4:421: AC_USE_SYSTEM_EXTENSIONS is expanded from...
/var/tmp/autoconf/autoconf-15~193/SRC/autoconf/lib/autoconf/functions.m4:1677: AC_FUNC_STRNLEN is expanded from...
configure.ac:46: the top level
configure.ac:46: warning: AC_RUN_IFELSE was called before AC_USE_SYSTEM_EXTENSIONS
configure.ac:46: warning: AC_COMPILE_IFELSE was called before AC_GNU_SOURCE
/var/tmp/autoconf/autoconf-15~193/SRC/autoconf/lib/autoconf/specific.m4:340: AC_GNU_SOURCE is expanded from...
configure.ac:46: warning: AC_RUN_IFELSE was called before AC_GNU_SOURCE
configure.ac:46: warning: AC_COMPILE_IFELSE was called before AC_AIX
/var/tmp/autoconf/autoconf-15~193/SRC/autoconf/lib/autoconf/specific.m4:455: AC_AIX is expanded from...
configure.ac:46: warning: AC_RUN_IFELSE was called before AC_AIX
configure.ac:46: warning: AC_COMPILE_IFELSE was called before AC_MINIX
/var/tmp/autoconf/autoconf-15~193/SRC/autoconf/lib/autoconf/specific.m4:474: AC_MINIX is expanded from...
configure.ac:46: warning: AC_RUN_IFELSE was called before AC_MINIX
Makefile.am: object `md5.$(OBJEXT)' created by `md5.cc' and `md5.c'
Relevant contents of configure.ac:
AC_INIT(testapp, 1.1, user#blah.com)
AM_INIT_AUTOMAKE(testapp,1.1)
AC_OUTPUT(Makefile)
Contents of Makefile.am:
AUTOMAKE_OPTIONS = foreign
CFLAGS=-O2
bin_PROGRAMS = testapp
testapp_SOURCES = interface.cc interface.hh keymgr.cc keymgr.hh main.cc manage.cc manage.hh md5.c md5.cc md5.h mm.cc mm.hh mysqldb.cc mysqldb.h testapp.cc testapp.h
I've been googling the issue but haven't found anything helpful.
Commands run were:
autoscan
mv configure.scan configure.ac
(edit configure.ac)
autoconf
(edit Makefile.am)
aclocal
automake --add-missing
Anyone seen anything like this before or know perhaps how I could turn on some additional debugging to troubleshoot the problem?

Answer 1

Makefile.am: object `md5.$(OBJEXT)' created by `md5.cc' and `md5.c'
is an error message that causes Automake to abort. These two files would have to be compiled to md5.o, so that is a problem.
Can you rename one of these two files?

Answer 2

I have one program that I configure with automake. That program has a script to do the setup, which consists of:
aclocal -I config &&
libtoolize --automake &&
autoheader &&
automake --foreign --add-missing &&
autoconf
The difference, as I see it, is that in this the autoconf step is last, not in the middle.

Answer 3

It complains on line 46, which you do not provide to your question.
Anyhow, to fix this issue you have to add AC_USE_SYSTEM_EXTENSIONS in your configure.ac.
example:
AC_INIT(testapp, 1.1, user#blah.com)
AM_INIT_AUTOMAKE(testapp,1.1)
AC_OUTPUT(Makefile)
AC_USE_SYSTEM_EXTENSIONS
AC_PROG_C
...