title: why automake fails to generate Makefile.in
body: <p>Trying to use automake/autoconf (versions 1.10 and 2.61, respectively).  Everything is working OK, except automake is not generating Makefile.in.</p>
  
  <p>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.</p>
  
  <pre><code>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'
  </code></pre>
  
  <p>Relevant contents of configure.ac:</p>
  
  <pre><code>AC_INIT(testapp, 1.1, user@blah.com)
  AM_INIT_AUTOMAKE(testapp,1.1)
  AC_OUTPUT(Makefile)
  </code></pre>
  
  <p>Contents of Makefile.am:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>I've been googling the issue but haven't found anything helpful.</p>
  
  <p>Commands run were:</p>
  
  <pre><code>autoscan
  mv configure.scan configure.ac
  (edit configure.ac)
  autoconf
  (edit Makefile.am)
  aclocal
  automake --add-missing
  </code></pre>
  
  <p>Anyone seen anything like this before or know perhaps how I could turn on some additional debugging to troubleshoot the problem?</p>