title: autoreconf failed with exit status 1
body: <p>I am trying to install a program by cloning it with git. I am running in an Ubuntu 14.04.4 LTS. I get the source code correctly with "git clone" but autoreconf fails giving the following error:</p>
  
  <pre><code>xray@silvia-desktop:~/Software/Gitsrc/simput$ autoreconf --install --verbose 
  autoreconf2.50: Entering directory `.'
  autoreconf2.50: configure.ac: not using Gettext
  autoreconf2.50: running: aclocal
  autoreconf2.50: configure.ac: tracing
  autoreconf2.50: configure.ac: adding subdirectory extlib/cfitsio to autoreconf
  autoreconf2.50: Entering directory `extlib/cfitsio'
  autoreconf2.50: configure.in: not using Gettext
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
  autoreconf2.50: configure.in: tracing
  autoreconf2.50: configure.in: not using Libtool
  autoreconf2.50: running: /usr/bin/autoconf
  configure.in:175: AC_PROG_CPP was called before AC_PROG_CC
  autoconf: Undefined macros:
  configure.in:11:AC_CONFIG_SRCDIR([fitscore.c])
  configure.in:178:  AC_MSG_NOTICE(cfitsio: == Fortran compiler search has been overridden)
  configure.in:179:  AC_MSG_NOTICE(cfitsio: == Cfitsio will be built without Fortran wrapper support)
  configure.in:186:    AC_MSG_NOTICE(cfitsio: == Adding wrapper support for GNU Fortran by default)
  configure.in:226:AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[void d( int , double) ]])],[PROTO=yes],[PROTO=no])dnl
  configure.in:248:    AC_LANG_PUSH([C])
  configure.in:249:    AC_COMPILE_IFELSE([AC_LANG_PROGRAM([])],[c_has_option=yes],[c_has_option=no])
  configure.in:250:    AC_MSG_RESULT($c_has_option)
  configure.in:251:    AC_LANG_POP([])
  configure.in:278:                AC_LANG_PUSH([C])
  configure.in:279:                AC_COMPILE_IFELSE([AC_LANG_PROGRAM([])],[c_has_option=yes],[c_has_option=no])
  configure.in:280:                AC_MSG_RESULT($c_has_option)
  configure.in:281:                AC_LANG_POP([])
  configure.in:288:        AC_DEFINE(_LARGEFILE_SOURCE)
  configure.in:289:        AC_DEFINE(_FILE_OFFSET_BITS,64)
  configure.in:304:        AC_DEFINE(_LARGEFILE_SOURCE)
  configure.in:305:        AC_DEFINE(_FILE_OFFSET_BITS,64)
  configure.in:309:        AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include &lt;stdio.h&gt;],
  configure.in:311:            AC_DEFINE(_LARGEFILE_SOURCE)
  configure.in:312:            AC_DEFINE(_FILE_OFFSET_BITS,64)
  configure.in:313:            AC_MSG_RESULT(yes)
  configure.in:314:        ],[AC_MSG_RESULT(no)])
  configure.in:323:        AC_DEFINE(_LARGEFILE_SOURCE)
  configure.in:324:        AC_DEFINE(_FILE_OFFSET_BITS,64)
  configure.in:454:AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include &lt;unistd.h&gt;
  configure.in:458:AC_DEFINE(HAVE_FTRUNCATE)
  configure.in:459:AC_MSG_RESULT("yes")
  configure.in:460:],[AC_MSG_RESULT("no") ])
  configure.in:467:AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include &lt;stdlib.h&gt;
  configure.in:471:AC_DEFINE(HAVE_LONGLONG)
  configure.in:472:AC_MSG_RESULT("yes")
  configure.in:473:],[AC_MSG_RESULT("no") ])
  configure.in:488:AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include &lt;sys/ipc.h&gt;
  configure.in:497:AC_DEFINE(HAVE_SHMEM_SERVICES)
  configure.in:499:AC_MSG_RESULT("yes")
  configure.in:500:],[AC_MSG_RESULT("no") ])
  configure.in:509:AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include &lt;sys/fcntl.h&gt;
  configure.in:513:AC_DEFINE(HAVE_FLOCK_T)
  configure.in:514:AC_MSG_RESULT("yes")
  configure.in:515:],[AC_MSG_RESULT("no") ])
  configure.in:519:   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include &lt;sys/flock.h&gt;
  configure.in:523:   AC_DEFINE(HAVE_FLOCK_T)
  configure.in:524:   AC_MSG_RESULT("yes")
  configure.in:525:   ],[AC_MSG_RESULT("no") ])
  configure.in:534:AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include &lt;sys/ipc.h&gt;
  configure.in:53:  AC_DEFINE(BUILD_HERA)
  configure.in:540:AC_DEFINE(HAVE_UNION_SEMUN)  
  configure.in:541:AC_MSG_RESULT("yes")
  configure.in:542:],[AC_MSG_RESULT("no") ])
  configure.in:552:   AC_DEFINE(HAVE_NET_SERVICES)
  configure.in:561:  AC_DEFINE(_REENTRANT)
  configure.in:566:AC_CONFIG_FILES([Makefile])
  configure.in:568:AC_CONFIG_FILES([cfitsio.pc])
  configure.in:572:AC_MSG_RESULT([])
  configure.in:573:AC_MSG_RESULT([    Congratulations, Makefile update was successful.])
  configure.in:574:AC_MSG_RESULT([    You may want to run \"make\" now.])
  configure.in:575:AC_MSG_RESULT([])
  configure.in:64:        AC_DEFINE(GSIFTP_FLAVOUR,1,[Define Globus Toolkit architecture])
  configure.in:79:        AC_DEFINE(HAVE_GSIFTP,1,[Define if you want Globus Toolkit gsiftp protocol support])
  configure.in:93:        AC_DEFINE(HAVE_BZIP2,1,[Define if you want bzip2 read support])
  configure.in:98:   AC_DEFINE(HAVE_BZIP2,1,[Define if you want bzip2 read support])
  autoreconf2.50: /usr/bin/autoconf failed with exit status: 1
  </code></pre>
  
  <p>I have been searching in this site and others. I found that the problem may be related to an old version of libtool, or to not having it installed, but I have already check this and my libtool package is up to date. I aso have autotools updated. </p>
  
  <p>An interesting point is that I have tryed to install it in a Debian I have installed in other computer in a virtual machine, and I get the same error, so it seems to be something related to an error I am committing maybe in system general configuration... </p>
  
  <p>I have been discussing with a mate thas has no problem in the installation, and get this output when doing outoreconf:</p>
  
  <pre><code>lenovo:~/tmp/simput&gt; autoreconf --install --verbose
  autoreconf: Entering directory `.'
  autoreconf: configure.ac: not using Gettext
  autoreconf: running: aclocal
  autoreconf: configure.ac: tracing
  autoreconf: configure.ac: adding subdirectory extlib/cfitsio to autoreconf
  autoreconf: Entering directory `extlib/cfitsio'
  autoreconf: configure.in: not using Gettext
  aclocal: warning: autoconf input should be named 'configure.ac', not
  'configure.in'
  autoreconf: configure.in: tracing
  </code></pre>
  
  <p>Any idea? </p>
  
  <p>Thanks a lot!</p>