Another team member generated the autotools scripts for the project using eclipse. After some time, Im trying to test the project in Linux, but I cant generate the makefile, the configure script halts at generating config.status, cannot find input file infig.status Im using automake 1.8.3 and autoconf 2.59. I have used all possible combinations to generate the scripts, by running bootstrap or automake/autoconf and the result is the same.

Could you post the scripts here so we could have a look. What versions of automake and autotools does the other team member use?

Here is configure.in

AC_INIT(configure.in)
AM_INIT_AUTOMAKE(Tower, 0.1)
AM_CONFIG_HEADER(config.h)

AC_ISC_POSIX
CXXFLAGS=""
AC_SUBST(CXXFLAGS)
AC_PROG_CXX
AM_PROG_CC_STDC
AC_HEADER_STDC
AM_PROG_LIBTOOL

dnl Checks for programs.
dnl Checks for libraries.
PKG_CHECK_MODULES(ogre, [OGRE >= 0.15])
AC_SUBST(ogre_CFLAGS)
AC_SUBST(ogre_LIBS)

PKG_CHECK_MODULES(vorbis, [vorbis >= 1.0.1])
AC_SUBST(vorbis_CFLAGS)
AC_SUBST(vorbis_LIBS)

dnl Checks for header files.
dnl Checks for typedefs, structures, and compiler characteristics.
dnl Checks for library functions.
dnl Checks for Additional stuffs.
GETTEXT_PACKAGE=Tower
AC_SUBST(GETTEXT_PACKAGE)
AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE, "$GETTEXT_PACKAGE", [Package name for gettext])


dnl Languages which your application supports
ALL_LINGUAS=""
AM_GNU_GETTEXT
AM_GNU_GETTEXT_VERSION(0.10.40)

dnl Set PACKAGE_LOCALE_DIR in config.h.
if test "x${prefix}" = "xNONE"; then
AC_DEFINE_UNQUOTED(PACKAGE_LOCALE_DIR, "${ac_default_prefix}/${DATADIRNAME}/locale")
else
AC_DEFINE_UNQUOTED(PACKAGE_LOCALE_DIR, "${prefix}/${DATADIRNAME}/locale")
fi


dnl Set PACKAGE SOURCE DIR in config.h.
packagesrcdir=`cd $srcdir && pwd`

dnl Set PACKAGE PREFIX
if test "x${prefix}" = "xNONE"; then
packageprefix=${ac_default_prefix}
else
packageprefix=${prefix}
fi

dnl Set PACKAGE DATA & DOC DIR
packagedatadir=share
packagedocdir=doc/${PACKAGE}

dnl Set PACKAGE DIRS in config.h.
packagepixmapsdir=${packagedatadir}/pixmaps
packagehelpdir=${packagedatadir}/help
packagemenudir=${packagedatadir}

dnl Subst PACKAGE_DATA_DIR.
NO_PREFIX_PACKAGE_DATA_DIR="${packagedatadir}"
AC_SUBST(NO_PREFIX_PACKAGE_DATA_DIR)
PACKAGE_DATA_DIR="${packageprefix}/${packagedatadir}"
AC_SUBST(PACKAGE_DATA_DIR)

dnl Subst PACKAGE_DOC_DIR.
NO_PREFIX_PACKAGE_DOC_DIR="${packagedocdir}"
AC_SUBST(NO_PREFIX_PACKAGE_DOC_DIR)
PACKAGE_DOC_DIR="${packageprefix}/${packagedocdir}"
AC_SUBST(PACKAGE_DOC_DIR)

dnl Subst PACKAGE_PIXMAPS_DIR.
NO_PREFIX_PACKAGE_PIXMAPS_DIR="${packagepixmapsdir}"
AC_SUBST(NO_PREFIX_PACKAGE_PIXMAPS_DIR)
PACKAGE_PIXMAPS_DIR="${packageprefix}/${packagepixmapsdir}"
AC_SUBST(PACKAGE_PIXMAPS_DIR)

dnl Subst PACKAGE_HELP_DIR.
NO_PREFIX_PACKAGE_HELP_DIR="${packagehelpdir}"
AC_SUBST(NO_PREFIX_PACKAGE_HELP_DIR)
PACKAGE_HELP_DIR="${packageprefix}/${packagehelpdir}"
AC_SUBST(PACKAGE_HELP_DIR)

dnl Subst PACKAGE_MENU_DIR.
NO_PREFIX_PACKAGE_MENU_DIR="${packagemenudir}"
AC_SUBST(NO_PREFIX_PACKAGE_MENU_DIR)
PACKAGE_MENU_DIR="${packageprefix}/${packagemenudir}"
AC_SUBST(PACKAGE_MENU_DIR)

AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${packageprefix}/${packagedatadir}")
AC_DEFINE_UNQUOTED(PACKAGE_DOC_DIR, "${packageprefix}/${packagedocdir}")
AC_DEFINE_UNQUOTED(PACKAGE_PIXMAPS_DIR, "${packageprefix}/${packagepixmapsdir}")
AC_DEFINE_UNQUOTED(PACKAGE_HELP_DIR, "${packageprefix}/${packagehelpdir}")
AC_DEFINE_UNQUOTED(PACKAGE_MENU_DIR, "${packageprefix}/${packagemenudir}")
AC_DEFINE_UNQUOTED(PACKAGE_SOURCE_DIR, "${packagesrcdir}")

AC_OUTPUT([
Makefile
intl/Makefile
po/Makefile.in
include/Makefile
src/Makefile
])

And this is Makefile.am

SUBDIRS = intl po include src

towerdocdir = ${prefix}/doc/Tower
towerdoc_DATA = README COPYING AUTHORS ChangeLog INSTALL NEWS TODO ABOUT-NLS

EXTRA_DIST = $(towerdoc_DATA)

# Copy all the spec files. Of cource, only one is actually used.
dist-hook:
for specfile in *.spec; do if test -f $$specfile; then cp -p $$specfile $(distdir); fi done

And I was wrong, they were generated by Anjuta, not eclipse.
I tried to clean all and generate with automake/autoconf, also copied bootstrap scripts and tried again, but in both cases i got the same problem.

Try removing every build-system related file from the top level directory except bootstrap, configure.in and Makefile.am. Most importantly, remove autom4te.cache. Then use bootstrap to recreate everything from scratch.

I got the error anyway.