newer versions of autotools are pickier about this file's name.

configure.ac

+
+# This file is part of QuickSched.
+# Coypright (c) 2013 pedro.gonnet@durham.ac.uk.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# init the project
+AC_INIT(src/qsched.c)
+VERSION="0.1.0"
+AC_SUBST(VERSION)
+AM_INIT_AUTOMAKE(QUICKSCHED,VERSION)
+AC_GNU_SOURCE
+AC_PROG_LIBTOOL
+
+# my own macro collection
+AC_CONFIG_MACRO_DIR([m4])
+
+# generate header file
+AM_CONFIG_HEADER(config.h)
+
+# compiler settings
+#CFLAGS="-Wall $(CFLAGS)"
+
+# find and test the compiler
+AM_PROG_CC_C_O
+AC_PROG_CC_C99
+AC_LANG_C
+# AX_CC_MAXOPT
+AX_FUNC_POSIX_MEMALIGN
+AX_GCC_ARCHFLAG([no])
+AX_EXT
+
+# autoconf stuff
+AC_PROG_INSTALL
+AC_PROG_MAKE_SET
+AC_HEADER_STDC
+
+# Check for pthreads
+ACX_PTHREAD([LIBS="$PTHREAD_LIBS $LIBS" CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+    CC="$PTHREAD_CC" LDFLAGS="$PTHREAD_LIBS $LIBS"
+    AC_DEFINE(HAVE_PTHREAD,1,[Define if you have POSIX threads libraries and header files.])],
+    AC_MSG_ERROR([Could not find a working version of
+    the pthread library. Make sure you have the library and header files installed
+    or use CPPFLAGS and LDFLAGS if the library is installed in a
+    non-standard location.]))
+    
+# Check for OpenMP
+AX_OPENMP
+AC_SUBST(OPENMP_CFLAGS)
+if test -z "${OPENMP_CFLAGS}"; then
+   echo $OPENMP_CFLAGS
+   AC_MSG_ERROR(Compiler does not support OpenMP, 1)
+fi
+
+# Check for timing functions needed by cycle.h
+AC_C_INLINE
+AC_HEADER_TIME
+AC_CHECK_HEADERS([sys/time.h c_asm.h intrinsics.h mach/mach_time.h])
+AC_CHECK_TYPE([hrtime_t],[AC_DEFINE(HAVE_HRTIME_T, 1, [Define to 1 if hrtime_t is defined in <sys/time.h>])],,[#if HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif])
+AC_CHECK_FUNCS([gethrtime read_real_time time_base_to_time clock_gettime mach_absolute_time])
+AC_MSG_CHECKING([for _rtc intrinsic])
+rtc_ok=yes
+AC_TRY_LINK([#ifdef HAVE_INTRINSICS_H
+#include <intrinsics.h>
+#endif], [_rtc()], [AC_DEFINE(HAVE__RTC,1,[Define if you have the UNICOS _rtc() intrinsic.])], [rtc_ok=no])
+AC_MSG_RESULT($rtc_ok)
+
+
+# make the documentation
+DX_INIT_DOXYGEN(libchebfun,doc/Doxyfile,doc/)
+
+# generate the Makefiles
+AC_OUTPUT(Makefile src/Makefile examples/Makefile doc/Makefile)
+