--- a/src/bootstrap	Tue Mar 04 12:09:26 2014 +0000
+++ b/src/bootstrap	Wed Mar 05 10:32:56 2014 +0000
@@ -1,5 +1,7 @@
 #!/bin/bash
 ## Octave-Forge: msh package bootstrap script
+set -e
+autoreconf --verbose --install --force
 
-set -e
-autoconf
+echo "$0: done.  Now you can run './configure'."
+

--- a/src/configure.ac	Tue Mar 04 12:09:26 2014 +0000
+++ b/src/configure.ac	Wed Mar 05 10:32:56 2014 +0000
@@ -1,22 +1,54 @@
 AC_PREREQ([2.67])
 AC_INIT([Msh Package], [1.0])
 
+AC_USE_SYSTEM_EXTENSIONS
+
 AC_PROG_CXX
 AC_LANG(C++)
 
+# Get Dense include locations
+AC_ARG_WITH([eigen-includedir],
+  [AS_HELP_STRING([--with-eigen-includedir=DIR],
+    [location of the Eigen headers, defaults to /usr/include/])],
+  [DENSE_CPPFLAGS="-I$withval"],
+  [DENSE_CPPFLAGS='-I/usr/include/'])
+AC_SUBST(DENSE_CPPFLAGS)
+echo $DENSE_CPPFLAGS
+
+CPPFLAGS="$DENSE_CPPFLAGS $CPPFLAGS"
+
+# Check for Dense and dolfin
+have_dense_ok=no
+AC_CHECK_HEADERS([Eigen/Dense],[have_dense_ok=yes;break],[],[])
+
+if test $have_dense_ok = no; then
+  AC_MSG_WARN([Dense headers could not be found,
+                some functionalities will be disabled,
+                don't worry your package will still be
+                working, though.])
+fi
+
+have_dolfin_ok=no
+AC_CHECK_HEADERS([dolfin.h], [have_dolfin_ok=yes; break], [],
+  [#ifdef HAVE_DOLFIN_H
+   #include<dolfin.h>
+   #endif])
+if test $have_dolfin_ok = no; then
+  AC_MSG_WARN([dolfin headers could not be found,
+                some functionalities will be disabled,
+                don't worry your package will still be
+                working, though.])
+fi
+
+AC_CHECK_PROG([HAVE_FFC], [ffc], [yes], [no])
+if [test $HAVE_FFC = "no"]; then
+  AC_MSG_ERROR([ffc required to install $PACKAGE_NAME])
+fi
+
 AC_CHECK_PROG([HAVE_MKOCTFILE], [mkoctfile], [yes], [no])
 if [test $HAVE_MKOCTFILE = "no"]; then
   AC_MSG_ERROR([mkoctfile required to install $PACKAGE_NAME])
 fi
 
-AC_CHECK_HEADERS([dolfin.h], [ ],
-  [AC_MSG_ERROR([dolfin required to install $PACKAGE_NAME])]
-)
-
-AC_CHECK_PROG([HAVE_FFC], [ffc], [yes], [no])
-if [test $HAVE_FFC = "no"]; then
-  AC_MSG_ERROR([ffc required to install $PACKAGE_NAME])
-fi
-
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT