Index: /issm/trunk-jpl/externalpackages/autotools/install-win.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/autotools/install-win.sh	(revision 19587)
+++ /issm/trunk-jpl/externalpackages/autotools/install-win.sh	(revision 19588)
@@ -45,4 +45,9 @@
 
 # This patch takes care of removing options passed to the linker that casuse 
-# the build to fail.
+# the build to fail, as well as changing some flags to match up to Microsoft
+# compilers.
 patch ./install/share/aclocal/libtool.m4 < ./patches/libtool.m4.patch
+
+# Small change to Automake in order to get the right flags for Microsoft's
+# compiler.
+patch ./install/bin/automake < ./patches/automake.patch
Index: /issm/trunk-jpl/externalpackages/autotools/patches/automake.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/autotools/patches/automake.patch	(revision 19588)
+++ /issm/trunk-jpl/externalpackages/autotools/patches/automake.patch	(revision 19588)
@@ -0,0 +1,13 @@
+--- ./externalpackages/autotools/install/bin/automake	2015-09-24 19:26:11.796659200 -0700
++++ /home/daeden/tmp/automake	2015-09-25 11:32:53.557609300 -0700
+@@ -702,8 +702,8 @@
+ 		   'compile' => "\$(CXX) @cpplike_flags \$(AM_CXXFLAGS) \$(CXXFLAGS)",
+ 		   'ccer' => 'CXX',
+ 		   'compiler' => 'CXXCOMPILE',
+-		   'compile_flag' => '-c',
+-		   'output_flag' => '-o',
++		   'compile_flag' => '/c',
++		   'output_flag' => '/Fo:',
+ 		   'libtool_tag' => 'CXX',
+ 		   'lder' => 'CXXLD',
+ 		   'ld' => '$(CXX)',
Index: /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch	(revision 19587)
+++ /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch	(revision 19588)
@@ -1,4 +1,13 @@
---- ./externalpackages/autotools/install/share/aclocal/libtool.m4	2015-05-22 18:31:17.780392900 -0700
-+++ ./m4/libtool.m4	2015-05-22 18:35:16.669058700 -0700
+--- ./externalpackages/autotools/install/share/aclocal/libtool.m4	2015-09-24 19:28:57.393566400 -0700
++++ /home/daeden/tmp/libtool.m4	2015-09-25 11:30:45.133747600 -0700
+@@ -2382,7 +2382,7 @@
+     # Native MSVC
+     libname_spec='$name'
+     soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+-    library_names_spec='${libname}.dll.lib'
++    library_names_spec='${libname}${shrext_cmds}'
+ 
+     case $build_os in
+     mingw*)
 @@ -3142,7 +3142,7 @@
  case $host_os in
@@ -15,5 +24,5 @@
        if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
 -        _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+        _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags -o $output_objdir/$soname '
++        _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname '
  	# If the export-symbols file already is a .def file (1st line
  	# is EXPORTS), use it as is; otherwise, prepend...
@@ -24,8 +33,41 @@
  	fi~
 -	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	$CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname '
++	$CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname '
        else
  	_LT_TAGVAR(ld_shlibs, $1)=no
        fi
+@@ -5130,13 +5130,13 @@
+ 	# Tell ltmain to make .dll files, not .so files.
+ 	shrext_cmds=".dll"
+ 	# FIXME: Setting linknames here is a bad hack.
+-	_LT_TAGVAR(archive_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames='
++	_LT_TAGVAR(archive_cmds, $1)='$CC /OUT:$output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames='
+ 	_LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+-	    sed -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp;
++	    sed -n -e 's/\\\\\\\(.*\\\\\\\)/\/link\\\ \/EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp;
+ 	  else
+-	    sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp;
++	    sed -e 's/\\\\\\\(.*\\\\\\\)/\/link\\\ \/EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp;
+ 	  fi~
+-	  $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~
++	  $CC /OUT:$tool_output_objdir$soname $libobjs $compiler_flags $deplibs~
+ 	  linknames='
+ 	# The linker will not automatically build a static lib if we build a DLL.
+ 	# _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
+@@ -6131,11 +6131,11 @@
+ 	  # FIXME: Setting linknames here is a bad hack.
+ 	  _LT_TAGVAR(archive_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames='
+ 	  _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+-	      $SED -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp;
++	      $SED -n -e 's/\\\\\\\(.*\\\\\\\)/\/link\\\ \/EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp;
+ 	    else
+-	      $SED -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp;
++	      $SED -e 's/\\\\\\\(.*\\\\\\\)/\/link\\\ \/EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp;
+ 	    fi~
+-	    $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~
++	    $CC /Fo:$tool_output_objdir$soname $libobjs $compiler_flags $deplibs~
+ 	    linknames='
+ 	  # The linker will not automatically build a static lib if we build a DLL.
+ 	  # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
 @@ -6168,7 +6168,7 @@
  	  _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
@@ -33,5 +75,5 @@
  	  if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
 -	    _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	    _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname '
++	    _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname '
  	    # If the export-symbols file already is a .def file (1st line
  	    # is EXPORTS), use it as is; otherwise, prepend...
@@ -42,5 +84,5 @@
  	    fi~
 -	    $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	    $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname '
++	    $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname '
  	  else
  	    _LT_TAGVAR(ld_shlibs, $1)=no