diff -up EMBOSS-6.3.1/m4/amd64.m4.BAD EMBOSS-6.3.1/m4/amd64.m4
--- EMBOSS-6.3.1/m4/amd64.m4.BAD	2010-11-10 11:13:27.153159001 -0500
+++ EMBOSS-6.3.1/m4/amd64.m4	2010-11-10 11:14:21.722159000 -0500
@@ -12,8 +12,8 @@ AC_DEFUN([CHECK_AMD64],
 [AC_MSG_CHECKING([if Linux x86_64])
 
 
-if test "`uname -a | grep Linux`"; then
-  if test "`uname -a | grep x86_64`"; then
+if test "`uname -o | grep Linux`"; then
+  if test "`uname -m | grep x86_64`"; then
     CFLAGS="${CFLAGS} -D__amd64__"
     AC_MSG_RESULT(yes)
   else