Author: Steffen Moeller <moeller@debian.org>, Tim Booth <tbooth@ceh.ac.uk>
Purpose: Comment MAC specific option
  Don't bother with any compilation flags, as the defaults are already sane
  on all architectures (and trying to set -m64 explicitly fails on ia64).
--- a/makefile
+++ b/makefile
@@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran
 FORTRAN_FLAGS = 
 
 # Optimize to level 3:
-CXXFLAGS += -O3 
+# Nope, let debuild set this.
+# CXXFLAGS += -O3
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
 	#CXX = g++44
 	
 	#if you are a mac user use the following line
-	TARGET_ARCH += -arch x86_64
+	#TARGET_ARCH += -arch x86_64
 	
 	#if you using cygwin to build Windows the following line
 	#CXX = x86_64-w64-mingw32-g++
@@ -38,9 +39,11 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
 
 	#if you are a linux user use the following line
 	#CXXFLAGS += -mtune=native -march=native -m64
+	# But not if you are trying to make a generic build for
+	# packaging, because your binary will end up being specific
+	# to your processor.
 	
 	CXXFLAGS += -DBIT_VERSION 
-    FORTRAN_FLAGS = -m64
 endif
 
 
@@ -120,4 +123,3 @@ install : mothur
 clean :
 	@rm -f $(OBJECTS)
 	@rm -f uchime
-
