diff --git a/apps/Makefile.common.in b/apps/Makefile.common.in
index 15c61ae..f15d71d 100644
--- a/apps/Makefile.common.in
+++ b/apps/Makefile.common.in
@@ -36,10 +36,10 @@ REGEX_CPP	= @REGEX_CPP@
 LIBS		= @LIBS@ -lm
 
 ALL_CPPFLAGS	= -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS)
-ALL_CXXFLAGS	= $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS)
-ALL_CFLAGS	= $(CC_DEBUGFLAGS) $(CC_OPTFLAGS)
+ALL_CXXFLAGS	= @CXXFLAGS@
+ALL_CFLAGS	= @CFLAGS@
 
-CXXLINK = $(CXX) $(ALL_CPPFLAGS) $(CXX_DEBUGFLAGS) $(CXX_OPTFLAGS) \
+CXXLINK = $(CXX) $(ALL_CPPFLAGS) @CXXFLAGS@ \
            $(LDFLAGS)
 
 .SUFFIXES: .cc .o
diff --git a/apps/libmso/Makefile.in b/apps/libmso/Makefile.in
index 249c25b..9d23665 100644
--- a/apps/libmso/Makefile.in
+++ b/apps/libmso/Makefile.in
@@ -35,8 +35,8 @@ INSTALL		= @INSTALL@
 INSTALL_PROGRAM	= @INSTALL_PROGRAM@
 
 ALL_CPPFLAGS	= -I. $(LOCALINCS) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS)
-ALL_CXXFLAGS	= $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS)
-ALL_CFLAGS	= $(CC_DEBUGFLAGS) $(CC_OPTFLAGS)
+ALL_CXXFLAGS	= @CXXFLAGS@
+ALL_CFLAGS	= @CFLAGS@
 
 .SUFFIXES:
 .SUFFIXES: .cc .o
diff --git a/apps/redti/Makefile.in b/apps/redti/Makefile.in
index c4aa5ca..9561bf3 100644
--- a/apps/redti/Makefile.in
+++ b/apps/redti/Makefile.in
@@ -21,7 +21,7 @@ CFLAGS	= @CFLAGS@
 redti_objs = redti.o rfixpro.o rfixprosee.o pfix.o tc.o
 
 redti : $(redti_objs)
-	$(CC) $(CFLAGS) $(redti_objs) -lm -o redti
+	$(CC) $(CFLAGS) $(LDFLAGS) $(redti_objs) -lm -o redti
 
 appname = redti
 include ../Makefile.common
diff --git a/libmead/Makefile.in b/libmead/Makefile.in
index 3d4d5f0..8b4a4ac 100644
--- a/libmead/Makefile.in
+++ b/libmead/Makefile.in
@@ -99,8 +99,8 @@ PYTHONINC	= @PYTHONINC@
 INCLUDES	= -I$(top_srcdir)
 
 ALL_CPPFLAGS	= $(INCLUDES) $(CPPFLAGS) $(REGEX_CPP) $(CXX_DEFS)
-ALL_CXXFLAGS	= $(CXX_OPTFLAGS) $(CXX_DEBUGFLAGS) $(CXX_SHAREDFLAGS)
-ALL_CFLAGS	= $(CC_DEBUGFLAGS) $(CC_OPTFLAGS)
+ALL_CXXFLAGS	= @CXXFLAGS@
+ALL_CFLAGS	= @CFLAGS@
 
 
 
diff --git a/swig/Makefile.in b/swig/Makefile.in
index 81b3b4e..8410307 100644
--- a/swig/Makefile.in
+++ b/swig/Makefile.in
@@ -58,7 +58,7 @@ CPP_FLAGS	= -DSWIG @CPPFLAGS@
 CXX_FLAGS	= @CXX_NOOPTFLAGS@ @CXX_DEBUGFLAGS@ @CXX_SHAREDFLAGS@
 CXX_DYNLIB_FLAGS = @CXX_DYNLIB_FLAGS@
 
-ALL_CXXFLAGS	= $(CPP_FLAGS) $(CXX_FLAGS)
+ALL_CXXFLAGS	= $(CPP_FLAGS) @CXXFLAGS@ @CXX_SHAREDFLAGS@
 
 MEADINC		= -I$(top_srcdir) -I$(srcdir)
 MEADLIBS	= -L../libmead -lmead