--- a/rp2gen/Makefile.in
+++ b/rp2gen/Makefile.in
@@ -198,7 +198,8 @@
 CCDEPMODE = @CCDEPMODE@
 
 # override any cross compilation target flags
-CFLAGS = -Wall
+AM_CFLAGS = -Wall
+CFLAGS = @CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CP = @CP@
 CPP = @CPP@
@@ -225,7 +226,7 @@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LD = @LD@
-LDFLAGS = 
+LDFLAGS = @LDFLAGS@
 LEX = @LEX@
 LEXLIB = @LEXLIB@
 LEX_OUTPUT_ROOT = @LEX_OUTPUT_ROOT@