diff --git a/build/bakefiles/Makefile b/build/bakefiles/Makefile
index 946efff91c..35dd92314e 100644
--- a/build/bakefiles/Makefile
+++ b/build/bakefiles/Makefile
@@ -91,9 +91,11 @@ clean:
 	rm -f ../../samples/internat/Makefile.in
 
 
+../../autoconf_inc.m4: ../../Makefile.in
 ../../configure: ../../autoconf_inc.m4
 	(cd ../.. ; aclocal && autoconf)
 
+../../samples/autoconf_inc.m4: ../../samples/Makefile.in
 ../../samples/configure: ../../samples/autoconf_inc.m4
 	(cd ../../samples ; aclocal && autoconf)
 
diff --git a/build/bakefiles/regenMakefile.py b/build/bakefiles/regenMakefile.py
index 23718bea3d..083895793f 100755
--- a/build/bakefiles/regenMakefile.py
+++ b/build/bakefiles/regenMakefile.py
@@ -108,9 +108,11 @@ clean:
 \trm -f ../../samples/autoconf_inc.m4
 %s
 
+../../autoconf_inc.m4: ../../Makefile.in
 ../../configure: ../../autoconf_inc.m4
 \t(cd ../.. ; aclocal && autoconf)
 
+../../samples/autoconf_inc.m4: ../../samples/Makefile.in
 ../../samples/configure: ../../samples/autoconf_inc.m4
 \t(cd ../../samples ; aclocal && autoconf)