--- a/Makefile.in
+++ b/Makefile.in
@@ -11,10 +11,10 @@
 all: binary docs
 
 binary: Makefile Source/Makefile
-	@cd Source && make && cd ..
+	@cd Source && $(MAKE) && cd ..
 
 docs:
-	@cd Docs && make && cd ..
+	@cd Docs && $(MAKE) && cd ..
 
 install: all
 	$(INSTALL) -d -m 755 $(SBINDIR)
@@ -29,7 +29,7 @@
 	$(INSTALL) -m 644 Docs/ippl.conf.5 $(MANDIR)/man5/ippl.conf.5
 
 clean:
-	@cd Source && make clean && cd .. && cd Docs && make clean && cd ..
+	@cd Source && $(MAKE) clean && cd .. && cd Docs && $(MAKE) clean && cd ..
 
 distclean: clean
 	$(RM) *~ Makefile.common Makefile Source/Makefile Docs/Makefile build-stamp install-stamp
--- a/Source/Makefile.in
+++ b/Source/Makefile.in
@@ -10,7 +10,7 @@
 CC=@CC@
 CFLAGS=@CFLAGS@
 WARNINGS=-Wall@PEDANTIC@
-LDFLAGS=
+LDFLAGS=@LDFLAGS@
 
 SRCS=	main.c \
 	configuration.c \
@@ -49,7 +49,7 @@
 y.tab.c: ippl.y Makefile ../Makefile.common
 	$(YACC) -d $<
 
-lex.yy.c: ippl.l Makefile ../Makefile.common
+lex.yy.c: ippl.l y.tab.c Makefile ../Makefile.common
 	$(LEX) $<
 
 clean: