paml (4.5-1) hardening.patch

Description: Enable propagation of hardening flags
Author: Andreas Tille <tille@debian.org>
Date: Tue, 15 May 2012 11:10:59 +0200

--- paml4.5.orig/src/Makefile
+++ paml4.5/src/Makefile
@@ -1,7 +1,7 @@
 PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 
 CC = cc # cc, gcc, cl
 
-CFLAGS = -O4 -funroll-loops -fomit-frame-pointer -finline-functions
+CFLAGS += -O4 -funroll-loops -fomit-frame-pointer -finline-functions
 
 #MAC OSX G5:
 #CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions
@@ -20,21 +20,21 @@
 all : $(PRGS)
 
 baseml : baseml.c tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.c tools.c $(LIBS)
 basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.c tools.c $(LIBS)
 codeml : codeml.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.c tools.c $(LIBS)
 evolver : evolver.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.c tools.c $(LIBS)
 pamp : pamp.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.c tools.c $(LIBS)
 mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
 yn00: yn00.c tools.c paml.h
-	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.c tools.c $(LIBS)
 chi2 : chi2.c
-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
 
 PREFIX=/usr
 DESTDIR=/