From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Thu, 9 Jul 2020 16:05:44 +0200
Subject: Enable proper flag appending so that Debian can harden the build.

Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/69
---
 Makefile                   | 4 ++--
 ext/safestringlib/makefile | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 359585f..717504d 100644
--- a/Makefile
+++ b/Makefile
@@ -111,11 +111,11 @@ multi:
 	$(MAKE) arch=avx2   EXE=bwa-mem2.avx2     CXX=$(CXX) all
 	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
 	$(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all
-	$(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2
 
 
 $(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@
 
 $(BWA_LIB):$(OBJS)
 	ar rcs $(BWA_LIB) $(OBJS)
diff --git a/ext/safestringlib/makefile b/ext/safestringlib/makefile
index f7cc268..23ad139 100644
--- a/ext/safestringlib/makefile
+++ b/ext/safestringlib/makefile
@@ -1,8 +1,8 @@
 IDIR = include
 MKDIR_P = mkdir -p
 CC=gcc
-CFLAGS=-I$(IDIR) -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
-LDFLAGS=-z noexecstack -z relo -z now
+CFLAGS+=-I$(IDIR) -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
+LDFLAGS+=-z noexecstack -z relo -z now
 
 ODIR=obj
 OTDIR=objtest
@@ -30,7 +30,7 @@ CLIB =$(addprefix $(SRCDIR)/,$(_CLIB))
 
 
 $(ODIR)/%.o: $(SRCDIR)/%.c $(DEPS) $(ODEPS)
-	$(CC) $(LDFLAGS) -c -o $@ $< $(CFLAGS)
+	$(CC) $(CPPFLAGS) $(LDFLAGS) -c -o $@ $< $(CFLAGS)
 
 libsafestring.a: $(OBJ)
 	ar rcs $@ $^
@@ -44,7 +44,7 @@ TCLIB =$(addprefix $(TESTDIR)/,$(_TESTFUNCS))
 
 
 $(OTDIR)/%.o: $(TESTDIR)/%.c $(TESTDIR)/test_private.h
-	$(CC) -c -o $@ $< $(CFLAGS)
+	$(CC) $(CPPFLAGS) -c -o $@ $< $(CFLAGS)
 
 
 safestringtest: directories libsafestring.a $(TOBJ)
