debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -12,8 +12,8 @@ export MANDIR      = ${prefix}/share/man
+ export PROGSUFFIX = 2
+ export MANSUFFIX = 1
+ 
+-export CFLAGS = -pipe -Wall -Wextra -fPIC -O3
+-export LIBS   = -lm -pthread
++export CFLAGS += -pipe -Wall -Wextra -fPIC -O3
++export LIBS    = -lm -pthread
+ 
+ # The program lists below for HMMER are not necessarily
+ # a complete manifest. They are the list of stable programs that the
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -45,7 +45,7 @@ HDRS =	config.h\
+ all:	 $(PROGS)
+ 
+ ${PROGS}: %: %.o ${OBJS}
+-	${CC} ${CFLAGS} ${MYLIBDIR} -o $@ $@.o ${OBJS} ${MYLIBS} ${PTHREAD_LIBS} ${LIBS}
++	${CC} ${CFLAGS} ${MYLIBDIR} -o $@ $@.o ${OBJS} ${MYLIBS} ${PTHREAD_LIBS} ${LIBS} $(LDFLAGS)
+ 
+ 
+ #################################################################

debian/patches/series

@@ -2,3 +2,5 @@ use_debian_packaged_biosquid.patch
 build_libhmmer.a_with-fPIC.patch
 fix_typo.patch
 fix_install.patch
+hardening.patch
+#static_lib.patch

debian/patches/static_lib.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
+Description: Try to create static library
+ Unfortunately this does not work - thus the patch is deactivated
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -54,9 +54,9 @@ ${PROGS}: %: %.o ${OBJS}
+ module: $(HMMLIB)
+ 
+ $(HMMLIB): $(OBJS)
+-#	$(AR) libhmmer.a $(OBJS)
+-#	$(RANLIB) libhmmer.a
+-#	chmod 644 libhmmer.a
++	$(AR) libhmmer.a $(OBJS)
++	$(RANLIB) libhmmer.a
++	chmod 644 libhmmer.a
+ 	gcc -shared $(OBJS) -o $@
+ 
+