debian/changelog

+soapaligner (2.20-2) unstable; urgency=medium
+
+  * Team upload.
+  * Drop -msse3 from compiler options
+    Closes: #902129
+  * debhelper 11
+  * Standards-Version: 4.1.4
+  * DEP3
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Sat, 30 Jun 2018 07:22:04 +0200
+
 soapaligner (2.20-1) unstable; urgency=low
 
   [ Steffen Moeller ]

debian/compat

-10
+11

debian/control

@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.3
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/soapaligner
 Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
 Homepage: http://soap.genomics.org.cn/soapaligner.html

debian/patches/UsageDoublette.patch

+Author: Steffen Moeller
+Last-Update: 2018-05-04 18:33:03 +0200
+Description: Deal with doublette of Usage function by making it static
+
 Index: soapaligner/soap.c
 ===================================================================
 --- soapaligner.orig/soap.c

debian/patches/compiler_options.patch

+Author: Steffen Moeller
+Last-Update: 2018-05-04 18:33:03 +0200
+Description: Adapt Makefile to accept Debian preset compiler options
+
 Index: soapaligner/Makefile
 ===================================================================
 --- soapaligner.orig/Makefile
@@ -24,7 +28,7 @@ Index: soapaligner/Makefile
 +CC            ?= gcc
 +DEBUG_FLAGS   ?= -g3 -Wall -O2
 +PROFILE_FLAGS ?= -fprofile-arcs -ftest-coverage -pg
-+RELEASE_FLAGS ?= -msse3 -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
++RELEASE_FLAGS ?= -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
 +STATIC_FLAGS  ?= -static
 +DFLAGS        ?= -DMAKE_TIME=\""`date`"\"
 +LDFLAGS       ?=

debian/patches/linkerror.patch

+Author: Steffen Moeller
+Last-Update: 2018-05-04 18:33:03 +0200
+Description: Fix build
+
 Index: soapaligner/Makefile
 ===================================================================
 --- soapaligner.orig/Makefile

debian/rules

@@ -9,5 +9,7 @@ export CFLAGS += -flto
 export CXXFLAGS += -flto
 export LDFLAGS += -Wl,-flto
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@