debian/changelog

+soapsnp (1.03-2) unstable; urgency=medium
+
+  * Team upload.
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Drop useless get-orig-source target
+  * Remove trailing whitespace in debian/rules
+  * d/copyright: Fix source URL
+  * Make sure binary gets installed
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Fri, 26 Oct 2018 15:30:46 +0200
+
 soapsnp (1.03-1) unstable; urgency=low
 
   [ Steffen Moeller ]

debian/compat

-10
+11

debian/control

@@ -3,11 +3,11 @@ 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),
+Build-Depends: debhelper (>= 11~),
                libboost-iostreams-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/soapsnp.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/soapsnp.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/soapsnp
+Vcs-Git: https://salsa.debian.org/med-team/soapsnp.git
 Homepage: http://soap.genomics.org.cn/soapsnp.html
 
 Package: soapsnp

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: soapsnp
-Source: <url://example.com>
+Source: http://soap.genomics.org.cn/soapsnp.html
 
 Files: *
 Copyright: 2008  BGI shenzhen <soap@genomics.org.cn>
@@ -8,6 +8,7 @@ License: GPL-3.0+
 
 Files: debian/*
 Copyright: 2012 Steffen Moeller <moeller@debian.org>
+           2017-2018 Andreas Tille <tille@debian.org>
 License: GPL-3.0+
 
 License: GPL-3.0+

debian/install

+soapsnp	usr/bin

debian/patches/Makefile.patch

-Index: soapsnp-1.03/makefile
-===================================================================
---- soapsnp-1.03.orig/makefile	2009-05-25 09:49:19.000000000 +0200
-+++ soapsnp-1.03/makefile	2012-04-22 01:27:43.714978426 +0200
+Author: Andreas Tille
+Last-Update: 2012-06-08 10:08:01 +0000
+Description: Drop unwanted options from CXXFLAGS
+
+--- a/makefile
++++ b/makefile
 @@ -1,6 +1,6 @@
  DEFINE =
  CXX = g++

debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 26 Oct 2018 15:10:20 +0200
+Description: Propagate hardening options
+
+--- a/makefile
++++ b/makefile
+@@ -1,6 +1,6 @@
+ DEFINE =
+ CXX = g++
+-CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops #-mmmx -msse -msse2 -msse3 -fmessage-length=0  #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
++CXXFLAGS += -fomit-frame-pointer -O3 -ffast-math -funroll-loops
+ 
+ LFLAGS = -lz
+ 
+@@ -11,7 +11,7 @@ objects: call_genotype.o chromosome.o ma
+ $(objects): %.o: soap_snp.h makefile
+ 
+ soapsnp: call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o makefile
+-	$(CXX) $(CXXFLAGS) call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o -o soapsnp $(LFLAGS)
++	$(CXX) $(CFLAGS) $(CXXFLAGS) call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o -o soapsnp $(LFLAGS) $(LDFLAGS)
+ 
+ .PHONY: clean
+ clean:

debian/patches/series

 Makefile.patch
+hardening.patch

debian/rules

@@ -3,9 +3,8 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@
 
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs