[med-svn] [Git][med-team/soapsnp][master] 10 commits: debhelper 11

Fri Oct 26 14:35:48 BST 2018

Andreas Tille pushed to branch master at Debian Med / soapsnp


Commits:
6b979169 by Andreas Tille at 2018-10-26T13:10:20Z
debhelper 11

- - - - -
0ce7ac99 by Andreas Tille at 2018-10-26T13:10:52Z
Point Vcs fields to salsa.debian.org

- - - - -
1bce80cf by Andreas Tille at 2018-10-26T13:10:52Z
Standards-Version: 4.2.1

- - - - -
ba623078 by Andreas Tille at 2018-10-26T13:10:53Z
Drop useless get-orig-source target

- - - - -
fae9f62c by Andreas Tille at 2018-10-26T13:10:53Z
Remove trailing whitespace in debian/rules

- - - - -
4ce08717 by Andreas Tille at 2018-10-26T13:21:29Z
Fix source URL

- - - - -
04b2b661 by Andreas Tille at 2018-10-26T13:22:36Z
DEP3

- - - - -
ad618209 by Andreas Tille at 2018-10-26T13:24:52Z
Make sure binary gets installed

- - - - -
af4e6ac0 by Andreas Tille at 2018-10-26T13:30:19Z
Propagate hardening options

- - - - -
48c74cfe by Andreas Tille at 2018-10-26T13:32:13Z
Upload to unstable

- - - - -


9 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/install
- debian/patches/Makefile.patch
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+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 at debian.org>  Fri, 26 Oct 2018 15:30:46 +0200
+
 soapsnp (1.03-1) unstable; urgency=low
 
   [ Steffen Moeller ]


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Steffen Moeller <moeller at 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
=====================================
@@ -1,6 +1,6 @@
 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 at genomics.org.cn>
@@ -8,6 +8,7 @@ License: GPL-3.0+
 
 Files: debian/*
 Copyright: 2012 Steffen Moeller <moeller at debian.org>
+           2017-2018 Andreas Tille <tille at debian.org>
 License: GPL-3.0+
 
 License: GPL-3.0+


=====================================
debian/install
=====================================
@@ -0,0 +1 @@
+soapsnp	usr/bin


=====================================
debian/patches/Makefile.patch
=====================================
@@ -1,7 +1,9 @@
-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
=====================================
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -1 +1,2 @@
 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 $@ 
+	dh $@
 
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs



View it on GitLab: https://salsa.debian.org/med-team/soapsnp/compare/10ba53f7b8cd6969900eb3c1748637cdc1c4c189...48c74cfeee50d5282f38f25a77fdb2c9dd93738c

-- 
View it on GitLab: https://salsa.debian.org/med-team/soapsnp/compare/10ba53f7b8cd6969900eb3c1748637cdc1c4c189...48c74cfeee50d5282f38f25a77fdb2c9dd93738c
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