debian/changelog

+snap-aligner (1.0~beta.18+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Install NOTICE.txt of Apache licensed files
+  * Propagate hardening options
+  TODO: With hardening options switched on build time test suite runs into
+    LandauVishkinTest:
+    - equal strings: [OK]
+    - prefixes: [OK]
+    - non-equal strings: [OK]
+    - overly distant strings: [OK]
+    - CIGAR strings: [OK]
+    
+    EventTest:
+    - many waiters: make[1]: *** [debian/rules:17: override_dh_auto_test] Segmentation fault
+
+
+ -- Andreas Tille <tille@debian.org>  Fri, 26 Oct 2018 14:23:56 +0200
+
 snap-aligner (1.0~beta.18+dfsg-2) unstable; urgency=medium
 
   * Team upload

debian/compat

-10
+11

debian/control

@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                help2man,
                zlib1g-dev
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snap-aligner.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/snap-aligner.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner
+Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git
 Homepage: http://snap.cs.berkeley.edu/
 
 Package: snap-aligner

debian/docs

 docs/Manual.pdf
 docs/QuickStart.pdf
 README.md
+import/pdclibhdfs/src/NOTICE.txt

debian/patches/hardening.patch

+Description: Propagate hardening options
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 26 Oct 2018 14:09:24 +0200
+
+--- a/Makefile
++++ b/Makefile
+@@ -2,7 +2,7 @@ ifndef CXXFLAGS
+   CXXFLAGS = -O3 -Wno-format
+ endif
+ 
+-CXXFLAGS += -MMD -ISNAPLib
++CXXFLAGS += -MMD -ISNAPLib $(CFLAGS)
+ 
+ LDFLAGS += -pthread
+ 

debian/patches/series

@@ -2,3 +2,4 @@ non-x86-and-kfreebsd
 drop-msse
 spelling
 finish-rename
+hardening.patch

debian/rules

@@ -12,8 +12,10 @@ export CXXFLAGS
 	dh $@
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test
 	./unit_tests
+endif
 
 override_dh_auto_build:
 	dh_auto_build