debian/changelog

-pbbam (0.18.0+dfsg-1) UNRELEASED; urgency=medium
+pbbam (0.18.0+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Team upload.
@@ -10,11 +10,13 @@ pbbam (0.18.0+dfsg-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.2.1
   * Use d-shlibs
   * Remove unneeded trigger
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test
+  * hardening=+all
 
   [ Fabian Kloetzl ]
   * fix dependency check for meson
 
- -- Andreas Tille <tille@debian.org>  Tue, 21 Aug 2018 21:31:37 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 06 Sep 2018 14:29:53 +0200
 
 pbbam (0.7.4+ds-1) unstable; urgency=medium
 

debian/copyright

@@ -9,16 +9,6 @@ Files: *
 Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
 License: PacBio-BSD-3-Clause
 
-Files: cmake/FindCSharp.cmake
-       cmake/FindMono.cmake
-       cmake/UseCSharp.cmake
-       cmake/UseDotNetFrameworkSdk.cmake
-       cmake/UseMono.cmake
-Copyright: 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com>
-Comment: These files are from GDCM (as indicated in the file headers).
-	 The license terms have been retrieved from there.
-License: MM-BSD-3-Clause
-
 Files: src/pugixml/*
 Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com>
 	   2003 Kristen Wegner <kristen@tima.net>
@@ -61,30 +51,6 @@ License: PacBio-BSD-3-Clause
  OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  SUCH DAMAGE.
 
-License: MM-BSD-3-clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- 1. Redistributions of source code must retain the above copyright notice,
-    this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright notice,
-    this list of conditions and the following disclaimer in the documentation
-    and/or other materials provided with the distribution.
- 3. Neither name of Mathieu Malaterre, or CREATIS, nor the names of any
-    contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to
-    endorse or promote products derived from this software without specific
-    prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 License: BSD-3-Clause
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions

debian/patches/fix_gtest_depcheck.patch

+Author: Andreas Tille, Fabian Klötzl
+Last-Update: 2018-09-05 14:50:07 +0000
+Description: Use Debian packaged gtest
+
 --- a/tests/meson.build
 +++ b/tests/meson.build
 @@ -6,7 +6,7 @@ if not pbbam_cram_script.found()

debian/rules

@@ -4,6 +4,8 @@
 export LC_ALL=C.UTF-8
 include /usr/share/dpkg/default.mk
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM))
 generated_data_dir = $(CURDIR)/gendata
 
@@ -23,6 +25,7 @@ generated_data_dir = $(CURDIR)/gendata
 ##	-DPacBioBAM_wrap_r=ON
 
 override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	mkdir -p $(generated_data_dir)
 	python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir)
 	# Fix broken PATH
@@ -32,6 +35,7 @@ override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
 	LIBDIR=`find $$PWD -name lib -type d`; \
 	PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \
 	cram -v $^
+endif
 
 override_dh_installchangelogs:
 	dh_installchangelogs CHANGELOG.md