debian/changelog

+spades (3.11.1+dfsg-2) unstable; urgency=medium
+
+  * Build-Depends: libnlopt-cxx-dev
+    Closes: #902592
+  * d/rules:
+     + filter nocheck,$(DEB_BUILD_OPTIONS)
+     + do not parse d/changelog
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Jul 2018 10:54:09 +0200
+
 spades (3.11.1+dfsg-1) unstable; urgency=medium
 
   [ Sascha Steinbiss ]

debian/compat

-9
+11

debian/control

 Source: spades
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders:
-	Andreas Tille <tille@debian.org>,
+Uploaders: Andreas Tille <tille@debian.org>,
            Afif Elghraoui <afif@debian.org>,
            Sascha Steinbiss <satta@debian.org>,
            Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                cmake,
                python-all-dev,
                zlib1g-dev,
@@ -19,6 +18,7 @@ Build-Depends: debhelper (>= 9),
                libhat-trie-dev,
                libhts-dev,
                libnlopt-dev,
+               libnlopt-cxx-dev,
                libssw-dev,
                python-yaml,
                python-joblib,
@@ -26,9 +26,9 @@ Build-Depends: debhelper (>= 9),
                bwa,
                libbwa-dev,
                lynx
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/spades.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/spades.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/spades
+Vcs-Git: https://salsa.debian.org/med-team/spades.git
 Homepage: http://cab.spbu.ru/software/spades/
 
 Package: spades

debian/patches/0103_use-debian-packaged-bwa.patch

@@ -11,7 +11,7 @@ Description: SPAdes originally contained a code copy of bwa since the version
  rather call /usr/bin/bwa but the test suite failed.  So as an alternative
  the package contains a symlink
     ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
- which enables successfull run of the test suite
+ which enables successful run of the test suite
 
 --- spades.orig/ext/tools/CMakeLists.txt
 +++ spades/ext/tools/CMakeLists.txt

debian/patches/0120_dont_rename_jemalloc_functionnames.patch

---- a/src/io/logger_impl.cpp
-+++ b/src/io/logger_impl.cpp
-@@ -17,6 +17,7 @@
- #include "config.hpp"
- 
- #ifdef SPADES_USE_JEMALLOC
-+#define JEMALLOC_NO_RENAME
- # include <jemalloc/jemalloc.h>
- #endif
- 

debian/rules

@@ -2,13 +2,14 @@
 
 # DH_VERBOSE := 1
 
+include /usr/share/dpkg/default.mk
+
 CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
 CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
 CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS)
 LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 TMPDIR     := $(CURDIR)/install_spades
-LIBDIR     := debian/$(DEBPKGNAME)/usr/lib/spades
+LIBDIR     := debian/$(DEB_SOURCE)/usr/lib/spades
 mandir     := $(CURDIR)/debian/man
 debfolder  := $(CURDIR)/debian
 
@@ -52,6 +53,7 @@ override_dh_installman:
 	dh_installman --
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	$(TMPDIR)/bin/spades.py --test
 	$(TMPDIR)/bin/dipspades.py --test
 	$(TMPDIR)/bin/metaspades.py --test
@@ -60,6 +62,7 @@ override_dh_auto_test:
 	# is still not in the right place. Let's do this later in an
 	# autopkgtest.
 	# $(TMPDIR)/bin/truspades.py --test
+endif
 
 override_dh_auto_install:
 	echo "Nothing to install"
@@ -67,12 +70,12 @@ override_dh_auto_install:
 override_dh_install:
 	dh_install
 	mkdir -p $(LIBDIR)
-	mv debian/$(DEBPKGNAME)/usr/bin $(LIBDIR)
-	mkdir -p debian/$(DEBPKGNAME)/usr/bin
-	install debian/bin/spades debian/$(DEBPKGNAME)/usr/bin/
-	chmod +x debian/$(DEBPKGNAME)/usr/bin/spades
-	rm -f debian/$(DEBPKGNAME)/usr/share/spades/GPLv2.txt
-	rm -f debian/$(DEBPKGNAME)/usr/share/spades/LICENSE
+	mv debian/$(DEB_SOURCE)/usr/bin $(LIBDIR)
+	mkdir -p debian/$(DEB_SOURCE)/usr/bin
+	install debian/bin/spades debian/$(DEB_SOURCE)/usr/bin/
+	chmod +x debian/$(DEB_SOURCE)/usr/bin/spades
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt
+	rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE
 
 override_dh_installdocs:
 	dh_installdocs