Andreas Tille pushed to branch master at Debian Med / spades
Commits: 38e0eadd by Andreas Tille at 2018-07-06T10:00:58+02:00 Build-Depends: libnlopt-cxx-dev - - - - - 499bf922 by Andreas Tille at 2018-07-06T10:03:06+02:00 filter nocheck,$(DEB_BUILD_OPTIONS) - - - - - f06d5aa5 by Andreas Tille at 2018-07-06T10:05:03+02:00 do not parse d/changelog - - - - - 1ec4c970 by Andreas Tille at 2018-07-06T10:07:03+02:00 Remove unneeded patch - - - - - e8547c8f by Andreas Tille at 2018-07-06T10:07:26+02:00 debhelper 11 - - - - - 69c6742d by Andreas Tille at 2018-07-06T10:30:46+02:00 Point Vcs fields to salsa.debian.org - - - - - 0d8a3a39 by Andreas Tille at 2018-07-06T10:30:46+02:00 Standards-Version: 4.1.4 - - - - - a22ad7ad by Andreas Tille at 2018-07-06T10:54:02+02:00 Spelling - - - - - 81b80c98 by Andreas Tille at 2018-07-06T11:33:04+02:00 Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/compat - debian/control - debian/patches/0103_use-debian-packaged-bwa.patch - − debian/patches/0120_dont_rename_jemalloc_functionnames.patch - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,16 @@ +spades (3.11.1+dfsg-2) unstable; urgency=medium + + * Build-Depends: libnlopt-cxx-dev + Closes: #902592 + * d/rules: + + filter nocheck,$(DEB_BUILD_OPTIONS) + + do not parse d/changelog + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.4 + + -- Andreas Tille <[email protected]> Fri, 06 Jul 2018 10:54:09 +0200 + spades (3.11.1+dfsg-1) unstable; urgency=medium [ Sascha Steinbiss ] ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -9 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -1,13 +1,12 @@ Source: spades Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: - Andreas Tille <[email protected]>, - Afif Elghraoui <[email protected]>, - Sascha Steinbiss <[email protected]>, - Michael R. Crusoe <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Afif Elghraoui <[email protected]>, + Sascha Steinbiss <[email protected]>, + Michael R. Crusoe <[email protected]> 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 ===================================== --- a/debian/patches/0103_use-debian-packaged-bwa.patch +++ b/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 deleted ===================================== --- a/debian/patches/0120_dont_rename_jemalloc_functionnames.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- 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 ===================================== --- a/debian/rules +++ b/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 View it on GitLab: https://salsa.debian.org/med-team/spades/compare/7901d289425a2d6a864c1a0adf56eec959ece86e...81b80c9801e5ea092d73e0f02230b41d0f2bf999 -- View it on GitLab: https://salsa.debian.org/med-team/spades/compare/7901d289425a2d6a864c1a0adf56eec959ece86e...81b80c9801e5ea092d73e0f02230b41d0f2bf999 You're receiving this email because of your account on salsa.debian.org.
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