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commit 59ea077bcdf0499dd14594dd341d0c7704854fee Author: Sascha Steinbiss <sa...@debian.org> Date: Sat Jan 14 11:22:04 2017 +0000 finish up packaging for new upstream release 2.3.0 --- debian/changelog | 11 ++++- debian/control | 4 +- debian/patches/do-not-rebuild-during-test.patch | 56 +++++++++++++++++++++++++ debian/patches/series | 2 + debian/patches/single-cpu-for-test.patch | 51 ++++++++++++++++++++++ debian/rules | 20 ++++++++- 6 files changed, 139 insertions(+), 5 deletions(-) diff --git a/debian/changelog b/debian/changelog index 263b07e..17f95ee 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,8 @@ -bowtie2 (2.3.0-1) UNRELEASED; urgency=medium +bowtie2 (2.3.0-1) unstable; urgency=medium + * Team upload. + + [ Andreas Tille ] * New upstream version * Code available on Github * debhelper 10 @@ -8,7 +11,11 @@ bowtie2 (2.3.0-1) UNRELEASED; urgency=medium libmath-random-perl * New Build-Depends to run build time test: liblocal-lib-perl - -- Andreas Tille <ti...@debian.org> Mon, 09 Jan 2017 12:43:48 +0100 + [ Sascha Steinbiss ] + * Even more new Build-Depends: libmath-random-perl, libtest-deep-perl + * Disable rebuilding during tests + + -- Sascha Steinbiss <sa...@debian.org> Sat, 14 Jan 2017 07:50:51 +0000 bowtie2 (2.2.9-4) unstable; urgency=medium diff --git a/debian/control b/debian/control index bb8c43f..a6beb02 100644 --- a/debian/control +++ b/debian/control @@ -9,7 +9,9 @@ Build-Depends: debhelper (>= 10), help2man, libtbb-dev, python, - liblocal-lib-perl + liblocal-lib-perl, + libtest-deep-perl, + libmath-random-perl Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bowtie2.git Vcs-Git: https://anonscm.debian.org/git/debian-med/bowtie2.git diff --git a/debian/patches/do-not-rebuild-during-test.patch b/debian/patches/do-not-rebuild-during-test.patch new file mode 100644 index 0000000..0d09145 --- /dev/null +++ b/debian/patches/do-not-rebuild-during-test.patch @@ -0,0 +1,56 @@ +Description: do not rebuild with default settings during test + The test suite builds the debug versions of the executables with default + flags, while is needs to be built with the flags in d/rules. +Author: Sascha Steinbiss <sa...@debian.org> +--- a/scripts/sim/run.sh ++++ b/scripts/sim/run.sh +@@ -21,15 +21,15 @@ + + CPUS=$1 + shift +-make -j$CPUS \ +- bowtie2-align-s \ +- bowtie2-align-l \ +- bowtie2-align-s-debug \ +- bowtie2-align-l-debug \ +- bowtie2-build-s \ +- bowtie2-build-l \ +- bowtie2-build-s-debug \ +- bowtie2-build-l-debug && \ ++#make -j$CPUS \ ++# bowtie2-align-s \ ++# bowtie2-align-l \ ++# bowtie2-align-s-debug \ ++# bowtie2-align-l-debug \ ++# bowtie2-build-s \ ++# bowtie2-build-l \ ++# bowtie2-build-s-debug \ ++# bowtie2-build-l-debug && \ + perl scripts/sim/run.pl \ + --bowtie2=./bowtie2 \ + --bowtie2-build=./bowtie2-build \ +--- a/scripts/test/simple_tests.sh ++++ b/scripts/test/simple_tests.sh +@@ -21,14 +21,14 @@ + + # simple_tests.sh + +-make $* bowtie2-align-s \ +- bowtie2-align-l \ +- bowtie2-align-s-debug \ +- bowtie2-align-l-debug \ +- bowtie2-build-s \ +- bowtie2-build-l \ +- bowtie2-build-s-debug \ +- bowtie2-build-l-debug && \ ++#make $* bowtie2-align-s \ ++# bowtie2-align-l \ ++# bowtie2-align-s-debug \ ++# bowtie2-align-l-debug \ ++# bowtie2-build-s \ ++# bowtie2-build-l \ ++# bowtie2-build-s-debug \ ++# bowtie2-build-l-debug && \ + perl scripts/test/simple_tests.pl \ + --bowtie2=./bowtie2 \ + --bowtie2-build=./bowtie2-build diff --git a/debian/patches/series b/debian/patches/series index aacdb8b..1b68131 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,5 @@ hardening.patch reproducible.patch skip_test_requiring_non-free_libmath-random-perl.patch +do-not-rebuild-during-test.patch +single-cpu-for-test.patch diff --git a/debian/patches/single-cpu-for-test.patch b/debian/patches/single-cpu-for-test.patch new file mode 100644 index 0000000..015dcfe --- /dev/null +++ b/debian/patches/single-cpu-for-test.patch @@ -0,0 +1,51 @@ +Description: only use single CPU for testing + This also frees us of the dependency to the non-packaged libsys-info-perl. +Author: Sascha Steinbiss <sa...@debian.org> +--- a/Makefile ++++ b/Makefile +@@ -491,7 +491,7 @@ + .PHONY: random-test perl-deps + random-test: all + eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ +- sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2) ++ sh ./scripts/sim/run.sh 1 #$(if $(NUM_CORES), $(NUM_CORES), 2) + + .PHONY: perl-deps + perl-deps: +--- a/scripts/sim/run.sh ++++ b/scripts/sim/run.sh +@@ -19,7 +19,7 @@ + # along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>. + # + +-CPUS=$1 ++CPUS=1 + shift + #make -j$CPUS \ + # bowtie2-align-s \ +--- a/scripts/sim/Sim.pm ++++ b/scripts/sim/Sim.pm +@@ -33,8 +33,8 @@ + use Math::Random; + use List::Util qw(max min); + use POSIX; +-use Sys::Info; +-use Sys::Info::Constants qw( :device_cpu ); ++#use Sys::Info; ++#use Sys::Info::Constants qw( :device_cpu ); + + ## + # Replacement for "die" that additionally writes error message to file so that +@@ -402,9 +402,9 @@ + if($r4 == 0) { + $args{"--offrate"} = int(rand(8))+1; + } +- my $info = Sys::Info->new; +- my $cpu = $info->device('CPU'); +- $args{"--threads"} = int(rand($cpu->count || 1)) + 1; ++# my $info = Sys::Info->new; ++# my $cpu = $info->device('CPU'); ++# $args{"--threads"} = int(rand($cpu->count || 1)) + 1; + $args{"--large-index"} = "" if $large_index; + return \%args; + } diff --git a/debian/rules b/debian/rules index 1de0ee8..486ec10 100755 --- a/debian/rules +++ b/debian/rules @@ -9,8 +9,8 @@ export LC_ALL=C.UTF-8 DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) EXTRA_OPTIONS = -ifeq ($(DEB_HOST_ARCH),amd64) - EXTRA_OPTIONS = WITH_TBB=1 +ifneq ($(DEB_HOST_ARCH),amd64) + EXTRA_OPTIONS = NO_TBB=1 endif export EXTRA_OPTIONS @@ -20,6 +20,22 @@ export EXTRA_OPTIONS override_dh_auto_build: dh_auto_build -- EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS) +override_dh_auto_test: + $(MAKE) EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS) \ + bowtie2-build-s-debug \ + bowtie2-build-l-debug \ + bowtie2-align-s-debug \ + bowtie2-align-l-debug \ + bowtie2-inspect-s-debug \ + bowtie2-inspect-l-debug + make -j1 test + +override_dh_auto_install: + dh_auto_install + +override_dh_install: + dh_install -X.gitignore + override_dh_installman: mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/ debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bowtie2.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit