[med-svn] [bowtie2] 02/02: finish up packaging for new upstream release 2.3.0
Sascha Steinbiss
satta at debian.org
Sat Jan 14 11:38:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository bowtie2.
commit 59ea077bcdf0499dd14594dd341d0c7704854fee
Author: Sascha Steinbiss <satta at 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 <tille at 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 <satta at 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 <satta at 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 <satta at 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-*"
--
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