[med-svn] [Git][med-team/mapsembler2][master] 9 commits: Fix hdf5 detection
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Apr 28 14:02:44 BST 2026
Andreas Tille pushed to branch master at Debian Med / mapsembler2
Commits:
a748f046 by Andreas Tille at 2026-04-28T14:44:53+02:00
Fix hdf5 detection
- - - - -
97ee9164 by Andreas Tille at 2026-04-28T14:48:37+02:00
Remove architecture kfreebsd-amd64
- - - - -
c5aa0d7b by Andreas Tille at 2026-04-28T14:49:57+02:00
Fix DEP3 format of Last-Update
- - - - -
d6787a26 by Andreas Tille at 2026-04-28T14:50:52+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
b56850f0 by Andreas Tille at 2026-04-28T14:50:55+02:00
Changes made by cme
- - - - -
8be39bfb by Andreas Tille at 2026-04-28T14:50:57+02:00
Drop default 'Rules-Requires-Root: no' from debian/control (routine- update)
- - - - -
0686122b by Andreas Tille at 2026-04-28T13:50:58+01:00
Rely on pre-initialized dpkg-architecture variables.
Changes-By: lintian-brush
- - - - -
cc88aafb by Andreas Tille at 2026-04-28T13:50:58+01:00
Reorder Files paragraphs in debian/copyright by directory depth.
Changes-By: lintian-brush
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
- - - - -
d5ae05dc by Andreas Tille at 2026-04-28T14:54:07+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/cmake4.patch
- debian/patches/gcc-5.patch
- debian/patches/libgomp.patch
- debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-mapsembler2 (2.2.4+dfsg1-6) UNRELEASED; urgency=medium
+mapsembler2 (2.2.4+dfsg1-6) unstable; urgency=medium
* Fix build with CMake 4
Closes: #1125550
-
- -- Andreas Tille <tille at debian.org> Tue, 28 Apr 2026 11:38:27 +0200
+ * Remove architecture kfreebsd-amd64
+ * Fix DEP3 format of Last-Update
+ * Standards-Version: 4.7.4 (routine-update)
+ * Remove Priority field (cme)
+ * Drop default 'Rules-Requires-Root: no' from debian/control (routine-
+ update)
+ * Rely on pre-initialized dpkg-architecture variables.
+ * Reorder Files paragraphs in debian/copyright by directory depth.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 Apr 2026 14:51:08 +0200
mapsembler2 (2.2.4+dfsg1-5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,12 +1,11 @@
Source: mapsembler2
-Standards-Version: 4.7.2
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Olivier Sallou <osallou at debian.org>,
Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>,
Section: science
-Priority: optional
Build-Depends:
debhelper-compat (= 13),
cmake,
@@ -18,10 +17,9 @@ Build-Depends:
Vcs-Browser: https://salsa.debian.org/med-team/mapsembler2
Vcs-Git: https://salsa.debian.org/med-team/mapsembler2.git
Homepage: http://colibread.inria.fr/mapsembler2/
-Rules-Requires-Root: no
Package: mapsembler2
-Architecture: amd64 arm64 kfreebsd-amd64 ppc64el s390x
+Architecture: amd64 arm64 ppc64el s390x
Depends:
${misc:Depends},
${shlibs:Depends},
=====================================
debian/copyright
=====================================
@@ -14,24 +14,11 @@ Files: *
Copyright: 2013 INRIA / IRISA
License: AGPL-3+
-Files: mapsembler2_extremities/thirdparty/gatb-core/*
-Copyright: 2014 INRIA R.Chikhi, G.Rizk, E.Drezen
+Files: minia/*
+Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
+ 2012 Guillaume Rizk
License: AGPL-3+
-Files: mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/*
-Copyright: 2013 Giuseppe Ottaviano <giuott at gmail.com>
-License: Apache-2.0
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
- .
- http://www.apache.org/licenses/LICENSE-2.0
- .
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-
Files: kissreads_graph/read_coherence_mapsembler/libchash.*
Copyright: 1998-2005 Google Inc.
License: BSD-3-clause
@@ -63,11 +50,24 @@ License: BSD-3-clause
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: minia/*
-Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
- 2012 Guillaume Rizk
+Files: mapsembler2_extremities/thirdparty/gatb-core/*
+Copyright: 2014 INRIA R.Chikhi, G.Rizk, E.Drezen
License: AGPL-3+
+Files: mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/*
+Copyright: 2013 Giuseppe Ottaviano <giuott at gmail.com>
+License: Apache-2.0
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
Files: debian/*
Copyright: 2013 Olivier Sallou <osallou at debian.org>
License: GPL-2+
=====================================
debian/patches/cmake4.patch
=====================================
@@ -24,7 +24,21 @@ Description: Fix build with CMake 4
################################################################################
# The version number.
-@@ -274,4 +274,4 @@ SET (CPACK_SOURCE_IGNORE_FILES
+@@ -218,7 +218,12 @@ ADD_SUBDIRECTORY(thirdparty)
+ # DEPENDENCIES
+ ################################################################################
+ # we must be sure that hdf5 is built and installed before building gatb-core
+-ADD_DEPENDENCIES (gatbcore-static hdf5)
++find_package (HDF5 REQUIRED)
++if (HDF5_FOUND)
++ include_directories (${HDF5_INCLUDE_DIRS})
++ set (gatb-core-libraries ${gatb-core-libraries} ${HDF5_LIBRARIES})
++ set (gatb-core-libraries ${gatb-core-libraries} PARENT_SCOPE)
++endif()
+
+ IF (DEFINED WITH_MPHF)
+ ADD_DEPENDENCIES(gatbcore-static emphf_copyasis)
+@@ -274,4 +279,4 @@ SET (CPACK_SOURCE_IGNORE_FILES
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
# We include the module and get all the delivery targets
include (Delivery)
=====================================
debian/patches/gcc-5.patch
=====================================
@@ -1,5 +1,5 @@
Author: Gianfranco Costamagna <costamagnagianfranco at yahoo.it>
-Last-Update: Tue, 1 Sep 2015 08:34:33 +0000 (UTC)
+Last-Update: 2015-09-01
Bug-Debian: http://bugs.debian.org/797526
Forwarded-Upstream: yes
Description: Fix type of prefix_trashable since gcc-5 is picky about it
=====================================
debian/patches/libgomp.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 21 Dec 2016 21:42:53 +0100
+Last-Update: 2016-12-21
Description: Add missing -lgomp
--- a/kissreads/Makefile
=====================================
debian/patches/spelling.patch
=====================================
@@ -1,6 +1,6 @@
Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
+Last-Update: 2018-10-10
--- mapsembler2.orig/kissreads_graph/KissReadsGraph.cpp
+++ mapsembler2/kissreads_graph/KissReadsGraph.cpp
=====================================
debian/rules
=====================================
@@ -5,7 +5,7 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+include /usr/share/dpkg/architecture.mk
include /usr/share/dpkg/default.mk
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/191e2ff54cea507a8c340d2fa8d4b6437178bd73...d5ae05dc1b4ae15f7f3a8f5343f6873635485c49
--
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/191e2ff54cea507a8c340d2fa8d4b6437178bd73...d5ae05dc1b4ae15f7f3a8f5343f6873635485c49
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