[med-svn] [Git][med-team/mrbayes][master] 9 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Sep 1 17:21:15 BST 2026
Andreas Tille pushed to branch master at Debian Med / mrbayes
Commits:
036e4768 by Andreas Tille at 2026-09-01T16:56:37+02:00
d/watch: version=5
- - - - -
6aaf432e by Andreas Tille at 2026-09-01T17:13:13+02:00
Controling build with MPI changed from --enable-mpi to --with-mpi Closes: #1143178
- - - - -
b67fbd9c by Andreas Tille at 2026-09-01T16:13:22+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/no_rpath.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/autoreconf.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/no_baseline_violation.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
- - - - -
e56ede8a by Andreas Tille at 2026-09-01T16:13:23+01:00
Remove redundant Priority: optional from source stanza.
Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html
- - - - -
77bc2481 by Andreas Tille at 2026-09-01T16:13:23+01:00
Replace FSF postal address with a reference to https://www.gnu.org/licenses/.
Changes-By: lintian-brush
Fixes: lintian: source: old-fsf-address-in-copyright-file
See-also: https://lintian.debian.org/tags/old-fsf-address-in-copyright-file.html
- - - - -
dc7cf2b8 by Andreas Tille at 2026-09-01T16:13:26+01:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.6.2 → 4.7.0:
* Package does not use dpkg-divert
4.7.0 → 4.7.1:
* Package does not install to non-/usr paths
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: source: ancient-standards-version 4.6.2 (released 2022-12-17) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/ancient-standards-version.html
- - - - -
40890abd by Andreas Tille at 2026-09-01T17:14:31+02:00
cme fix dpkg-control
- - - - -
762f94dd by Andreas Tille at 2026-09-01T18:02:49+02:00
Fix build with openmpi
- - - - -
86850247 by Andreas Tille at 2026-09-01T18:06:56+02:00
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/autoreconf.patch
- debian/patches/no_baseline_violation.patch
- debian/patches/no_rpath.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,17 @@
-mrbayes (3.2.7a-8) UNRELEASED; urgency=medium
+mrbayes (3.2.7a-8) unstable; urgency=medium
* Replace pkg-config with pkgconf in Build-Depends
+ * d/watch: version=5
+ * Controlling build with MPI changed from --enable-mpi to --with-mpi
+ Closes: #1143178
+ * Reformat the Last-Update date as ISO YYYY-MM-DD.
+ * Remove redundant Priority: optional from source stanza.
+ * Replace FSF postal address with a reference to
+ https://www.gnu.org/licenses/.
+ * Update standards version to 4.7.4, no changes needed.
+ * cme fix dpkg-control
- -- Andreas Tille <tille at debian.org> Tue, 10 Mar 2026 09:34:51 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 01 Sep 2026 18:03:08 +0200
mrbayes (3.2.7a-7) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,16 +1,18 @@
Source: mrbayes
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
+Uploaders:
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- libreadline-dev,
- mpi-default-dev,
- libhmsbeagle-dev,
- autoconf-archive,
- pkgconf
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 14),
+ libreadline-dev,
+ mpi-default-bin,
+ mpi-default-dev,
+ libhmsbeagle-dev,
+ autoconf-archive,
+ pkgconf,
Vcs-Browser: https://salsa.debian.org/med-team/mrbayes
Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git
Homepage: http://mrbayes.csit.fsu.edu/
@@ -18,9 +20,11 @@ Rules-Requires-Root: no
Package: mrbayes
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Suggests: mrbayes-doc
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Suggests:
+ mrbayes-doc,
Description: Bayesian Inference of Phylogeny
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
@@ -32,12 +36,14 @@ Description: Bayesian Inference of Phylogeny
Package: mrbayes-mpi
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- mpi-default-bin,
- ssh
-Suggests: mpi-default,
- mrbayes-doc
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ mpi-default-bin,
+ ssh,
+Suggests:
+ mpi-default,
+ mrbayes-doc,
Description: Bayesian Inference of Phylogeny - mpi version
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
@@ -51,10 +57,12 @@ Description: Bayesian Inference of Phylogeny - mpi version
Package: mrbayes-doc
Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Enhances: mrbayes
Multi-Arch: foreign
+Section: doc
+Depends:
+ ${misc:Depends},
+Enhances:
+ mrbayes,
Description: Bayesian Inference of Phylogeny - manual
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
=====================================
debian/copyright
=====================================
@@ -29,10 +29,8 @@ License: GPL-2+
PURPOSE. See the GNU General Public License for more
details.
.
- You should have received a copy of the GNU General Public
- License along with this package; if not, write to the Free
- Software Foundation, Inc., 51 Franklin St, Fifth Floor,
- Boston, MA 02110-1301 USA
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
.
On Debian systems, the full text of the GNU General Public
License version 2 can be found in the file
=====================================
debian/patches/autoreconf.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 11 Apr 2020 11:19:27 +0200
+Last-Update: 2020-04-11
Description: Fix autoconf issue
--- a/configure.ac
=====================================
debian/patches/no_baseline_violation.patch
=====================================
@@ -1,7 +1,7 @@
Description: Avoid baseline violation by disabling AX_EXT
Bug-Debian: https://bugs.debian.org/958125
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 18 Jul 2020 14:29:31 +0200
+Last-Update: 2020-07-18
--- a/configure.ac
+++ b/configure.ac
=====================================
debian/patches/no_rpath.patch
=====================================
@@ -1,6 +1,6 @@
Description: Do not include rpath
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 27 Jun 2018 08:45:36 +0200
+Last-Update: 2018-06-27
--- a/configure.ac
+++ b/configure.ac
=====================================
debian/rules
=====================================
@@ -12,7 +12,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
dh $@
override_dh_auto_configure:
- dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
+ dh_auto_configure -- --with-beagle=/usr --with-mpi=yes --enable-debug=yes CC=mpicc
override_dh_auto_build:
# build mb-mpi (from initial config)
@@ -20,7 +20,7 @@ override_dh_auto_build:
mv src/mb ./mb-mpi
# Now - build mb
( cd src ; make clean )
- dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes
+ dh_auto_configure -- --with-beagle=/usr --with-mpi=no --enable-debug=yes
LIBS="-Wl,--as-needed" dh_auto_build
mv src/mb .
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=4
+Version: 5
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/NBISweden/MrBayes/tags .*/v at ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Dist: https://github.com/NBISweden/MrBayes
View it on GitLab: https://salsa.debian.org/med-team/mrbayes/-/compare/1329a42053fd6169c1c8cdd9ee2e4f52484a9baa...86850247c16eaa7b97dfd37fea766456ded9ccd6
--
View it on GitLab: https://salsa.debian.org/med-team/mrbayes/-/compare/1329a42053fd6169c1c8cdd9ee2e4f52484a9baa...86850247c16eaa7b97dfd37fea766456ded9ccd6
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