[med-svn] [Git][med-team/phyml][master] 6 commits: d/p/series: disable cross.patch.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / phyml


Commits:
5506758c by Étienne Mollier at 2024-11-09T19:35:39+01:00
d/p/series: disable cross.patch.

The cross compilation procedure relies on mpi-c.pc to operate
properly, but mpich misses it for the moment.

- - - - -
4fc8039c by Étienne Mollier at 2024-11-09T19:38:30+01:00
d/control: migrate to mpi-default-*.

Closes: #1086912

- - - - -
ab5832e9 by Étienne Mollier at 2024-11-09T19:39:22+01:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
5b62f53a by Étienne Mollier at 2024-11-09T19:47:16+01:00
d/control: migrate to pkgconf.

- - - - -
b3c08edc by Étienne Mollier at 2024-11-09T19:50:11+01:00
d/patches/*: normalise header, notably Last-Update format.

- - - - -
cce462bb by Étienne Mollier at 2024-11-09T19:51:06+01:00
d/changelog: ready for upload to unstable.

- - - - -


7 changed files:

- debian/changelog
- debian/control
- debian/patches/cross.patch
- debian/patches/fix_declaration_of_temp.patch
- debian/patches/fix_wrong_initialisation_of_array.patch
- debian/patches/series
- debian/patches/sse_only_if_supported.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+phyml (3:3.3.20220408-4) unstable; urgency=medium
+
+  * d/p/series: disable cross.patch.
+    The cross compilation procedure relies on mpi-c.pc to operate
+    properly, but mpich misses it for the moment.
+  * d/control: migrate to mpi-default-*. (Closes: #1086912)
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/control: migrate to pkgconf.
+  * d/patches/*: normalise header, notably Last-Update format.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 09 Nov 2024 19:50:59 +0100
+
 phyml (3:3.3.20220408-3) unstable; urgency=medium
 
   * d/watch: move to git tag scanning; fixes uscan following github changes.


=====================================
debian/control
=====================================
@@ -7,11 +7,11 @@ Uploaders: Charles Plessy <plessy at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               pkg-config,
+               pkgconf,
 #               libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
-               libopenmpi-dev,
+               mpi-default-dev,
                chrpath
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/phyml
 Vcs-Git: https://salsa.debian.org/med-team/phyml.git
 Homepage: http://www.atgc-montpellier.fr/phyml
@@ -21,7 +21,7 @@ Package: phyml
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         openmpi-bin
+         mpi-default-bin
 Description: Phylogenetic estimation using Maximum Likelihood
  PhyML is a software that estimates maximum likelihood phylogenies from
  alignments of nucleotide or amino acid sequences. It provides a wide
@@ -49,7 +49,7 @@ Description: Phylogenetic estimation using Maximum Likelihood
 #Architecture: any-amd64 any-i386 arm64 armhf
 #Depends: ${shlibs:Depends},
 #         ${misc:Depends},
-#         openmpi-bin
+#         mpi-default-bin
 #Description: Phylogenetic estimation using Maximum Likelihood
 # PhyML is a software that estimates maximum likelihood phylogenies from
 # alignments of nucleotide or amino acid sequences. It provides a wide


=====================================
debian/patches/cross.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Helmut Grohne <helmut at subdivi.de>
-Last-Update: Tue, 26 Jun 2018 17:32:08 +0200
+Last-Update: 2018-06-26
 Bug-Debian: https://bugs.debian.org/902433
 Description: Use MPI_C to enable cross building
 


=====================================
debian/patches/fix_declaration_of_temp.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
+Last-Update: 2017-06-24
 Description: Add missing declaration, fix name of BEAGLE constant
 
 --- phyml.orig/src/utilities.c


=====================================
debian/patches/fix_wrong_initialisation_of_array.patch
=====================================
@@ -1,6 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
         Thomas Schmitt <scdbackup at gmx.net>
-Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
+Last-Update: 2017-06-24
 Description: avoid initialisation an array with a scalar value
  Quoting James Cowgill <jcowgill at debian.org> on debian-mentors list:
  .


=====================================
debian/patches/series
=====================================
@@ -3,7 +3,9 @@ no-configure-ac-date.patch
 fix_declaration_of_temp.patch
 fix_wrong_initialisation_of_array.patch
 no-march-native.patch
-cross.patch
+# FIXME: cross.patch is disabled due to missing support for mpi-c.pc in mpich,
+# as described in #1086912 message #19.
+#cross.patch
 apply-cflags.patch
 filter-sse3-intrinsics.patch
 apply-ldflags.patch


=====================================
debian/patches/sse_only_if_supported.patch
=====================================
@@ -1,6 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
-LastChanged: Mon, 05 Aug 2013 09:56:27 +0200
-BugsClosed: http://bugs.debian.org/718747
+Last-Update: 2013-08-05
+Bug-Debian: http://bugs.debian.org/718747
 Forwarded: guindon at lirmm.fr
 Description: Verify architecture whether we comiple on i386 or amd64 and
  only in this case use -msse



View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/119f3bf37d5e98afbaab9c197542d03691d959d2...cce462bb3bfc7bb72ff92ab4d04b4fc733a76656

-- 
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/119f3bf37d5e98afbaab9c197542d03691d959d2...cce462bb3bfc7bb72ff92ab4d04b4fc733a76656
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