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 <[email protected]> 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 <[email protected]>, 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 <[email protected]> -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 <[email protected]> -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 <[email protected]> Thomas Schmitt <[email protected]> -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 <[email protected]> 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 <[email protected]> -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: [email protected] 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 You're receiving this email because of your account on salsa.debian.org.
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