Étienne Mollier pushed to branch master at Debian Med / raxml
Commits: 283363ca by Étienne Mollier at 2025-12-19T20:25:05+01:00 d/control: fix standards version declaration. - - - - - 768fad61 by Étienne Mollier at 2025-12-19T20:25:26+01:00 d/copyright: drop the old FSF mail address. - - - - - 67eee0cf by Étienne Mollier at 2025-12-19T20:27:09+01:00 d/watch: convert to v5 Github template. - - - - - 2faf7a81 by Étienne Mollier at 2025-12-19T20:27:37+01:00 d/control: drop redundant Rules-Requires-Root: no. - - - - - 1af89930 by Étienne Mollier at 2025-12-19T20:35:08+01:00 stabilize-makefiles.patch: new. This patche makes the "all" target more robust to unordered invocations by dropping the dependency on the "clean" target. Closes: #1105678 - - - - - 1526f6b7 by Étienne Mollier at 2025-12-19T20:36:52+01:00 d/changelog: ready for upload to unstable. - - - - - 6 changed files: - debian/changelog - debian/control - debian/copyright - debian/patches/series - + debian/patches/stabilize-makefiles.patch - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +raxml (8.2.13+dfsg-3) unstable; urgency=medium + + * d/control: fix standards version declaration. + * d/copyright: drop the old FSF mail address. + * d/watch: convert to v5 Github template. + * d/control: drop redundant Rules-Requires-Root: no. + * stabilize-makefiles.patch: new. + This patche makes the "all" target more robust to unordered + invocations by dropping the dependency on the "clean" target. + (Closes: #1105678) + + -- Étienne Mollier <[email protected]> Fri, 19 Dec 2025 20:36:27 +0100 + raxml (8.2.13+dfsg-2) unstable; urgency=medium * d/control: declare compliance to standards version 4.7.2. ===================================== debian/control ===================================== @@ -6,11 +6,10 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), libsimde-dev -Standards-Version: 4.7.2. +Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/raxml Vcs-Git: https://salsa.debian.org/med-team/raxml.git Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html -Rules-Requires-Root: no Package: raxml Architecture: any ===================================== debian/copyright ===================================== @@ -24,10 +24,6 @@ License: GPL-2+ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 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 program; if not, write to the Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. ===================================== debian/patches/series ===================================== @@ -3,3 +3,4 @@ hardening c23.patch typos.patch interpreter-path.patch +stabilize-makefiles.patch ===================================== debian/patches/stabilize-makefiles.patch ===================================== @@ -0,0 +1,44 @@ +Description: stabilize makefiles. + Note that there are many makefiles addressing a whole range of + configurations. This patch only addresses the ones in use during the + Debian build process and would need modifications, or more like + extension, if forwarded upstream. +Author: Étienne Mollier <emollier +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105678 +Forwarded: no +Last-Update: 2025-12-19 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- raxml.orig/Makefile.AVX.PTHREADS.gcc ++++ raxml/Makefile.AVX.PTHREADS.gcc +@@ -15,7 +15,7 @@ + + objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o eigen.o + +-all : clean raxmlHPC-PTHREADS-AVX ++all : raxmlHPC-PTHREADS-AVX + + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h + +--- raxml.orig/Makefile.PTHREADS.gcc ++++ raxml/Makefile.PTHREADS.gcc +@@ -19,7 +19,7 @@ + + objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +-all : clean raxmlHPC-PTHREADS ++all : raxmlHPC-PTHREADS + + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h + +--- raxml.orig/Makefile.SSE3.PTHREADS.gcc ++++ raxml/Makefile.SSE3.PTHREADS.gcc +@@ -19,7 +19,7 @@ + + objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +-all : clean raxmlHPC-PTHREADS-SSE3 ++all : raxmlHPC-PTHREADS-SSE3 + + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h + ===================================== debian/watch ===================================== @@ -1,3 +1,7 @@ -version=4 -opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ - https://github.com/stamatak/standard-RAxML/tags .*/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$ +Version: 5 + +Template: Github +Owner: stamatak +Project: standard-RAxML +Dversionmangle: auto +Repacksuffix: +dfsg View it on GitLab: https://salsa.debian.org/med-team/raxml/-/compare/74137cb1c767f4ee9f056f0f9d83b544f574fdba...1526f6b708adb0516a4965e20b7aaf282843a3f6 -- View it on GitLab: https://salsa.debian.org/med-team/raxml/-/compare/74137cb1c767f4ee9f056f0f9d83b544f574fdba...1526f6b708adb0516a4965e20b7aaf282843a3f6 You're receiving this email because of your account on salsa.debian.org.
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