[med-svn] [Git][med-team/raxml][master] 6 commits: d/control: fix standards version declaration.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Dec 19 19:37:23 GMT 2025
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 <emollier at debian.org> 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 at -$1.tar.gz%" \
- https://github.com/stamatak/standard-RAxML/tags .*/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$
+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
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