[med-svn] [Git][med-team/velvet][master] 10 commits: stabilize-makefile.patch: new: fix unordered build steps.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Jan 14 21:17:50 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / velvet
Commits:
04f0a7b5 by Étienne Mollier at 2026-01-14T21:41:02+01:00
stabilize-makefile.patch: new: fix unordered build steps.
Closes: #1105569
- - - - -
b7081e2f by Étienne Mollier at 2026-01-14T21:41:55+01:00
d/rules: allow parallel builds.
- - - - -
3dcc70cb by Étienne Mollier at 2026-01-14T21:42:21+01:00
d/copyright: drop the old FSF mail address.
- - - - -
b4089f3b by Étienne Mollier at 2026-01-14T21:42:42+01:00
d/patches/*: normalise Last-Update timestamps.
- - - - -
aad5a161 by Étienne Mollier at 2026-01-14T21:43:03+01:00
d/watch: convert to v5 Github template.
- - - - -
1ac64528 by Étienne Mollier at 2026-01-14T21:43:36+01:00
d/control: drop redundant Priority: optional.
- - - - -
96862153 by Étienne Mollier at 2026-01-14T21:43:55+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
ab658b21 by Étienne Mollier at 2026-01-14T21:44:21+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
36d36b9c by Étienne Mollier at 2026-01-14T22:00:07+01:00
d/control: declare velvet-example Multi-Arch: foreign.
- - - - -
c85fe507 by Étienne Mollier at 2026-01-14T22:17:23+01:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/2to3.patch
- debian/patches/series
- debian/patches/spelling.patch
- + debian/patches/stabilize-makefile.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+velvet (1.2.10+dfsg1-10) unstable; urgency=medium
+
+ * Team upload.
+ * stabilize-makefile.patch: new: fix unordered build steps. (Closes: #1105569)
+ * d/rules: allow parallel builds.
+ * d/copyright: drop the old FSF mail address.
+ * d/patches/*: normalise Last-Update timestamps.
+ * d/watch: convert to v5 Github template.
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/control: declare velvet-example Multi-Arch: foreign.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 14 Jan 2026 22:17:14 +0100
+
velvet (1.2.10+dfsg1-9) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -3,16 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
texlive-latex-base,
texlive-latex-recommended
-Standards-Version: 4.7.0
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/velvet
Vcs-Git: https://salsa.debian.org/med-team/velvet.git
Homepage: https://github.com/dzerbino/velvet
-Rules-Requires-Root: no
Package: velvet
Architecture: any
@@ -52,6 +50,7 @@ Architecture: all
Depends: ${misc:Depends},
velvet-tests
Recommends: python3
+Multi-Arch: foreign
Description: Example data for the Velvet sequence assembler
Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and
=====================================
debian/copyright
=====================================
@@ -97,8 +97,7 @@ License: GPL-2+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with Velvet; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
Comment: 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/2to3.patch
=====================================
@@ -1,7 +1,7 @@
Description: Use 2to3 to port to Python3
Bug-Debian: https://bugs.debian.org/945743
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 02 Dec 2019 13:36:55 +0100
+Last-Update: 2019-12-02
--- a/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
+++ b/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ hardening.patch
spelling.patch
2to3.patch
gcc-14.patch
+stabilize-makefile.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -1,6 +1,6 @@
Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 05 Jul 2018 09:22:07 +0200
+Last-Update: 2018-07-05
--- a/src/correctedGraph.c
+++ b/src/correctedGraph.c
=====================================
debian/patches/stabilize-makefile.patch
=====================================
@@ -0,0 +1,71 @@
+Description: stabilise makefile runs.
+ This fixes running make targets with --shuffle=reverse and hopefully
+ allows stable parallel builds.
+ .
+ Targets unused by debian/rules may need further refinement before
+ forwarding upstream.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105569
+Forwarded: no
+Last-Update: 2026-01-13
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- velvet.orig/Makefile
++++ velvet/Makefile
+@@ -39,7 +39,7 @@
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+
+-default : cleanobj zlib obj velveth velvetg doc
++default : zlib obj velveth velvetg doc
+
+ clean : clean-zlib
+ -rm obj/*.o obj/dbg/*.o ./velvet*
+@@ -74,36 +74,40 @@
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+ debug : override DEF := $(DEF) -D DEBUG
+-debug : cleanobj obj/dbg
++debug : obj/dbg
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+ color : override DEF := $(DEF) -D COLOR
+-color : cleanobj obj_de
++color : obj_de
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+ colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
+-colordebug : cleanobj obj/dbg_de
++colordebug : obj/dbg_de
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
+
+ objdir:
+ mkdir -p obj
+
+-obj: zlib cleanobj objdir $(OBJ)
++obj: zlib
++ $(MAKE) objdir
++ $(MAKE) $(OBJ)
+
+ obj_de: override DEF := $(DEF) -D COLOR
+-obj_de: zlib cleanobj objdir $(OBJ)
++obj_de: zlib
++ $(MAKE) objdir
++ $(MAKE) $(OBJ)
+
+ obj/dbgdir:
+ mkdir -p obj/dbg
+
+ obj/dbg: override DEF := $(DEF) -D DEBUG
+-obj/dbg: zlib cleanobj obj/dbgdir $(OBJDBG)
++obj/dbg: zlib obj/dbgdir $(OBJDBG)
+
+ obj/dbg_de: override DEF := $(DEF) -D COLOR -D DEBUG
+-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
++obj/dbg_de: zlib obj/dbgdir $(OBJDBG)
+
+ obj/%.o: src/%.c
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
=====================================
debian/rules
=====================================
@@ -4,7 +4,7 @@
#export DH_VERBOSE=1
%:
- dh $@ --no-parallel
+ dh $@
pkg=velvet
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="dversionmangle=auto,repacksuffix=+dfsg,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/dzerbino/velvet/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Template: Github
+Project: dzerbino
+Owner: velvet
+Dversionmangle: auto
+Repacksuffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/velvet/-/compare/f16ca3bb85bac720c033cc3e72f1e5e202a5b47e...c85fe507a879ada660b534f323fafdf5ca7a3829
--
View it on GitLab: https://salsa.debian.org/med-team/velvet/-/compare/f16ca3bb85bac720c033cc3e72f1e5e202a5b47e...c85fe507a879ada660b534f323fafdf5ca7a3829
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