[med-svn] [Git][med-team/skesa][master] 5 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 20 22:33:04 GMT 2025
Andreas Tille pushed to branch master at Debian Med / skesa
Commits:
2c337c8d by Andreas Tille at 2025-12-20T22:15:59+01:00
d/watch: version=5
- - - - -
83030391 by Andreas Tille at 2025-12-20T22:17:46+01:00
Do not use variable CC for the C++ compiler Closes: #1112688
- - - - -
cf364c33 by Andreas Tille at 2025-12-20T22:17:59+01:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
fc14e496 by Andreas Tille at 2025-12-20T23:12:20+01:00
Remove trailing whitespace in debian/changelog (routine-update)
- - - - -
551c130e by Andreas Tille at 2025-12-20T23:16:03+01:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/cross.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,20 @@
+skesa (2.4.0-7) unstable; urgency=medium
+
+ [ Andreas Tille ]
+ * d/watch: version=5
+ * Standards-Version: 4.7.2 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+
+ [ Helmut Grohne ]
+ * Do not use variable CC for the C++ compiler
+ Closes: #1112688
+
+ -- Andreas Tille <tille at debian.org> Sat, 20 Dec 2025 23:12:25 +0100
+
skesa (2.4.0-6) unstable; urgency=medium
* debian/patches/hardening.patch: Reinstate use of dpkg-supplied CFLAGS.
- The addition accidentally got lost in the course of updating
+ The addition accidentally got lost in the course of updating
use_debian_packaged_ngs-sdk.patch.
* debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a
baseline violation on x86, and entirely unavailable elsewhere.
=====================================
debian/control
=====================================
@@ -1,19 +1,22 @@
Source: skesa
+Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>, Aaron M. Ucko <ucko at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Aaron M. Ucko <ucko at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- libboost-dev,
- libboost-chrono-dev,
- libboost-iostreams-dev,
- libboost-program-options-dev,
- libboost-regex-dev,
- libboost-system-dev,
- libboost-timer-dev,
- libncbi-vdb-dev (>= 3),
- libngs-c++-dev
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 13),
+ libboost-dev,
+ libboost-chrono-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libboost-regex-dev,
+ libboost-system-dev,
+ libboost-timer-dev,
+ libncbi-vdb-dev,
+ libngs-c++-dev,
Vcs-Browser: https://salsa.debian.org/med-team/skesa
Vcs-Git: https://salsa.debian.org/med-team/skesa.git
Homepage: https://github.com/ncbi/SKESA
@@ -21,8 +24,9 @@ Rules-Requires-Root: no
Package: skesa
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: strategic Kmer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for
assembling reads of microbial genomes sequenced using Illumina.
=====================================
debian/patches/cross.patch
=====================================
@@ -0,0 +1,48 @@
+Author: Helmut Grohne <helmut at subdivi.de>
+Last-Update: 2025-08-31
+Bug-Debian: https://bugs.debian.org/1112688
+Description: Do not use variable CC for the C++ compiler
+
+--- skesa-2.4.0.orig/Makefile
++++ skesa-2.4.0/Makefile
+@@ -39,7 +39,11 @@
+ NGS_INCL := -I $(NGS_PATH)/include
+ NGS_LIB := -L $(NGS_PATH)/lib64
+
+-CC = c++ -std=c++11 -fdiagnostics-color=never
++ifeq ($(origin CXX),default)
++CXX = c++
++endif
++CFLAGS += -std=c++11 -fdiagnostics-color=never
++LDLAGS += -std=c++11 -fdiagnostics-color=never
+ CFLAGS += -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
+ -fomit-frame-pointer $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
+
+@@ -54,7 +58,7 @@
+ -lrt -ldl -lm -lpthread -lz
+
+ %.o: %.cpp
+- $(CC) -c -o $@ $< $(CFLAGS)
++ $(CXX) -c -o $@ $< $(CFLAGS)
+
+ binaries=skesa gfa_connector kmercounter
+
+@@ -69,15 +73,15 @@
+
+ skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
+ skesa: skesa.o glb_align.o
+- $(CC) -o $@ $^ $(LIBS) $(LDFLAGS)
++ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
+
+ gfa_connector.o: gfa.hpp glb_align.hpp common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp graphdigger.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile
+ gfa_connector: gfa_connector.o glb_align.o
+- $(CC) -o $@ $^ $(LIBS)
++ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
+
+ kmercounter.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile
+ kmercounter: kmercounter.o glb_align.o
+- $(CC) -o $@ $^ $(LIBS)
++ $(CXX) -o $@ $^ $(LIBS) $(LDFLAGS)
+
+
+ $(NGS_DIR)/ngs.done:
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_ngs-sdk.patch
hardening.patch
link_boost_dynamically.patch
no_sse4.2.patch
+cross.patch
=====================================
debian/watch
=====================================
@@ -1,4 +1,5 @@
-version=4
+Version: 5
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/ncbi/SKESA/tags .*/v?@ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Owner: ncbi
+Project: SKESA
View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/c903620376731d46db778c6bdb693873aea6a0cb...551c130e3c6b5f6aea35043f3450019cb8ef7551
--
View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/c903620376731d46db778c6bdb693873aea6a0cb...551c130e3c6b5f6aea35043f3450019cb8ef7551
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