[med-svn] [Git][med-team/soapdenovo2][master] 8 commits: gcc-15.patch: new: fix build failure with gcc-15.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Oct 24 18:54:59 BST 2025
Étienne Mollier pushed to branch master at Debian Med / soapdenovo2
Commits:
8ea8c21a by Étienne Mollier at 2025-10-24T19:34:24+02:00
gcc-15.patch: new: fix build failure with gcc-15.
Closes: #1097909
- - - - -
ac05f086 by Étienne Mollier at 2025-10-24T19:35:10+02:00
reproducible patch: normalise Last-Update timestamp.
- - - - -
9784afae by Étienne Mollier at 2025-10-24T19:37:23+02:00
d/watch: bump to watch file version 5.
- - - - -
b9d46c0f by Étienne Mollier at 2025-10-24T19:38:48+02:00
d/u/metadata: locate upstream repository.
- - - - -
9f4e1440 by Étienne Mollier at 2025-10-24T19:39:14+02:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
28ef92a3 by Étienne Mollier at 2025-10-24T19:39:44+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
4f6fc315 by Étienne Mollier at 2025-10-24T19:52:41+02:00
fix-deps.patch: new: stabilise make rules ordering.
Closes: #1105578
- - - - -
fdc7b222 by Étienne Mollier at 2025-10-24T19:53:39+02:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-deps.patch
- + debian/patches/gcc-15.patch
- debian/patches/reproducible
- debian/patches/series
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+soapdenovo2 (242+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097909)
+ * fix-deps.patch: new: stabilise make rules ordering. (Closes: #1105578)
+ * reproducible patch: normalise Last-Update timestamp.
+ * d/watch: bump to watch file version 5.
+ * d/u/metadata: locate upstream repository.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org> Fri, 24 Oct 2025 19:53:20 +0200
+
soapdenovo2 (242+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,11 +9,10 @@ Build-Depends: debhelper-compat (= 13),
libbam-dev,
libaio-dev,
rename
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo2
Vcs-Git: https://salsa.debian.org/med-team/soapdenovo2.git
Homepage: http://soap.genomics.org.cn/soapdenovo.html
-Rules-Requires-Root: no
Package: soapdenovo2
Architecture: any-amd64 any-ppc64 any-ia64
=====================================
debian/patches/fix-deps.patch
=====================================
@@ -0,0 +1,30 @@
+Description: stabilise make rules ordering.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105578
+Forwarded: no
+Last-Update: 2025-10-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapdenovo2.orig/Makefile
++++ soapdenovo2/Makefile
+@@ -57,12 +57,16 @@
+ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS)
+ else
+ SOAPdenovo-63mer:
+- @cd sparsePregraph;make 63mer=1 clean all;cd ..;
+- @cd standardPregraph;make 63mer=1 clean all;cd ..;
++ @cd sparsePregraph;$(MAKE) 63mer=1 clean;cd ..;
++ @cd standardPregraph;$(MAKE) 63mer=1 clean;cd ..;
++ @cd sparsePregraph;$(MAKE) 63mer=1 all;cd ..;
++ @cd standardPregraph;$(MAKE) 63mer=1 all;cd ..;
+ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer $(LDFLAGS)
+ SOAPdenovo-127mer:
+- @cd sparsePregraph;make 127mer=1 clean all;cd ..;
+- @cd standardPregraph;make 127mer=1 clean all;cd ..;
++ @cd sparsePregraph;$(MAKE) 127mer=1 clean;cd ..;
++ @cd standardPregraph;$(MAKE) 127mer=1 clean;cd ..;
++ @cd sparsePregraph;$(MAKE) 127mer=1 all;cd ..;
++ @cd standardPregraph;$(MAKE) 127mer=1 all;cd ..;
+ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS)
+ endif
+
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,40 @@
+Description: fix build failure with gcc-15.
+ This patch fixes the following build failure by completing the
+ debugging2 function declaration with the missing argument type:
+ .
+ Compiling orderContig.c...
+ orderContig.c:1965:13: error: conflicting types for ‘debugging2’; have ‘void(unsigned int)’
+ 1965 | static void debugging2 ( unsigned int ctg )
+ | ^~~~~~~~~~
+ orderContig.c:86:13: note: previous declaration of ‘debugging2’ with type ‘void(void)’
+ 86 | static void debugging2();
+ | ^~~~~~~~~~
+ Error in command: gcc -c -O3 -fomit-frame-pointer -w -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBDATE="Aug 11 2024" -DBTIME="17:08:09" -DMER63 -m64 -Iinc -I/usr/include/samtools orderContig.c
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097909
+Forwarded: no
+Last-Update: 2025-10-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapdenovo2.orig/fusion/orderContig.c
++++ soapdenovo2/fusion/orderContig.c
+@@ -50,7 +50,7 @@
+ static int setConnectWP(unsigned int from_c, unsigned int to_c, char flag);
+
+ static void general_linearization(boolean strict);
+-static void debugging2();
++static void debugging2(unsigned int);
+ static void smallScaf();
+ static void detectBreakScaf();
+ static boolean checkSimple(DARRAY *ctgArray, int count);
+--- soapdenovo2.orig/standardPregraph/orderContig.c
++++ soapdenovo2/standardPregraph/orderContig.c
+@@ -83,7 +83,7 @@
+ static int setConnectWP ( unsigned int from_c, unsigned int to_c, char flag );
+
+ static void general_linearization ( boolean strict );
+-static void debugging2();
++static void debugging2(unsigned int);
+ static void smallScaf();
+ static void clearNewInsFlag();
+ static void detectBreakScaff();
=====================================
debian/patches/reproducible
=====================================
@@ -1,5 +1,5 @@
Author: Sascha Steinbiss <sascha at steinbiss.name>
-Last-Update: Fri, 27 May 2016 20:24:56 +0000
+Last-Update: 2016-05-27
Description: Enable reproducible build
--- a/sparsePregraph/Makefile
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,5 @@ use_debian_zlib
reproducible
gcc-10.patch
gcc-14.patch
+gcc-15.patch
+fix-deps.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,7 @@
Bug-Database: https://github.com/aquaskyline/SOAPdenovo2/issues
Bug-Submit: https://github.com/aquaskyline/SOAPdenovo2/issues/new
+Repository: https://github.com/aquaskyline/SOAPdenovo2.git
+Repository-Browse: https://github.com/aquaskyline/SOAPdenovo2
Reference:
Author: >
Ruibang Luo and Binghang Liu and Yinlong Xie and Zhenyu Li and Weihua
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/aquaskyline/SOAPdenovo2/tags .*/r(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Source: https://github.com/aquaskyline/SOAPdenovo2/tags
+Matching-Pattern: .*/r(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Dversionmangle: auto
+Filenamemangle: s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%
+Repacksuffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/-/compare/08aeed139d001f31f24b21c4a58c3f73298ce1a7...fdc7b2229d4b0e8e6d0d94e69178d464a62cf295
--
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/-/compare/08aeed139d001f31f24b21c4a58c3f73298ce1a7...fdc7b2229d4b0e8e6d0d94e69178d464a62cf295
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