[med-svn] [Git][med-team/soapdenovo][master] 7 commits: gcc-15.patch: new: fix build failure with gcc-15.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Oct 22 22:26:50 BST 2025
Étienne Mollier pushed to branch master at Debian Med / soapdenovo
Commits:
cd9ccddf by Étienne Mollier at 2025-10-22T23:12:21+02:00
gcc-15.patch: new: fix build failure with gcc-15.
Closes: #1097907
- - - - -
15da18d1 by Étienne Mollier at 2025-10-22T23:12:47+02:00
d/watch: convert to untrackable watch file v5.
- - - - -
3c1da3da by Étienne Mollier at 2025-10-22T23:24:08+02:00
build-flags.patch: new: propagate build flags.
This notably fixes missing binaries hardening.
- - - - -
e84b1e8b by Étienne Mollier at 2025-10-22T23:24:51+02:00
add_debug_symbols.patch: normalize Last-Update timestamp.
- - - - -
a4a0da07 by Étienne Mollier at 2025-10-22T23:25:14+02:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
1c93aac9 by Étienne Mollier at 2025-10-22T23:25:37+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
f402dded by Étienne Mollier at 2025-10-22T23:26:16+02:00
d/changelog: ready for upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/add_debug_symbols.patch
- + debian/patches/build-flags.patch
- + debian/patches/gcc-15.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+soapdenovo (1.05-7) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097907)
+ * d/watch: convert to untrackable watch file v5.
+ * build-flags.patch: new: propagate build flags.
+ This notably fixes missing binaries hardening.
+ * add_debug_symbols.patch: normalize Last-Update timestamp.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 22 Oct 2025 23:26:00 +0200
+
soapdenovo (1.05-6) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,11 +5,10 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
rename
-Standards-Version: 4.5.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo
Vcs-Git: https://salsa.debian.org/med-team/soapdenovo.git
Homepage: http://soap.genomics.org.cn/soapdenovo.html
-Rules-Requires-Root: no
Package: soapdenovo
Architecture: any-amd64 any-ppc64 any-ia64
=====================================
debian/patches/add_debug_symbols.patch
=====================================
@@ -1,5 +1,5 @@
Author: Liubov Chuprikova <chuprikovalv at gmail.com>
-Last-Update: Sat, 9 June 2018 11:25:43 +0200
+Last-Update: 2018-06-09
Description: Add debug symbols
=====================================
debian/patches/build-flags.patch
=====================================
@@ -0,0 +1,72 @@
+Description: propagate Debian build flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2025-10-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapdenovo.orig/src/127mer/Makefile
++++ soapdenovo/src/127mer/Makefile
+@@ -44,8 +44,8 @@
+ .SUFFIXES:.c .o
+
+ .c.o:
+- @printf "Compiling $<... \r"; \
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
++ @printf "Compiling $<... \r";
++ $(CC) $(CPPFLAGS) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
+
+ all: SOAPdenovo
+
+@@ -55,7 +55,7 @@
+ @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;'
+
+ SOAPdenovo: envTest $(OBJS)
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "Linking...\r"
+ @printf "$(PROG) compilation done.\n";
+
+--- soapdenovo.orig/src/31mer/Makefile
++++ soapdenovo/src/31mer/Makefile
+@@ -44,8 +44,8 @@
+ .SUFFIXES:.c .o
+
+ .c.o:
+- @printf "Compiling $<... \r"; \
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
++ @printf "Compiling $<... \r";
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
+
+ all: SOAPdenovo
+
+@@ -55,7 +55,7 @@
+ @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;'
+
+ SOAPdenovo: envTest $(OBJS)
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "Linking...\r"
+ @printf "$(PROG) compilation done.\n";
+
+--- soapdenovo.orig/src/63mer/Makefile
++++ soapdenovo/src/63mer/Makefile
+@@ -44,8 +44,8 @@
+ .SUFFIXES:.c .o
+
+ .c.o:
+- @printf "Compiling $<... \r"; \
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
++ @printf "Compiling $<... \r";
++ $(CC) $(CPPFLAGS) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) $(CPPFLAGS) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
+
+ all: SOAPdenovo
+
+@@ -55,7 +55,7 @@
+ @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;'
+
+ SOAPdenovo: envTest $(OBJS)
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "Linking...\r"
+ @printf "$(PROG) compilation done.\n";
+
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,40 @@
+Description: fix build failure with gcc-15.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097907
+Forwarded: no
+Last-Update: 2025-10-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapdenovo.orig/src/127mer/orderContig.c
++++ soapdenovo/src/127mer/orderContig.c
+@@ -73,7 +73,7 @@
+ 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 );
+--- soapdenovo.orig/src/31mer/orderContig.c
++++ soapdenovo/src/31mer/orderContig.c
+@@ -73,7 +73,7 @@
+ 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 );
+--- soapdenovo.orig/src/63mer/orderContig.c
++++ soapdenovo/src/63mer/orderContig.c
+@@ -73,7 +73,7 @@
+ 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 );
=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
add_debug_symbols.patch
+gcc-15.patch
+build-flags.patch
=====================================
debian/watch
=====================================
@@ -1,6 +1,6 @@
-version=4
-opts=dversionmangle=s/.*/0.No-Release/ \
-https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
+Version: 5
+Untrackable: not available any more.
-# Not available there any more
-# opts=filenamemangle=s/down\/SOAPdenovo-V/soapdenovo-/ http://soap.genomics.org.cn/soapdenovo.html#down2 down/SOAPdenovo-V(.*)\.src\.tgz
+Source: http://soap.genomics.org.cn/soapdenovo.html#down2
+Matching-Pattern: down/SOAPdenovo-V(.*)\.src\.tgz
+Filenamemangle: s/down\/SOAPdenovo-V/soapdenovo-/
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/-/compare/2016bd7682dabf1d07a7eba43eb9146fac47665a...f402ddedd57857758d68f7ec34f7ffc456b7a03a
--
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/-/compare/2016bd7682dabf1d07a7eba43eb9146fac47665a...f402ddedd57857758d68f7ec34f7ffc456b7a03a
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