[med-svn] [Git][med-team/soapaligner][master] 8 commits: gcc-15.patch: new: fix build failure with gcc-15.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Oct 22 22:01:08 BST 2025
Étienne Mollier pushed to branch master at Debian Med / soapaligner
Commits:
6b75a86f by Étienne Mollier at 2025-10-22T22:48:49+02:00
gcc-15.patch: new: fix build failure with gcc-15.
Closes: #1097906
- - - - -
39c150bf by Étienne Mollier at 2025-10-22T22:50:28+02:00
d/patches/*: normalize Last-Update timestamp.
- - - - -
b5992984 by Étienne Mollier at 2025-10-22T22:50:47+02:00
d/watch: convert to untrackable watch file v5.
- - - - -
a2f0e0c2 by Étienne Mollier at 2025-10-22T22:51:12+02:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
1dc26f58 by Étienne Mollier at 2025-10-22T22:51:38+02:00
d/control: declare complianct to standards version 4.7.2.
- - - - -
3561de27 by Étienne Mollier at 2025-10-22T22:55:57+02:00
d/rules: simplify passing lto flags.
- - - - -
00d0d855 by Étienne Mollier at 2025-10-22T22:59:52+02:00
cppflags.patch: new: propagate CPPFLAGS.
This improves binaries hardening by fortifying sources.
- - - - -
94c494f5 by Étienne Mollier at 2025-10-22T23:00:42+02:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/patches/cppflags.patch
- + debian/patches/gcc-15.patch
- debian/patches/linkerror.patch
- debian/patches/series
- debian/patches/spelling.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+soapaligner (2.20-6) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097906)
+ * d/patches/*: normalize Last-Update timestamp.
+ * d/watch: convert to untrackable watch file v5.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare complianct to standards version 4.7.2.
+ * d/rules: simplify passing lto flags.
+ * cppflags.patch: new: propagate CPPFLAGS.
+ This improves binaries hardening by fortifying sources.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 22 Oct 2025 23:00:20 +0200
+
soapaligner (2.20-5) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -4,11 +4,10 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/soapaligner
Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
Homepage: https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html
-Rules-Requires-Root: no
Package: soapaligner
Architecture: any-amd64 x32
=====================================
debian/patches/cppflags.patch
=====================================
@@ -0,0 +1,31 @@
+Description: propagate CPPFLAGS C preprocessor flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2025-10-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapaligner.orig/Makefile
++++ soapaligner/Makefile
+@@ -11,6 +11,7 @@
+ STATIC_FLAGS ?= -static
+ DFLAGS ?= -DMAKE_TIME=\""`date`"\"
+ LDFLAGS ?=
++CPPFLAGS ?=
+ LIBS ?= -lm
+ #TARBALL_EXCLUDE = "*.(o,gz,zip)"
+ #ZIP_EXCLUDE = *.o *.gz *.zip
+@@ -42,12 +43,12 @@
+ .SUFFIX: .c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $< -o $@
++ $(CC) $(CPPFLAGS) -c $(CFLAGS) $< -o $@
+
+ all: $(PROG)
+
+ $(PROG): $(OBJ)
+- $(CC) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)
+
+ SeqIO.o:SeqIO.h
+ r250.o: r250.h
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,18 @@
+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=1097906
+Forwarded: no
+Last-Update: 2025-10-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapaligner.orig/r250.c
++++ soapaligner/r250.c
+@@ -16,7 +16,7 @@
+ #include "r250.h"
+
+ // static functions
+-static unsigned int randlcg();
++static unsigned int randlcg(int);
+
+
+ #define MSB 0x80000000L
=====================================
debian/patches/linkerror.patch
=====================================
@@ -1,5 +1,5 @@
Author: Steffen Moeller
-Last-Update: 2018-05-04 18:33:03 +0200
+Last-Update: 2018-05-04
Description: Fix build
--- a/Makefile
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ linkerror.patch
UsageDoublette.patch
spelling.patch
gcc-10.patch
+gcc-15.patch
+cppflags.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 13:04:29 +0200
+Last-Update: 2018-07-05
--- a/soap.1
+++ b/soap.1
=====================================
debian/rules
=====================================
@@ -2,13 +2,9 @@
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all optimize=+lto
export DH_VERBOSE=1
export DFLAGS = -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\"
-export CFLAGS:=-flto $(shell dpkg-buildflags --get CFLAGS)
-export CXXFLAGS:=-flto $(shell dpkg-buildflags --get CXXFLAGS)
-export LDFLAGS:=-Wl,-flto $(shell dpkg-buildflags --get LDFLAGS)
-
%:
dh $@
=====================================
debian/watch
=====================================
@@ -1,7 +1,5 @@
-version=4
+Version: 5
+Untrackable: upstream site vanished.
-# Upstream site vanished
-opts=dversionmangle=s/.*/0.No-Site/ \
- https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
-
-# http://soap.genomics.org.cn/soapaligner.html down/SOAPaligner-v(\d[.\d]+)-src.tar.gz
+Source: http://soap.genomics.org.cn/soapaligner.html
+Matching-Pattern: down/SOAPaligner-v(\d[.\d]+)-src.tar.gz
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/-/compare/7df32561e1133479b325a5917dab13681a7e044e...94c494f52cac918cc1f5e336acd69f24297e6ad2
--
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/-/compare/7df32561e1133479b325a5917dab13681a7e044e...94c494f52cac918cc1f5e336acd69f24297e6ad2
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20251022/5887c8b5/attachment-0001.htm>
More information about the debian-med-commit
mailing list