[med-svn] [Git][med-team/readseq][master] 10 commits: gcc-15.patch: new: fix build failure with gcc-15.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Sep 24 20:52:10 BST 2025
Étienne Mollier pushed to branch master at Debian Med / readseq
Commits:
41157c63 by Étienne Mollier at 2025-09-24T21:31:15+02:00
gcc-15.patch: new: fix build failure with gcc-15.
Closes: #1097779
- - - - -
9c699049 by Étienne Mollier at 2025-09-24T21:32:17+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
d2167112 by Étienne Mollier at 2025-09-24T21:32:46+02:00
d/control: remove redundant Rules-Requires-Root.
- - - - -
89837fa1 by Étienne Mollier at 2025-09-24T21:34:10+02:00
d/watch: migrate to untrackable v5 watch file.
- - - - -
99c0e97d by Étienne Mollier at 2025-09-24T21:34:41+02:00
d/control: add myself to uploaders.
- - - - -
c9ac9f2f by Étienne Mollier at 2025-09-24T21:35:32+02:00
d/get-orig-source: delete: unneeded.
- - - - -
912cf9f2 by Étienne Mollier at 2025-09-24T21:49:08+02:00
buffer_overflow.patch: normalize Last-Update.
- - - - -
f9ac7e4b by Étienne Mollier at 2025-09-24T21:49:37+02:00
d/rules: convert Stdfiles to Unicode.
- - - - -
7c3df3dd by Étienne Mollier at 2025-09-24T21:50:31+02:00
hardening.patch: also propagate CPPFLAGS.
- - - - -
a0c88fbc by Étienne Mollier at 2025-09-24T21:51:42+02:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- − debian/get-orig-source
- debian/patches/buffer_overflow.patch
- + debian/patches/gcc-15.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+readseq (1-16) unstable; urgency=medium
+
+ * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097779)
+ * d/control: declare compliance to standards version 4.7.2.
+ * d/control: remove redundant Rules-Requires-Root.
+ * d/watch: migrate to untrackable v5 watch file.
+ * d/control: add myself to uploaders.
+ * d/get-orig-source: delete: unneeded.
+ * buffer_overflow.patch: normalize Last-Update.
+ * d/rules: convert Stdfiles to Unicode.
+ * hardening.patch: also propagate CPPFLAGS.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 24 Sep 2025 21:50:54 +0200
+
readseq (1-15) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,15 +1,15 @@
Source: readseq
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
ncbi-tools-dev
-Standards-Version: 4.6.2
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/readseq
Vcs-Git: https://salsa.debian.org/med-team/readseq.git
Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/
-Rules-Requires-Root: no
Package: readseq
Architecture: any
=====================================
debian/get-orig-source deleted
=====================================
@@ -1,38 +0,0 @@
-#!/bin/sh
-prog=readseq
-version=1
-dir="$prog"-"$version"
-tardir=`pwd`/../tarballs/"$dir"
-# url="ftp://ftp.bio.indiana.edu/molbio/readseq/version1/src"
-url="http://iubio.bio.indiana.edu/soft/molbio/readseq/version1/src/"
-
-mkdir -p "$tardir"
-cd "$tardir"
-
-files="add.gdemenu
- alphabet.std
- Formats
- macinit.c
- macinit.r
- Make.com
- Makefile
- Make.ncbi
- multi.std
- nucleic.std
- Readme
- readseq.c
- Readseq.help
- readseqSIOW.make
- Stdfiles
- upper.std
- ureadasn.c
- ureadseq.c
- ureadseq.h"
-
-for file in $files ; do
- wget "$url/$file"
-done
-
-cd ..
-GZIP="--best --no-name" tar -czf "$prog"_"$version".orig.tar.gz "$dir"
-rm -rf "$dir"
=====================================
debian/patches/buffer_overflow.patch
=====================================
@@ -1,5 +1,5 @@
Author: Michael Bienia <geser at ubuntu.com>
-Last-Update: 30 Dec 2013 18:34:52 +0100
+Last-Update: 2013-12-30
Bug-Debian: http://bugs.debian.org/733650
Description: Fix buffer overflow in ureadseq.c
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,21 @@
+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=1097779
+Forwarded: no
+Last-Update: 2025-09-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- readseq.orig/ureadseq.c
++++ readseq/ureadseq.c
+@@ -105,9 +105,9 @@
+ char s[256], *sp;
+
+ #ifdef ARB
+- int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/
++ int (*isseqcharfirst8)(int); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/
+ #endif
+- int (*isseqchar)();
++ int (*isseqchar)(int);
+ /* int (*isseqchar)(int c); << sgi cc hates (int c) */
+ };
+
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,10 +1,11 @@
Author: Andreas Tille <tille at debian.org>
-LastChanged: Mon, 18 Nov 2013 14:22:50 +0100
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Last-Update: 2013-11-18
Description: Propagate hardening options
---- a/Makefile
-+++ b/Makefile
-@@ -10,7 +10,7 @@ CC=gcc # Gnu C Compiler
+--- readseq.orig/Makefile
++++ readseq/Makefile
+@@ -10,7 +10,7 @@
#CC=cc # SGI Irix
#CC=vcc # some DEC Ultrix
@@ -13,12 +14,12 @@ Description: Propagate hardening options
#CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
# instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
-@@ -48,7 +48,7 @@ all: build
+@@ -48,7 +48,7 @@
# if using NCBI, uncomment these lines in place of build: above
build: $(SOURCES)
@echo "Compiling readseq with NCBI toolkit support and ARB patches";
- $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
-+ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS) $(LDFLAGS)
++ $(CC) $(CPPFLAGS) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS) $(LDFLAGS)
test:
@echo ""
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ hardening.patch
buffer_overflow.patch
fix_tests.patch
fix-gets.patch
+gcc-15.patch
=====================================
debian/rules
=====================================
@@ -7,6 +7,12 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
-override_dh_clean:
- dh_clean
+execute_after_dh_clean:
rm -f readseq
+
+DOCDIR = $(CURDIR)/debian/readseq/usr/share/doc/readseq
+execute_after_dh_installdocs:
+ iconv -f ISO-8859-1 -t UTF-8 \
+ < $(DOCDIR)/Stdfiles \
+ > $(DOCDIR)/Stdfiles.converted
+ mv -vf $(DOCDIR)/Stdfiles.converted $(DOCDIR)/Stdfiles
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=4
-opts=dversionmangle=s/.*/0.No-Release/ \
- https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
+Version: 5
+Untrackable: upstream vanished.
+Source: http://iubio.bio.indiana.edu/soft/molbio/readseq/
View it on GitLab: https://salsa.debian.org/med-team/readseq/-/compare/a90817c6038aa23167be9708823602d024e2ca62...a0c88fbc49ff95c0cc0b3b1aa51ced031da83d27
--
View it on GitLab: https://salsa.debian.org/med-team/readseq/-/compare/a90817c6038aa23167be9708823602d024e2ca62...a0c88fbc49ff95c0cc0b3b1aa51ced031da83d27
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