[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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