[med-svn] [Git][med-team/sim4][master] 8 commits: rename-type-bool.patch: new: fix build failure.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Oct 6 20:48:46 BST 2025
Étienne Mollier pushed to branch master at Debian Med / sim4
Commits:
57c6e1f8 by Étienne Mollier at 2025-10-06T21:31:38+02:00
rename-type-bool.patch: new: fix build failure.
Closes: #1097885
- - - - -
95a81cc9 by Étienne Mollier at 2025-10-06T21:33:37+02:00
d/copyright: remove the old fsf address.
- - - - -
28348143 by Étienne Mollier at 2025-10-06T21:38:05+02:00
d/watch: convert to version 5 watch file.
This change also adjusts the scanner for a working https page.
- - - - -
2507d862 by Étienne Mollier at 2025-10-06T21:38:55+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
236fe011 by Étienne Mollier at 2025-10-06T21:39:14+02:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
f8ca39a7 by Étienne Mollier at 2025-10-06T21:41:36+02:00
cppflags.patch: new: propagate more hardening flags.
- - - - -
ceeda98d by Étienne Mollier at 2025-10-06T21:47:46+02:00
d/rules: activate hardening support.
- - - - -
eae5a7f7 by Étienne Mollier at 2025-10-06T21:48:17+02:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/cppflags.patch
- + debian/patches/rename-type-bool.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+sim4 (0.0.20121010-9) unstable; urgency=medium
+
+ * Team upload.
+ * rename-type-bool.patch: new: fix build failure. (Closes: #1097885)
+ * d/copyright: remove the old fsf address.
+ * d/watch: convert to version 5 watch file.
+ This change also adjusts the scanner for a working https page.
+ * d/control: declare compliance to standards version 4.7.2.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * cppflags.patch: new: propagate more hardening flags.
+ * d/rules: activate hardening support.
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 06 Oct 2025 21:48:07 +0200
+
sim4 (0.0.20121010-8) unstable; urgency=medium
* Nelson A. de Oliveira <naoliv at debian.org> has retired so remove him
=====================================
debian/control
=====================================
@@ -4,11 +4,10 @@ Uploaders: Andreas Tille <tille 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/sim4
Vcs-Git: https://salsa.debian.org/med-team/sim4.git
Homepage: https://globin.bx.psu.edu/html/docs/sim4.html
-Rules-Requires-Root: no
Package: sim4
Architecture: any
=====================================
debian/copyright
=====================================
@@ -23,11 +23,6 @@ License: GPL-2+
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
- MA 02110-1301, USA.
.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-2'.
=====================================
debian/patches/cppflags.patch
=====================================
@@ -0,0 +1,18 @@
+Description: propagate CPPFLAGS.
+ This change is necessary for complete executable hardening using the
+ standard Debian build flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2025-10-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- sim4.orig/Makefile
++++ sim4/Makefile
+@@ -8,6 +8,6 @@
+ LDLIBS=-lm
+
+ sim4:
+- $(CC) -o sim4 -I. $(CFLAGS) `LC_ALL=C ls *.c` $(LDLIBS) $(LDFLAGS)
++ $(CC) $(CPPFLAGS) -o sim4 -I. $(CFLAGS) `LC_ALL=C ls *.c` $(LDLIBS) $(LDFLAGS)
+ clean:
+ rm -f sim4 *.o
=====================================
debian/patches/rename-type-bool.patch
=====================================
@@ -0,0 +1,178 @@
+Description: rename type definition to Bool.
+ The type bool is part of the C language since the specification 2023.
+ Its redefinition provokes build failures like:
+ .
+ types.h:7:13: error: ‘bool’ cannot be defined via ‘typedef’
+ 7 | typedef int bool;
+ | ^~~~
+ types.h:7:13: note: ‘bool’ is a keyword with ‘-std=c23’ onwards
+ .
+ The original code bases its type on "int", which is larger than the one
+ byte size of the standardized bool type, therefore, a proper fix to
+ preserve the legacy behavior is rename the type to Bool.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097885
+Forwarded: no
+Last-Update: 2025-10-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- sim4.orig/args.c
++++ sim4/args.c
+@@ -28,7 +28,7 @@
+ }
+
+ /* get_argval --------------------- get the value of a command-line argument */
+-bool get_argval(int c, int *val_ptr)
++Bool get_argval(int c, int *val_ptr)
+ {
+ int i;
+
+@@ -42,7 +42,7 @@
+ }
+
+ /* get_fargval --------------- get the float value of a command-line argument */
+-bool get_fargval(int c, double *val_ptr)
++Bool get_fargval(int c, double *val_ptr)
+ {
+ int i;
+
+@@ -56,7 +56,7 @@
+ }
+
+ /* get_strargval ---------- get the string value of a command-line argument */
+-bool get_strargval(int c, char **val_ptr)
++Bool get_strargval(int c, char **val_ptr)
+ {
+ int i;
+
+@@ -70,7 +70,7 @@
+ return 0;
+ }
+
+-bool get_cargval(int c, char **valp)
++Bool get_cargval(int c, char **valp)
+ {
+ int i;
+
+--- sim4.orig/args.h
++++ sim4/args.h
+@@ -10,10 +10,10 @@
+ int V;
+ } argv_scores_t;
+
+-bool get_argval(int, int *);
+-bool get_fargval(int, double *);
+-bool get_strargval(int, char **);
+-bool get_cargval(int, char **);
++Bool get_argval(int, int *);
++Bool get_fargval(int, double *);
++Bool get_strargval(int, char **);
++Bool get_cargval(int, char **);
+ void ckargs(const char *, int , char **, int );
+ void fprintf_argv(FILE* fp);
+ void ck_argc(const char *);
+--- sim4.orig/discrim.c
++++ sim4/discrim.c
+@@ -16,7 +16,7 @@
+
+ static int is_dchar(int ch);
+
+-bool is_DNA(uchar *s, int len)
++Bool is_DNA(uchar *s, int len)
+ {
+ int ACGT, i;
+
+--- sim4.orig/discrim.h
++++ sim4/discrim.h
+@@ -2,6 +2,6 @@
+ #define SIM_DISCRIM_H
+ /* $Id: discrim.h,v 1.1 2000/06/05 22:23:15 florea Exp $ */
+
+-bool is_DNA(uchar *s, int len);
++Bool is_DNA(uchar *s, int len);
+
+ #endif
+--- sim4.orig/misc.c
++++ sim4/misc.c
+@@ -123,7 +123,7 @@
+ }
+
+ /* strsame --------------------------- tell whether two strings are identical */
+-bool same_string(const char *s, const char *t)
++Bool same_string(const char *s, const char *t)
+ {
+ return (strcmp(s, t) == 0);
+ }
+--- sim4.orig/misc.h
++++ sim4/misc.h
+@@ -23,7 +23,7 @@
+ /*@only@*/ void *ckalloc(size_t amount);
+ /*@only@*/ void *ckallocz(size_t amount);
+ void *ckfree(void *p);
+-bool same_string(const char *s, const char *t);
++Bool same_string(const char *s, const char *t);
+ char *copy_string(const char *s);
+ char *copy_substring(const char *s, int n);
+ long ckftell(FILE*);
+--- sim4.orig/sim4b1.c
++++ sim4/sim4b1.c
+@@ -44,7 +44,7 @@
+ static Exon_ptr exon_list;
+
+ static void merge(Exon **,Exon **);
+-static bool get_sync_flag(Exon *, Exon *, int);
++static Bool get_sync_flag(Exon *, Exon *, int);
+ static void slide_intron(int w, Exon **,uchar *,uchar *);
+ static void sync_slide_intron(int w, Exon **,uchar *,uchar *);
+ static void wobble(Exon **,Exon **,const char *,const char *,uchar *seq1);
+@@ -75,7 +75,7 @@
+ static void relink(Msp_ptr *,int,int,int,int,int,uchar *,uchar *);
+ static int dispatch_find_ends(int,int,int *,int *,edit_script_list *,int,int,int);
+ static int find_ends(edit_script_list *,int);
+-static bool get_match_quality(Exon *,Exon *,sim4_stats_t *,int);
++static Bool get_match_quality(Exon *,Exon *,sim4_stats_t *,int);
+ static int check_consistency_intron_ori(Exon *,int,char *);
+
+ Exon *find_previous(Exon *,Exon *);
+@@ -102,7 +102,7 @@
+ {
+ int cflag, diff, cost, rollbflag, sync_flag;
+ int u, v, I, J;
+- bool good_match;
++ Bool good_match;
+ Exon *Lblock, *Rblock=NULL, *tmp_block, *last, *prev, *tmp_block1,
+ *tmp_Lblock=NULL, *tmp_Rblock=NULL, *new;
+
+@@ -2701,7 +2701,7 @@
+ }
+ }
+
+-static bool get_sync_flag(Exon *lblock, Exon *rblock, int w)
++static Bool get_sync_flag(Exon *lblock, Exon *rblock, int w)
+ {
+ int numx=0, e2;
+ Exon *t;
+@@ -3078,10 +3078,10 @@
+ return t;
+ }
+
+-static bool get_match_quality(Exon *lblock, Exon *rblock, sim4_stats_t *st, int N)
++static Bool get_match_quality(Exon *lblock, Exon *rblock, sim4_stats_t *st, int N)
+ {
+ int tcov;
+- bool good_match;
++ Bool good_match;
+ Exon *t;
+
+ good_match = TRUE; st->icoverage = 0;
+--- sim4.orig/types.h
++++ sim4/types.h
+@@ -4,7 +4,7 @@
+
+ #define NACHARS 128
+
+-typedef int bool;
++typedef int Bool;
+ typedef int ss_t[NACHARS][NACHARS];
+ typedef unsigned char uchar;
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
hardening.patch
compilation_order.patch
+rename-type-bool.patch
+cppflags.patch
=====================================
debian/rules
=====================================
@@ -1,8 +1,6 @@
#!/usr/bin/make -f
-## This does not help to solve
-## I: sim4: hardening-no-fortify-functions usr/bin/sim4
-# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
-version=4
-opts="uversionmangle=s/^/0.0./;s/-//g" \
-http://globin.cse.psu.edu/ftp/dist/sim4/ sim4.(.*)\.tar\.gz
+Version: 5
+
+Source: https://globin.bx.psu.edu/ftp/dist/sim4/
+Matching-Pattern: sim4.(.*)\.tar\.gz
+Uversionmangle: s/^/0.0./;s/-//g
View it on GitLab: https://salsa.debian.org/med-team/sim4/-/compare/a76eaead6c79497d250dd8d3cd5edaeebdc01be5...eae5a7f73ed29b2df41fb6baaaed719e4c03669e
--
View it on GitLab: https://salsa.debian.org/med-team/sim4/-/compare/a76eaead6c79497d250dd8d3cd5edaeebdc01be5...eae5a7f73ed29b2df41fb6baaaed719e4c03669e
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