[med-svn] [Git][med-team/dialign][master] 4 commits: d/control: declare compliance to standards version 4.7.0.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Thu Jul 4 21:43:31 BST 2024



Étienne Mollier pushed to branch master at Debian Med / dialign


Commits:
d2ead755 by Étienne Mollier at 2024-07-04T21:42:42+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
31a60985 by Étienne Mollier at 2024-07-04T21:43:59+02:00
d/control: add myself to uploaders.

- - - - -
3951822e by Étienne Mollier at 2024-07-04T22:24:40+02:00
gcc-14.patch: new: fix implicit types flagged by gcc-14.

Closes: #1074909

- - - - -
2f0723a6 by Étienne Mollier at 2024-07-04T22:42:46+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc-14.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+dialign (2.2.1-13) unstable; urgency=medium
+
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/control: add myself to uploaders.
+  * gcc-14.patch: new: fix implicit types flagged by gcc-14. (Closes: #1074909)
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 04 Jul 2024 22:25:10 +0200
+
 dialign (2.2.1-12) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -1,11 +1,12 @@
 Source: dialign
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Charles Plessy <plessy at debian.org>,
-           Andreas Tille <tille at debian.org>
+           Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/dialign
 Vcs-Git: https://salsa.debian.org/med-team/dialign.git
 Homepage: https://dialign.gobics.de/


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,99 @@
+Description: fix build failure with gcc 14
+ Since gcc 14, implicit int types are flagged as errors.  This results
+ in multiple issues when trying to compile dialign:
+ .
+ 	output.c:64:9: error: type defaults to ‘int’ in declaration of ‘plot_calc’ [-Wimplicit-int]
+ 	   64 |  extern plot_calc( int num , int e_len, float *w_count, float *pl,
+ 	      |         ^~~~~~~~~
+ 	output.c:66:9: error: type defaults to ‘int’ in declaration of ‘wgt_type_count’ [-Wimplicit-int]
+ 	   66 |  extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+ 	      |         ^~~~~~~~~~~~~~
+ 	dialign.c:260:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 	  260 | main(int argc, char **argv)
+ 	      | ^~~~
+ 	make[2]: *** [makefile:44: output.o] Error 1
+ 	make[2]: *** Waiting for unfinished jobs....
+ 	functions.c:856:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 	  856 | wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+ 	      | ^~~~~~~~~~~~~~
+ 	functions.c:885:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 	  885 | plot_calc( int num , int e_len, float *w_count, float *pl,
+ 	      | ^~~~~~~~~
+ 	make[2]: *** [makefile:34: dialign.o] Error 1
+ 	regex.c:154:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 	  154 | seq_parse( char *mot_regex ) {
+ 	      | ^~~~~~~~~
+ 	regex.c:154:1: warning: conflicting types for ‘seq_parse’
+ 	In file included from regex.c:18:
+ 	dialign.h:70:6: note: previous declaration of ‘seq_parse’ with type ‘void(char *)’
+ 	   70 | void seq_parse( char *mot_regex );
+ 	      |      ^~~~~~~~~
+ .
+ This patch declares the appropriate types to functions missing them,
+ usually "void" instead of the default "int", as the affected functions
+ do not explicitly return any value.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1074909
+Forwarded: no
+Last-Update: 2024-07-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- dialign.orig/src/dialign.c
++++ dialign/src/dialign.c
+@@ -256,7 +256,7 @@
+                     /******************************/
+ 
+ 
+-
++int
+ main(int argc, char **argv)
+ {
+  int k,  anc1, dia_counter, tmpi1, tmpi2 ;
+--- dialign.orig/src/functions.c
++++ dialign/src/functions.c
+@@ -853,7 +853,7 @@
+       }
+   }
+ 
+-wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
++void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+            int *nuc_cnt , int *frg_inv, struct multi_frag *dia )      {
+ 
+ int i, dc, pc, s1, pos;
+@@ -882,8 +882,8 @@
+ 
+ 
+ 
+-plot_calc( int num , int e_len, float *w_count, float *pl, 
+-           struct multi_frag *dia , FILE *fp_csc )
++void plot_calc( int num , int e_len, float *w_count, float *pl,
++                struct multi_frag *dia , FILE *fp_csc )
+   {
+     int i, dc, pc, s1, pos;
+     float max_weight = 0;     /* maximum value of `weight_count' */
+--- dialign.orig/src/output.c
++++ dialign/src/output.c
+@@ -61,9 +61,9 @@
+  extern void mini(int *a, int b);
+  extern void maxi(int *a, int b);
+  extern int int_test(float f);
+- extern plot_calc( int num , int e_len, float *w_count, float *pl,
++ extern void plot_calc( int num , int e_len, float *w_count, float *pl,
+            struct multi_frag *dia , FILE *fp_csc ) ;
+- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
++ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+            int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ;  
+ 
+ 
+--- dialign.orig/src/regex.c
++++ dialign/src/regex.c
+@@ -151,7 +151,7 @@
+ 
+ }
+  
+-seq_parse( char *mot_regex ) { 
++void seq_parse( char *mot_regex ) {
+   int sn, ok , i ; 
+   int sp, ap, rp, hv, match;
+   max_mot_offset = sqrt ( - log ( 0.1 ) *  10 / mot_factor ) * mot_offset_factor; 


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ hardening.patch
 fix_excess_argument.patch
 spelling.patch
 fix-declarations.patch
+gcc-14.patch



View it on GitLab: https://salsa.debian.org/med-team/dialign/-/compare/757fc2724f90425bbd970adfc428a1116ec4f652...2f0723a62c10108759fa8a10488a6da6739da59f

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View it on GitLab: https://salsa.debian.org/med-team/dialign/-/compare/757fc2724f90425bbd970adfc428a1116ec4f652...2f0723a62c10108759fa8a10488a6da6739da59f
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