[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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