[med-svn] [Git][med-team/dialign][master] 4 commits: fix-declarations.patch: new: fix build failure.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / dialign


Commits:
f4c663c1 by Étienne Mollier at 2024-03-16T15:53:02+01:00
fix-declarations.patch: new: fix build failure.

Closes: #1066659

- - - - -
dffa1008 by Étienne Mollier at 2024-03-16T14:53:25+00:00
Use secure URI in Homepage field.

Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

- - - - -
a847cce9 by Étienne Mollier at 2024-03-16T14:53:27+00:00
Update standards version to 4.6.2, no changes needed.

Changes-By: lintian-brush
Fixes: lintian: out-of-date-standards-version
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html

- - - - -
757fc272 by Étienne Mollier at 2024-03-16T15:55:54+01:00
ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix-declarations.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+dialign (2.2.1-12) unstable; urgency=medium
+
+  * Team upload.
+  * fix-declarations.patch: new: fix build failure. (Closes: #1066659)
+  * Use secure URI in Homepage field.
+  * Update standards version to 4.6.2, no changes needed.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 16 Mar 2024 15:55:11 +0100
+
 dialign (2.2.1-11) unstable; urgency=medium
 
   [ Jelmer Vernooij ]


=====================================
debian/control
=====================================
@@ -5,10 +5,10 @@ Uploaders: Charles Plessy <plessy at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/dialign
 Vcs-Git: https://salsa.debian.org/med-team/dialign.git
-Homepage: http://dialign.gobics.de/
+Homepage: https://dialign.gobics.de/
 Rules-Requires-Root: no
 
 Package: dialign


=====================================
debian/patches/fix-declarations.patch
=====================================
@@ -0,0 +1,48 @@
+Description: fix missing C function declarations.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1066659
+Forwarded: no
+Last-Update: 2024-03-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- dialign.orig/src/input.c
++++ dialign/src/input.c
+@@ -17,6 +17,7 @@
+ #include "define.h"
+ #include "dialign.h"
+ #include "alig_graph_closure.h"
++#include "pratique.h"
+ 
+ extern int max_dia , self_comparison ; 
+ extern int sim_score[21][21]; 
+--- dialign.orig/src/anchor.c
++++ dialign/src/anchor.c
+@@ -17,6 +17,7 @@
+ #include "define.h"
+ #include "dialign.h"
+ #include "alig_graph_closure.h"
++#include "pratique.h"
+ 
+ 
+ extern int  anc_num, *seqlen ;
+--- dialign.orig/src/dialign.h
++++ dialign/src/dialign.h
+@@ -66,4 +66,7 @@
+ struct subtree { int member_num, valid ; int *member; char *name ;
+                  float depth; };         
+ 
+-
++void regex_parse( char *mot_regex );
++void seq_parse( char *mot_regex );
++void exclude_frg_read( char *file_name , int ***exclude_list);
++int word_count( char *seq ) ;
+--- dialign.orig/src/dialign.c
++++ dialign/src/dialign.c
+@@ -214,7 +214,6 @@
+ /********************************/
+ 
+  extern float mot_dist_factor ( int offset , float parameter ) ;
+- extern int word_count( char *seq ) ; 
+  extern void subst_mat(char *file_name, int fragno , struct  multi_frag *smp );
+  extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ;
+  extern int anc_read( char *file_name ) ;


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



View it on GitLab: https://salsa.debian.org/med-team/dialign/-/compare/3184a2913a6b7ce5c1e276c3b3071995a1d6b357...757fc2724f90425bbd970adfc428a1116ec4f652

-- 
View it on GitLab: https://salsa.debian.org/med-team/dialign/-/compare/3184a2913a6b7ce5c1e276c3b3071995a1d6b357...757fc2724f90425bbd970adfc428a1116ec4f652
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