[med-svn] [Git][med-team/prime-phylo][master] Apply patch from Zixing Liu @ Canonical to fix FTBFS with GCC 13. Thanks!

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / prime-phylo


Commits:
e409ac42 by Michael R. Crusoe at 2024-04-12T14:16:30+03:00
Apply patch from Zixing Liu @ Canonical to fix FTBFS with GCC 13. Thanks!

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-ftbfs-with-gcc13.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+prime-phylo (1.0.11-11) unstable; urgency=medium
+
+  * Team upload.
+  * Apply patch from Zixing Liu @ Canonical to fix FTBFS with GCC 13.
+    Thanks!
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Fri, 12 Apr 2024 14:16:27 +0300
+
 prime-phylo (1.0.11-10) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/patches/fix-ftbfs-with-gcc13.patch
=====================================
@@ -0,0 +1,55 @@
+Description: Fix missing headers and missing prototypes
+Author: Zixing Liu <zixing.liu at canonical.com>
+Bug-Ubuntu: https://bugs.launchpad.net/debian/+source/prime-phylo/+bug/2061032
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066653
+Forwarded: no
+Last-Update: 2024-04-11
+Index: prime-phylo/src/cxx/libraries/prime/NHXparse.y
+===================================================================
+--- prime-phylo.orig/src/cxx/libraries/prime/NHXparse.y
++++ prime-phylo/src/cxx/libraries/prime/NHXparse.y
+@@ -2,6 +2,7 @@
+ #include <string.h>
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <unistd.h>
+ #include "NHXnode.h"
+ #include "NHXtree.h"
+ #include "NHXannotation.h"
+@@ -14,7 +15,9 @@
+ /* #define YYERROR_VERBOSE */ 
+ 
+ /* Here comes some C declarations */
+-
++extern int yylex (void);
++extern void read_from_string(char *str);
++extern void close_string_buffer();
+ extern FILE *yytree_in;
+ extern char *yytree_text;
+ extern unsigned int lineno; /* Current line number in input file */
+Index: prime-phylo/src/cxx/libraries/sfile/gb.y
+===================================================================
+--- prime-phylo.orig/src/cxx/libraries/sfile/gb.y
++++ prime-phylo/src/cxx/libraries/sfile/gb.y
+@@ -23,7 +23,8 @@
+ #include "entry.h"
+ #include "sfile.h"
+ 
+-
++extern int yylex (void);
++unsigned linenumber();
+ static int yyerror();
+ 
+ #define YYDEBUG 1
+Index: prime-phylo/src/cxx/libraries/sfile/gbread.c
+===================================================================
+--- prime-phylo.orig/src/cxx/libraries/sfile/gbread.c
++++ prime-phylo/src/cxx/libraries/sfile/gbread.c
+@@ -3,6 +3,7 @@
+ 
+ extern int yydebug;
+ 
++#include <string.h>
+ #include "sfile.h"
+ #include "gb.tab.h"
+  


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix-ftbfs-with-Boost160.patch
 fix-gcc-8.patch
 0003-Fix-build-with-Boost-1.67.patch
 0004-fix-gcc10-build.patch
+fix-ftbfs-with-gcc13.patch



View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/commit/e409ac424018ba7e07705669e131407e7c74576f

-- 
View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/commit/e409ac424018ba7e07705669e131407e7c74576f
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