[Debian-med-packaging] Bug#1066653: prime-phylo: FTBFS: gb.tab.c:1096:16: error: implicit declaration of function ‘yylex’ [-Werror=implicit-function-declaration]

[Zixing Liu]

Package: prime-phylo
Followup-For: Bug #1066653
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu noble ubuntu-patch
Control: tags -1 patch

Dear Maintainer,

In Ubuntu, the attached patch was applied to achieve the following:

  * debian/patches/fix-ftbfs-with-gcc13.patch: Fix missing headers and
    missing prototypes.  Closes LP: #2061032.


Thanks for considering the patch.


-- System Information:
Debian Release: bookworm/sid
  APT prefers jammy-updates
  APT policy: (500, 'jammy-updates'), (500, 'jammy-security'), (500, 'jammy'), (100, 'jammy-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.5.0-26-generic (SMP w/10 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_CA.UTF-8, LC_CTYPE=en_CA.UTF-8 (charmap=UTF-8), LANGUAGE=en_CA:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
diff -Nru prime-phylo-1.0.11/debian/patches/fix-ftbfs-with-gcc13.patch prime-phylo-1.0.11/debian/patches/fix-ftbfs-with-gcc13.patch
--- prime-phylo-1.0.11/debian/patches/fix-ftbfs-with-gcc13.patch	1969-12-31 17:00:00.000000000 -0700
+++ prime-phylo-1.0.11/debian/patches/fix-ftbfs-with-gcc13.patch	2024-04-11 16:13:25.000000000 -0600
@@ -0,0 +1,54 @@
+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
+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"
+  
diff -Nru prime-phylo-1.0.11/debian/patches/series prime-phylo-1.0.11/debian/patches/series
--- prime-phylo-1.0.11/debian/patches/series	2021-05-20 05:51:42.000000000 -0600
+++ prime-phylo-1.0.11/debian/patches/series	2024-04-11 16:10:29.000000000 -0600
@@ -3,3 +3,4 @@
 fix-gcc-8.patch
 0003-Fix-build-with-Boost-1.67.patch
 0004-fix-gcc10-build.patch
+fix-ftbfs-with-gcc13.patch