1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
Description: fix multiple issues gone fatal with gcc 14.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075638
Forwarded: not-needed
Last-Update: 2024-08-15
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- wise.orig/src/socket/functionclient.dy
+++ wise/src/socket/functionclient.dy
@@ -190,7 +190,7 @@
bcopy( hp->h_addr, &server.sin_addr, hp->h_length);
server.sin_port = htons(port);
- connect(out->socket, &server, sizeof(server));
+ connect(out->socket, (const struct sockaddr *)&server, sizeof(server));
return out;
--- wise.orig/src/dyc/dynafunc.dy
+++ wise/src/dyc/dynafunc.dy
@@ -6,6 +6,7 @@
#include "labelmaster.h"
#include "linesubs.h"
#include "dynashadow.h"
+#include "dyshatter.h"
#include "dynadb.h"
#include "dpimpl.h"
#include "dbthread.h"
--- wise.orig/src/dyc/inputfile.c
+++ wise/src/dyc/inputfile.c
@@ -5,7 +5,7 @@
static FILE * watch_file = NULL;
-static linecount = 0;
+static int linecount = 0;
# line 18 "inputfile.dy"
--- wise.orig/src/dyc/dynafunc.h
+++ wise/src/dyc/dynafunc.h
@@ -14,6 +14,7 @@
#include "dbthread.h"
#include "probal.h"
#include "dynadebug.h"
+#include "dyshatter.h"
--- wise.orig/src/dyc/lex.yy.c
+++ wise/src/dyc/lex.yy.c
@@ -411,11 +411,7 @@
#endif
#ifndef YY_NO_INPUT
-#ifdef __cplusplus
static int yyinput YY_PROTO(( void ));
-#else
-static int input YY_PROTO(( void ));
-#endif
#endif
#if YY_STACK_USED
@@ -1061,11 +1057,7 @@
#endif /* ifndef YY_NO_UNPUT */
-#ifdef __cplusplus
static int yyinput()
-#else
-static int input()
-#endif
{
int c;
@@ -1111,11 +1103,7 @@
if ( ! yy_did_buffer_switch_on_eof )
YY_NEW_FILE;
-#ifdef __cplusplus
return yyinput();
-#else
- return input();
-#endif
}
case EOB_ACT_CONTINUE_SCAN:
--- wise.orig/src/dnaindex/compressed_protein_index.dy
+++ wise/src/dnaindex/compressed_protein_index.dy
@@ -220,7 +220,7 @@
{
fatal("For compressed protein indexes, impossible to add numbers directly");
- return NULL;
+ return FALSE;
}
ArraySeqHead * lookup_array_head_CompressedProteinIndex(void * data,int seq_number)
--- wise.orig/src/dnaindex/kmer_assembly_untangler.dy
+++ wise/src/dnaindex/kmer_assembly_untangler.dy
@@ -565,7 +565,14 @@
if( have_link == 1 ) {
/* fprintf(stderr," ..reverse TAIL.. untangling...\n"); */
- lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
+ lift_backward_tangled_tail(
+ kai,
+ newpath->stack[newpath->stack_len-1],
+ path,
+ (int*)transferred_label,
+ transferred_pos,
+ transferred_len
+ );
}
/* pop off the top of this path */
--- wise.orig/src/models/est_evidence.dy
+++ wise/src/models/est_evidence.dy
@@ -139,7 +139,7 @@
in->utr_pot = est_utr_pot;
in->cds_intron_pot = est_intron_pot;
in->utr_intron_pot = est_intron_pot;
- in->geu_free = free_EstEvidence;
+ in->geu_free = (int(*)(void*))free_EstEvidence;
in->frameshift_cds = est_cds_frameshift;
in->stop_pot = est_stop_pot;
in->start_pot = est_start_pot;
|
