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Description: Fix FTBFS with GCC-15
Author: Lance Lin <lq27267@gmail.com>
Last-Update: 2025-03-27
Forwarded: not-needed
--- a/src/HMMer2/gnuregex.c
+++ b/src/HMMer2/gnuregex.c
@@ -824,13 +824,6 @@
"Unmatched ) or \\)", /* REG_ERPAREN */
};
-/* Subroutine declarations and macros for regex_compile. */
-
-static void store_op1 (), store_op2 ();
-static void insert_op1 (), insert_op2 ();
-static boolean at_begline_loc_p (), at_endline_loc_p ();
-static boolean group_in_compile_stack ();
-static reg_errcode_t compile_range ();
/* Fetch the next character in the uncompiled pattern---translating it
if necessary. Also cast from a signed character in the constant
@@ -984,6 +977,14 @@
unsigned avail; /* Offset of next open position. */
} compile_stack_type;
+/* Subroutine declarations and macros for regex_compile. */
+
+static void store_op1 (re_opcode_t, unsigned char *, int), store_op2 (re_opcode_t, unsigned char *,int, int);
+static void insert_op1 (re_opcode_t, unsigned char *, int, unsigned char *), insert_op2 (re_opcode_t, unsigned char *, int, int, unsigned char *);
+static boolean at_begline_loc_p (char *, char *, reg_syntax_t), at_endline_loc_p (char *, char *, int);
+static boolean group_in_compile_stack (compile_stack_type, regnum_t);
+static reg_errcode_t compile_range (char **, char *, char *, reg_syntax_t, unsigned char *);
+
#define INIT_COMPILE_STACK_SIZE 32
@@ -2976,12 +2977,6 @@
return -1;
} /* re_search_2 */
-/* Declarations and macros for re_match_2. */
-
-static int bcmp_translate ();
-static boolean alt_match_null_string_p (),
- common_op_match_null_string_p (),
- group_match_null_string_p ();
/* Structure for per-register (a.k.a. per-group) information.
This must not be longer than one word, because we push this value
@@ -3009,6 +3004,14 @@
} bits;
} register_info_type;
+/* Declarations and macros for re_match_2. */
+
+static int bcmp_translate (unsigned char *, unsigned char *, register int, char *);
+static boolean alt_match_null_string_p (unsigned char *, unsigned char *, register_info_type *),
+ common_op_match_null_string_p (unsigned char **, unsigned char *, register_info_type *),
+ group_match_null_string_p (unsigned char **, unsigned char *, register_info_type *);
+
+
#define REG_MATCH_NULL_STRING_P(R) ((R).bits.match_null_string_p)
#define IS_ACTIVE(R) ((R).bits.is_active)
#define MATCHED_SOMETHING(R) ((R).bits.matched_something)
--- a/src/dnaindex/kmer_assembly_error.dy
+++ b/src/dnaindex/kmer_assembly_error.dy
@@ -13,9 +13,9 @@
boolean lift_indel_error_KmerAssembly(KmerAssemblyIndex * kai,KmerAssemblyPath * real,KmerAssemblyPath * error,long int * start_labels,int label_len,int error_position,int error_len)
{
- int i,j,k,true;
+ int i,j,k,true_int;
- for(i=0,true=0;i<error->stack_len && true<real->stack_len;i++,true++) {
+ for(i=0,true_int=0;i<error->stack_len && true_int<real->stack_len;i++,true_int++) {
if( i == error_position ) {
if( error_len > 0 ) {
for(j=0;j<error_len;) {
@@ -25,7 +25,7 @@
} else {
error_len = abs(error_len);
for(j=0;j<error_len;) {
- true++;
+ true_int++;
j++;
}
}
@@ -39,10 +39,10 @@
remove_sequence_label_KmerAssemblyLink(error->stack[i],start_labels[k]+i);
}
- if( real->stack[true] == NULL ) {
+ if( real->stack[true_int] == NULL ) {
fprintf(stderr,"issue - true path is missing a link!");
} else {
- add_sequence_label_KmerAssemblyLink(real->stack[true],start_labels[k]+i);
+ add_sequence_label_KmerAssemblyLink(real->stack[true_int],start_labels[k]+i);
}
if( error->stack[i] != NULL && error->stack[i]->sequence_label_len == 0 ) {
detach_KmerAssemblyLink(kai,error->stack[i]);
@@ -415,7 +415,7 @@
/* recursively call for each possible path: if any return
- true, return TRUE */
+ true_int, return TRUE */
/* fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
@@ -542,7 +542,7 @@
/* recursively call for each possible path: if any return
- true, return TRUE */
+ true_int, return TRUE */
/* fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
--- a/src/models/genewisehsp.h
+++ b/src/models/genewisehsp.h
@@ -270,7 +270,7 @@
#define show_help_GeneWiseRunPara Wise2_show_help_GeneWiseRunPara
DPEnvelope * Wise2_DPEnvelope_from_protein_gen(Sequence * prot,Sequence * dna,CompMat * mat,CodonTable * ct,GeneWiseRunPara *p);
#define DPEnvelope_from_protein_gen Wise2_DPEnvelope_from_protein_gen
-int Wise2_consistent_GeneWiseHSP(GeneWiseHSP * true,GeneWiseHSP * proposed);
+int Wise2_consistent_GeneWiseHSP(GeneWiseHSP * true_val,GeneWiseHSP * proposed);
#define consistent_GeneWiseHSP Wise2_consistent_GeneWiseHSP
int Wise2_compare_GeneWiseHSP_start(GeneWiseHSP * one,GeneWiseHSP * two);
#define compare_GeneWiseHSP_start Wise2_compare_GeneWiseHSP_start
--- a/src/models/genewisehsp.dy
+++ b/src/models/genewisehsp.dy
@@ -288,30 +288,30 @@
-int consistent_GeneWiseHSP(GeneWiseHSP * true,GeneWiseHSP * proposed)
+int consistent_GeneWiseHSP(GeneWiseHSP * true_val,GeneWiseHSP * proposed)
{
int query_centre;
int target_centre;
- assert(true);
+ assert(true_val);
assert(proposed);
/* is this left or right of the true HSP */
query_centre = (proposed->query_start + proposed->query_end) / 2;
target_centre = (proposed->target_start + proposed->target_end) / 2;
/* overlap criteria first */
- if( query_centre >= true->query_start && query_centre <= true->query_end ) {
+ if( query_centre >= true_val->query_start && query_centre <= true_val->query_end ) {
return 0;
}
/* left or right */
- if( query_centre > true->query_end ) {
- if( target_centre < true->target_end ) {
+ if( query_centre > true_val->query_end ) {
+ if( target_centre < true_val->target_end ) {
/* no - inconsistent */
return 0;
}
} else {
- if( target_centre > true->target_start ) {
+ if( target_centre > true_val->target_start ) {
return 0;
}
}
@@ -319,7 +319,7 @@
/* overlap */
- if( target_centre >= true->target_start && target_centre <= true->target_end ) {
+ if( target_centre >= true_val->target_start && target_centre <= true_val->target_end ) {
return 0;
}
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