Description: Fix FTBFS with GCC-15 Author: Lance Lin 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;istack_len && truestack_len;i++,true++) { + for(i=0,true_int=0;istack_len && true_intstack_len;i++,true_int++) { if( i == error_position ) { if( error_len > 0 ) { for(j=0;jstack[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; }