[med-svn] [Git][med-team/wise][master] Add patch to fix FTBFS with GCC-15 (#1098098)
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Thu Mar 27 13:41:57 GMT 2025
Lance Lin pushed to branch master at Debian Med / wise
Commits:
c92fe095 by Lance Lin at 2025-03-27T20:21:48+07:00
Add patch to fix FTBFS with GCC-15 (#1098098)
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/fix_ftbfs_with_gcc-15.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+wise (2.4.1-27) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * d/patches: Add patch to fix FTBFS with GCC-15
+
+ -- Lance Lin <lq27267 at gmail.com> Thu, 27 Mar 2025 20:15:36 +0700
+
wise (2.4.1-26) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/fix_ftbfs_with_gcc-15.patch
=====================================
@@ -0,0 +1,177 @@
+Description: Fix FTBFS with GCC-15
+Author: Lance Lin <lq27267 at 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;
+ }
+
=====================================
debian/patches/series
=====================================
@@ -15,3 +15,4 @@ implicit-function-declaration.patch
executable-is-script.patch
gcc-14.patch
fix_blhc.patch
+fix_ftbfs_with_gcc-15.patch
View it on GitLab: https://salsa.debian.org/med-team/wise/-/commit/c92fe0950ef28ab72075a3483961bfc42c8357c5
--
View it on GitLab: https://salsa.debian.org/med-team/wise/-/commit/c92fe0950ef28ab72075a3483961bfc42c8357c5
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