gentoo-overlay/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch

Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252
https://bugs.gentoo.org/show_bug.cgi?id=570252

In addition, fixed multiple -Wformat= warnings, such as

io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
   while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
                    ^
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]

--- DIALIGN-TX_1.0.2/source/alig.c
+++ DIALIGN-TX_1.0.2/source/alig.c
@@ -10,9 +10,9 @@
 
 extern void error(char *message);
 extern void merror(char *msg1, char *msg2);
-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
 			struct prob_dist *pdist);
-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
 		    struct prob_dist *pdist);
 //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
 extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, 
@@ -520,7 +520,7 @@
  * datastructure (i.e. frontiers). The given diag must be consistent
  * to the given alignment !
  */
-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
 
   char alignedSomething = 0;
   int i,j,k;
--- DIALIGN-TX_1.0.2/source/assemble.c
+++ DIALIGN-TX_1.0.2/source/assemble.c
@@ -10,9 +10,9 @@
 
 extern void error(char *message);
 extern void merror(char *msg1, char *msg2);
-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
 			struct prob_dist *pdist);
-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
 		    struct prob_dist *pdist);
 //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
 extern long double** create_tmp_pdist(struct prob_dist *pdist);
@@ -22,7 +22,7 @@
                          int n2, struct seq* sq2, unsigned int sp2,
                          int dlength);
 extern void free_diag(struct diag* dg);
-extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
+extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
 							struct prob_dist *pdist, 
 							struct gt_node* n1,  
 							struct gt_node* n2, 
@@ -34,10 +34,10 @@
 
 extern struct alignment* create_empty_alignment(struct seq_col *scol);
 extern void free_alignment(struct alignment *algn);
-extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
+extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
 extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
 //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
 //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
 //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
 
--- DIALIGN-TX_1.0.2/source/diag.c
+++ DIALIGN-TX_1.0.2/source/diag.c
@@ -183,7 +183,7 @@
  * omitScore = 0:  normal 
  * omitScore = 1:  no score calculation 
  */ 
-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
+void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
 		 struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { 
    
   if(dg->multi_dg) {
@@ -302,7 +302,7 @@
   } 
 } 
  
-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
 		 struct prob_dist *pdist) { 
   real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); 
 } 
--- DIALIGN-TX_1.0.2/source/io.c
+++ DIALIGN-TX_1.0.2/source/io.c
@@ -267,7 +267,7 @@
     for( c=r; c<length; c++) {
       // check whether it is a regular acid or a special character like '$',...
       if( (r<length-additional) && (c<length-additional)) {
-		fscanf( fp, "%i", &is);
+		if( fscanf( fp, "%i", &is) ){};
       } else {
 		is = 0;
       }
@@ -279,7 +279,7 @@
       // ensure symmetry of the weight matrix
       data[length*c+r] = is;
     }
-    fscanf(fp, "%s\n", rline);
+    if( fscanf(fp, "%s\n", rline) ){};
   }
   fclose(fp);
 
@@ -368,7 +368,7 @@
     }
     for(scr=0;scr<=mxscr;scr++) {
       dist[i][scr]=1.0;
-      fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
+      if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){};
       //if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename);
       scr = tscr;
       if(weight==0.0) weight = 1.0;
@@ -532,7 +532,7 @@
   sdcol->data = malloc(sizeof (struct diag*)*alloc_size);
   sdcol->length=0;
 
-  while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
+  while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
     if(sdcol->length >= alloc_size) {
       alloc_size+=16;
       sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size);