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sci-biology/dialign-tx: fixes GCC-5 inline semantics and -Wformat= warnings, #570252
Package-Manager: portage-2.2.26
This commit is contained in:
Ted Tanberry
@@ -22,7 +22,8 @@ S=${WORKDIR}/${MY_P}
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src_prepare() {
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sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \
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-i source/Makefile || die #336533
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epatch "${FILESDIR}"/${P}-implicits.patch
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epatch "${FILESDIR}"/${P}-implicits.patch \
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"${FILESDIR}"/${P}-modernize.patch
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}
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src_compile() {
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130
sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
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130
sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
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@@ -0,0 +1,130 @@
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Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252
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https://bugs.gentoo.org/show_bug.cgi?id=570252
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In addition, fixed multiple -Wformat= warnings, such as
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io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
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while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
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^
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io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
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io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
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io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
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io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
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--- DIALIGN-TX_1.0.2/source/alig.c
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+++ DIALIGN-TX_1.0.2/source/alig.c
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@@ -10,9 +10,9 @@
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extern void error(char *message);
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extern void merror(char *msg1, char *msg2);
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-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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//extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
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extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2,
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@@ -520,7 +520,7 @@
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* datastructure (i.e. frontiers). The given diag must be consistent
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* to the given alignment !
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*/
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-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
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+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
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char alignedSomething = 0;
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int i,j,k;
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--- DIALIGN-TX_1.0.2/source/assemble.c
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+++ DIALIGN-TX_1.0.2/source/assemble.c
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@@ -10,9 +10,9 @@
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extern void error(char *message);
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extern void merror(char *msg1, char *msg2);
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-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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//extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
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extern long double** create_tmp_pdist(struct prob_dist *pdist);
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@@ -22,7 +22,7 @@
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int n2, struct seq* sq2, unsigned int sp2,
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int dlength);
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extern void free_diag(struct diag* dg);
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-extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
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+extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
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struct prob_dist *pdist,
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struct gt_node* n1,
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struct gt_node* n2,
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@@ -34,10 +34,10 @@
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extern struct alignment* create_empty_alignment(struct seq_col *scol);
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extern void free_alignment(struct alignment *algn);
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-extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
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+extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
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extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
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//extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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//extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
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//extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
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--- DIALIGN-TX_1.0.2/source/diag.c
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+++ DIALIGN-TX_1.0.2/source/diag.c
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@@ -183,7 +183,7 @@
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* omitScore = 0: normal
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* omitScore = 1: no score calculation
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*/
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-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) {
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if(dg->multi_dg) {
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@@ -302,7 +302,7 @@
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}
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}
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-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist) {
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real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL);
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}
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--- DIALIGN-TX_1.0.2/source/io.c
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+++ DIALIGN-TX_1.0.2/source/io.c
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@@ -267,7 +267,7 @@
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for( c=r; c<length; c++) {
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// check whether it is a regular acid or a special character like '$',...
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if( (r<length-additional) && (c<length-additional)) {
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- fscanf( fp, "%i", &is);
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+ if( fscanf( fp, "%i", &is) ){};
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} else {
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is = 0;
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}
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@@ -279,7 +279,7 @@
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// ensure symmetry of the weight matrix
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data[length*c+r] = is;
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}
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- fscanf(fp, "%s\n", rline);
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+ if( fscanf(fp, "%s\n", rline) ){};
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}
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fclose(fp);
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@@ -368,7 +368,7 @@
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}
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for(scr=0;scr<=mxscr;scr++) {
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dist[i][scr]=1.0;
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- fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
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+ if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){};
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//if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename);
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scr = tscr;
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if(weight==0.0) weight = 1.0;
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@@ -532,7 +532,7 @@
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sdcol->data = malloc(sizeof (struct diag*)*alloc_size);
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sdcol->length=0;
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- while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
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+ while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
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if(sdcol->length >= alloc_size) {
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alloc_size+=16;
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sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size);
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