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dialign-tx adding patch for gcc@5.4.0 (#6413)

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peetsv 2017-11-26 15:14:18 -08:00 committed by Christoph Junghans
parent 257d968259
commit 09eeb991a2
2 changed files with 82 additions and 0 deletions
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80
var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch Normal file
View file

@ -0,0 +1,80 @@
--- a/source/alig.c 2008-12-06 04:10:05.000000000 -0800
+++ b/source/alig.c 2017-11-21 10:58:31.000000000 -0800
@@ -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;
diff -Naur a/source/assemble.c b/source/assemble.c
--- a/source/assemble.c 2008-12-06 04:10:05.000000000 -0800
+++ b/source/assemble.c 2017-11-21 10:57:55.000000000 -0800
@@ -10,7 +10,7 @@
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,
struct prob_dist *pdist);
@@ -37,7 +37,7 @@
extern inline 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);
@@ -574,7 +574,7 @@
* returns a value <0 if there is an non-conflicting overlap
* returns 0 in all other non-conflicting cases
*/
-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
+static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
// if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
int s1_1 = dg1->seq_p1.num;
int s1_2 = dg1->seq_p2.num;
diff -Naur a/source/diag.c b/source/diag.c
--- a/source/diag.c 2008-12-06 04:10:05.000000000 -0800
+++ b/source/diag.c 2017-11-21 10:55:43.000000000 -0800
@@ -183,7 +183,7 @@
* omitScore = 0: normal
* omitScore = 1: no score calculation
*/
-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+static inline 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);
}
@@ -312,7 +312,7 @@
/**
* calculates the overlap weight for the given diag
*/
-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
+static inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
struct prob_dist *pdist) {
int sn1 = dg->seq_p1.num;
int sn2 = dg->seq_p2.num;
@@ -958,7 +958,7 @@
* The pointer returned (and the ones included in the struct)
* has to be deallocted explicitely from memory.
*/
-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,
+static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,
struct prob_dist *pdist, struct seq* seq1,
struct seq* seq2, struct alignment *algn,
long double **tmp_dist, int round) {

2
var/spack/repos/builtin/packages/dialign-tx/package.py
View file

@ -50,3 +50,5 @@ def install(self, spec, prefix):
install('dialign-tx', prefix.bin)
# t-coffee recognizes as dialign-t
install('dialign-tx', join_path(prefix.bin, 'dialign-t'))
patch('dialign-1-0-2-gcc-5-4-0.patch', when='%gcc@5.4.0')