[med-svn] r17629 - in trunk/packages/dialign-t/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Aug 7 13:13:18 UTC 2014
Author: tille
Date: 2014-08-07 13:13:18 +0000 (Thu, 07 Aug 2014)
New Revision: 17629
Added:
trunk/packages/dialign-t/trunk/debian/patches/clang-ftbfs.diff
Modified:
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/patches/series
Log:
Fix clang bug
Modified: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog 2014-08-07 11:58:29 UTC (rev 17628)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2014-08-07 13:13:18 UTC (rev 17629)
@@ -1,8 +1,17 @@
-dialign-t (1.0.2-7) UNRELEASED; urgency=medium
+dialign-t (1.0.2-7) unstable; urgency=medium
+ [ Andreas Tille ]
* moved debian/upstream to debian/upstream/metadata
+
+ [ Arthur Marble ]
+ * Fix FTBFS with clang
+ - Fixed the undefined reference error in
+ source/alig.c
+ source/assemble.c
+ source/diag.c
+ Closes: #757281
- -- Andreas Tille <tille at debian.org> Fri, 09 May 2014 11:59:49 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 06 Aug 2014 15:52:44 -0500
dialign-t (1.0.2-6) unstable; urgency=medium
Added: trunk/packages/dialign-t/trunk/debian/patches/clang-ftbfs.diff
===================================================================
--- trunk/packages/dialign-t/trunk/debian/patches/clang-ftbfs.diff (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/patches/clang-ftbfs.diff 2014-08-07 13:13:18 UTC (rev 17629)
@@ -0,0 +1,84 @@
+Author: Arthur Marble <arthur at info9.net>
+Bug-Debian: http://bugs.debian.org/757281
+Last-Update: Wed, 06 Aug 2014 15:52:44 -0500
+Forwarded-Upstream: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-August/028291.html
+Description: Fix FTBFS with clang instead of gcc
+
+--- a/source/diag.c
++++ b/source/diag.c
+@@ -183,7 +183,7 @@ void fill_tmp_pdist(struct prob_dist *pd
+ * 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 real_calc_weight(struct diag
+ }
+ }
+
+-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 @@ inline void calc_weight(struct diag* dg,
+ /**
+ * 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 @@ inline struct simple_diag_col* find_diag
+ * 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) {
+--- a/source/assemble.c
++++ b/source/assemble.c
+@@ -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 void free_alignment(struct alignm
+ 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 @@ char simple_aligner(struct seq_col *scol
+ * 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;
+--- a/source/alig.c
++++ b/source/alig.c
+@@ -520,7 +520,7 @@ struct alignment* copy_alignment( struct
+ * 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;
Modified: trunk/packages/dialign-t/trunk/debian/patches/series
===================================================================
--- trunk/packages/dialign-t/trunk/debian/patches/series 2014-08-07 11:58:29 UTC (rev 17628)
+++ trunk/packages/dialign-t/trunk/debian/patches/series 2014-08-07 13:13:18 UTC (rev 17629)
@@ -1,3 +1,4 @@
prevent_enforcing_arch.patch
hardening.patch
consistent_declarations.patch
+clang-ftbfs.diff
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