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 <[email protected]> Fri, 09 May 2014 11:59:49 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
