Package: dialign-t
Severity: minor
Tags: patch
User: pkg-llvm-t...@lists.alioth.debian.org
Usertags: clang-ftbfs
Hello,
Using the rebuild infrastructure, your package fails to build with clang
(instead of gcc).
Detected this kind of error:
http://clang.debian.net/status.php?version=3.4.2&key=UNDEF_REF
Full build log is available here:
http://clang.debian.net/logs/2014-06-16/dialign-t_1.0.2-6_unstable_clang.log
Thanks,
Arthur
-- System Information:
Debian Release: jessie/sid (unstable)
Architecture: amd64 (x86_64)
Kernel: Linux 3.14-2-amd64
Locale: LANG=en_US.UTF-8, LC_CTYPE="en_US.UTF-8"
Shell: /bin/sh linked to /bin/dash
Compiler: Debian clang version 3.5.0-+rc1-2 (tags/RELEASE_35/rc1) (based on
LLVM 3.5.0)
diff -Naur dialign-t.orig/dialign-t-1.0.2/debian/changelog dialign-t/dialign-t-1.0.2/debian/changelog
--- dialign-t.orig/dialign-t-1.0.2/debian/changelog 2014-08-06 15:44:15.135034437 -0500
+++ dialign-t/dialign-t-1.0.2/debian/changelog 2014-08-06 15:52:44.235043303 -0500
@@ -1,3 +1,13 @@
+dialign-t (1.0.2-7) unstable; urgency=low
+
+ * Fix FTBFS with clang
+ - Fixed the undefined reference error in
+ source/alig.c
+ source/assemble.c
+ source/diag.c
+
+ -- Arthur Marble <art...@info9.net> Wed, 06 Aug 2014 15:52:44 -0500
+
dialign-t (1.0.2-6) unstable; urgency=medium
* debian/patches/consistent_declarations.patch: Make sure declarations
diff -Naur dialign-t.orig/dialign-t-1.0.2/debian/patches/clang-ftbfs.diff dialign-t/dialign-t-1.0.2/debian/patches/clang-ftbfs.diff
--- dialign-t.orig/dialign-t-1.0.2/debian/patches/clang-ftbfs.diff 1969-12-31 18:00:00.000000000 -0600
+++ dialign-t/dialign-t-1.0.2/debian/patches/clang-ftbfs.diff 2014-08-06 15:51:34.219042084 -0500
@@ -0,0 +1,78 @@
+--- 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;
diff -Naur dialign-t.orig/dialign-t-1.0.2/debian/patches/series dialign-t/dialign-t-1.0.2/debian/patches/series
--- dialign-t.orig/dialign-t-1.0.2/debian/patches/series 2014-08-06 15:44:15.135034437 -0500
+++ dialign-t/dialign-t-1.0.2/debian/patches/series 2014-08-06 15:44:40.243034875 -0500
@@ -1,3 +1,4 @@
prevent_enforcing_arch.patch
hardening.patch
consistent_declarations.patch
+clang-ftbfs.diff
