Dear Amarendran, six year after my previous email to you, DIALIGN and DIALIGN-TX are still distributed in Debian, where they have a stable user base as you can see from the graph at the link below.
https://qa.debian.org/popcon-graph.php?packages=dialign-tx+dialign&show_vote=on&want_legend=on&beenhere=1 We run frequently quality tests over the whole Debian archive, and one of them let to the production of a patch to compile DIALIGN-TX with Clang. You can refer to the message below for details. A clean version of the patch can be downloaded from the following link. https://bugs.debian.org/cgi-bin/bugreport.cgi?msg=5;filename=undef-ref.patch;att=1;bug=757281 Also, in a previous quality control run by a third party, some crashes were found. You an see details at the following URL. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=715816 Have a nice day, -- Charles Plessy, Debian Med packaging team, Tsurumi, Kanagawa, Japan. Le Wed, Aug 06, 2014 at 03:57:26PM -0500, Arthur Marble a écrit : > 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 > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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