[med-svn] [Git][med-team/wise][master] 7 commits: Fix clean target.
Santiago Vila (@sanvila)
gitlab at salsa.debian.org
Fri Feb 20 09:58:12 GMT 2026
Santiago Vila pushed to branch master at Debian Med / wise
Commits:
57127063 by Santiago Vila at 2026-02-20T10:39:00+01:00
Fix clean target.
- - - - -
89b2de3a by Santiago Vila at 2026-02-20T10:40:00+01:00
Fix old-fsf-address-in-copyright-file.
- - - - -
c45ed656 by Santiago Vila at 2026-02-20T10:41:00+01:00
d/control: Drop "Rules-Requires-Root: no" (default).
- - - - -
507781b7 by Santiago Vila at 2026-02-20T10:42:00+01:00
d/control: Drop "Priority: optional" (default).
- - - - -
e0663072 by Santiago Vila at 2026-02-20T10:43:00+01:00
d/control: Update standards-version.
- - - - -
66c90da9 by Santiago Vila at 2026-02-20T10:44:00+01:00
d/salsa-ci.yml: Use the simplified version.
- - - - -
fc6ae2ab by Santiago Vila at 2026-02-20T10:45:00+01:00
Upload for unstable as 2.4.1-28
- - - - -
7 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/side-effects.patch
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+wise (2.4.1-28) unstable; urgency=medium
+
+ * Team upload.
+ * Fix clean target.
+ * Fix old-fsf-address-in-copyright-file.
+ * Drop "Rules-Requires-Root: no" (default).
+ * Drop "Priority: optional" (default).
+ * Update standards-version.
+ * Simplify salsa-ci.yml.
+
+ -- Santiago Vila <sanvila at debian.org> Thu, 19 Feb 2026 21:03:40 +0100
+
wise (2.4.1-27) unstable; urgency=medium
* Team upload.
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+src/dyc/dyc
=====================================
debian/control
=====================================
@@ -4,7 +4,6 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
texlive-latex-base,
texlive-extra-utils,
@@ -12,11 +11,10 @@ Build-Depends: debhelper-compat (= 13),
docbook-to-man,
libglib2.0-dev,
libfl-dev
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
Homepage: https://www.ebi.ac.uk/~birney/wise2/
-Rules-Requires-Root: no
Package: wise
Architecture: any
=====================================
debian/copyright
=====================================
@@ -80,8 +80,7 @@ License: GPL-2+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ with this program; if not, see <https://www.gnu.org/licenses/>.
Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public
License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the
complete text of the GNU Lesser General Public License can be found in
=====================================
debian/patches/series
=====================================
@@ -16,3 +16,4 @@ executable-is-script.patch
gcc-14.patch
fix_blhc.patch
fix_ftbfs_with_gcc-15.patch
+side-effects.patch
=====================================
debian/patches/side-effects.patch
=====================================
@@ -0,0 +1,192 @@
+From: Santiago Vila <sanvila at debian.org>
+Subject: Apply changes to generated files
+
+--- a/src/dnaindex/compressed_protein_index.c
++++ b/src/dnaindex/compressed_protein_index.c
+@@ -199,7 +199,7 @@
+ {
+ fatal("For compressed protein indexes, impossible to add numbers directly");
+
+- return NULL;
++ return FALSE;
+ }
+
+ # line 226 "compressed_protein_index.dy"
+--- a/src/dnaindex/kmer_assembly_error.c
++++ b/src/dnaindex/kmer_assembly_error.c
+@@ -7,9 +7,9 @@
+ # line 14 "kmer_assembly_error.dy"
+ boolean lift_indel_error_KmerAssembly(KmerAssemblyIndex * kai,KmerAssemblyPath * real,KmerAssemblyPath * error,long int * start_labels,int label_len,int error_position,int error_len)
+ {
+- int i,j,k,true;
++ int i,j,k,true_int;
+
+- for(i=0,true=0;i<error->stack_len && true<real->stack_len;i++,true++) {
++ for(i=0,true_int=0;i<error->stack_len && true_int<real->stack_len;i++,true_int++) {
+ if( i == error_position ) {
+ if( error_len > 0 ) {
+ for(j=0;j<error_len;) {
+@@ -19,7 +19,7 @@
+ } else {
+ error_len = abs(error_len);
+ for(j=0;j<error_len;) {
+- true++;
++ true_int++;
+ j++;
+ }
+ }
+@@ -33,10 +33,10 @@
+ remove_sequence_label_KmerAssemblyLink(error->stack[i],start_labels[k]+i);
+ }
+
+- if( real->stack[true] == NULL ) {
++ if( real->stack[true_int] == NULL ) {
+ fprintf(stderr,"issue - true path is missing a link!");
+ } else {
+- add_sequence_label_KmerAssemblyLink(real->stack[true],start_labels[k]+i);
++ add_sequence_label_KmerAssemblyLink(real->stack[true_int],start_labels[k]+i);
+ }
+ if( error->stack[i] != NULL && error->stack[i]->sequence_label_len == 0 ) {
+ detach_KmerAssemblyLink(kai,error->stack[i]);
+@@ -416,7 +416,7 @@
+
+
+ /* recursively call for each possible path: if any return
+- true, return TRUE */
++ true_int, return TRUE */
+
+ /* fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
+
+@@ -545,7 +545,7 @@
+
+
+ /* recursively call for each possible path: if any return
+- true, return TRUE */
++ true_int, return TRUE */
+
+ /* fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
+
+--- a/src/dnaindex/kmer_assembly_untangler.c
++++ b/src/dnaindex/kmer_assembly_untangler.c
+@@ -547,7 +547,14 @@
+
+ if( have_link == 1 ) {
+ /* fprintf(stderr," ..reverse TAIL.. untangling...\n"); */
+- lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
++ lift_backward_tangled_tail(
++ kai,
++ newpath->stack[newpath->stack_len-1],
++ path,
++ (int*)transferred_label,
++ transferred_pos,
++ transferred_len
++ );
+ }
+
+ /* pop off the top of this path */
+@@ -578,7 +585,7 @@
+ }
+
+
+-# line 599 "kmer_assembly_untangler.dy"
++# line 606 "kmer_assembly_untangler.dy"
+ void lift_forward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyPath * tail,long int * start_label,int label_len)
+ {
+ int i;
+@@ -640,7 +647,7 @@
+
+
+
+-# line 660 "kmer_assembly_untangler.dy"
++# line 667 "kmer_assembly_untangler.dy"
+ void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len)
+ {
+ int i;
+@@ -698,7 +705,7 @@
+ /* finished lift */
+ }
+
+-# line 717 "kmer_assembly_untangler.dy"
++# line 724 "kmer_assembly_untangler.dy"
+ KmerAssemblyPath * lift_forward_tangled_KmerAssemblyPath(KmerAssemblyIndex * kai,KmerAssemblyPath * kap,long int * start_label,int label_len)
+ {
+ int i,j;
+@@ -779,7 +786,7 @@
+
+
+
+-# line 781 "kmer_assembly_untangler.c"
++# line 788 "kmer_assembly_untangler.c"
+ /* Function: hard_link_KmerAssemblyPath(obj)
+ *
+ * Descrip: Bumps up the reference count of the object
+--- a/src/models/est_evidence.c
++++ b/src/models/est_evidence.c
+@@ -115,7 +115,7 @@
+ in->utr_pot = est_utr_pot;
+ in->cds_intron_pot = est_intron_pot;
+ in->utr_intron_pot = est_intron_pot;
+- in->geu_free = free_EstEvidence;
++ in->geu_free = (int(*)(void*))free_EstEvidence;
+ in->frameshift_cds = est_cds_frameshift;
+ in->stop_pot = est_stop_pot;
+ in->start_pot = est_start_pot;
+--- a/src/models/genewisehsp.c
++++ b/src/models/genewisehsp.c
+@@ -262,30 +262,30 @@
+
+
+ # line 291 "genewisehsp.dy"
+-int consistent_GeneWiseHSP(GeneWiseHSP * true,GeneWiseHSP * proposed)
++int consistent_GeneWiseHSP(GeneWiseHSP * true_val,GeneWiseHSP * proposed)
+ {
+ int query_centre;
+ int target_centre;
+
+- assert(true);
++ assert(true_val);
+ assert(proposed);
+ /* is this left or right of the true HSP */
+ query_centre = (proposed->query_start + proposed->query_end) / 2;
+ target_centre = (proposed->target_start + proposed->target_end) / 2;
+
+ /* overlap criteria first */
+- if( query_centre >= true->query_start && query_centre <= true->query_end ) {
++ if( query_centre >= true_val->query_start && query_centre <= true_val->query_end ) {
+ return 0;
+ }
+
+ /* left or right */
+- if( query_centre > true->query_end ) {
+- if( target_centre < true->target_end ) {
++ if( query_centre > true_val->query_end ) {
++ if( target_centre < true_val->target_end ) {
+ /* no - inconsistent */
+ return 0;
+ }
+ } else {
+- if( target_centre > true->target_start ) {
++ if( target_centre > true_val->target_start ) {
+ return 0;
+ }
+ }
+@@ -293,7 +293,7 @@
+
+ /* overlap */
+
+- if( target_centre >= true->target_start && target_centre <= true->target_end ) {
++ if( target_centre >= true_val->target_start && target_centre <= true_val->target_end ) {
+ return 0;
+ }
+
+--- a/src/socket/functionclient.c
++++ b/src/socket/functionclient.c
+@@ -181,7 +181,7 @@
+ bcopy( hp->h_addr, &server.sin_addr, hp->h_length);
+ server.sin_port = htons(port);
+
+- connect(out->socket, &server, sizeof(server));
++ connect(out->socket, (const struct sockaddr *)&server, sizeof(server));
+
+
+ return out;
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
---
include:
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/6183e375cd851090561c45f920a9a3cce5bece7d...fc6ae2abc4001f71eeb82a0b8281d9fcf8aa9a64
--
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/6183e375cd851090561c45f920a9a3cce5bece7d...fc6ae2abc4001f71eeb82a0b8281d9fcf8aa9a64
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