[med-svn] [Git][med-team/vienna-rna][master] 6 commits: Adding perl-xs-dev to Build-Depends

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Sat Sep 20 22:43:01 BST 2025



Pierre Gruet pushed to branch master at Debian Med / vienna-rna


Commits:
6387a17f by Pierre Gruet at 2025-09-06T17:23:49+02:00
Adding perl-xs-dev to Build-Depends

- - - - -
06ad964f by Pierre Gruet at 2025-09-06T17:24:01+02:00
Raising Standards version to 4.7.2 (no change)

- - - - -
59920a85 by Pierre Gruet at 2025-09-20T22:57:50+02:00
Building with gcc-15

- - - - -
d6d340a2 by Pierre Gruet at 2025-09-20T22:58:13+02:00
Adding missing inclusion of parent directory to find headers

- - - - -
cba05573 by Pierre Gruet at 2025-09-20T22:58:57+02:00
Updating changelog

- - - - -
fe625cf3 by Pierre Gruet at 2025-09-20T22:59:30+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc-15.patch
- + debian/patches/missing_include_header.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,12 +1,15 @@
-vienna-rna (2.7.0+dfsg-1) UNRELEASED; urgency=medium
+vienna-rna (2.7.0+dfsg-1) unstable; urgency=medium
 
+  * Team upload
   * New upstream version 2.7.0+dfsg
   * Refreshing patches
-  * Raising Standards version to 4.7.0 (no change)
+  * Raising Standards version to 4.7.2 (no change)
   * Updating the list of files to remove when repacking
-  TODO: build fails, certainly missing -I flags for the compiler
+  * Adding perl-xs-dev to Build-Depends (Closes: #1102852)
+  * Building with gcc-15 (Closes: #1114434)
+  * Adding missing inclusion of parent directory to find headers
 
- -- Pierre Gruet <pgt at debian.org>  Tue, 15 Oct 2024 21:02:47 +0200
+ -- Pierre Gruet <pgt at debian.org>  Sat, 20 Sep 2025 22:59:19 +0200
 
 vienna-rna (2.6.4+dfsg-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -20,6 +20,7 @@ Build-Depends: debhelper-compat (= 13),
                liblapack-dev,
                libmpfr-dev,
                libsvm-dev,
+               perl-xs-dev,
                xxd,
                texlive-latex-extra,
                help2man,
@@ -29,7 +30,7 @@ Build-Depends: debhelper-compat (= 13),
                doxygen,
                texinfo
 #               libg2-dev,
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/vienna-rna
 Vcs-Git: https://salsa.debian.org/med-team/vienna-rna.git
 Homepage: https://www.tbi.univie.ac.at/RNA/


=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,34 @@
+Description: building with gcc-15: putting the list of argument types in
+ prototypes
+Author: Pierre Gruet <pgt at debian.org>
+Bug-Debian: https://bugs.debian.org/1114434
+Forwarded: no
+Last-Update: 2025-09-20
+
+--- a/src/ViennaRNA/datastructures/lists.h
++++ b/src/ViennaRNA/datastructures/lists.h
+@@ -55,11 +55,11 @@
+ /*@only@*//*@out@*/ void *lst_newnode (int size);
+ void lst_freenode (/*@only@*/ void *node);
+ /*@only@*//*@out@*/  LIST *lst_init (void);
+-void lst_kill (LIST * l, void (*freeNode) ());
++void lst_kill (LIST * l, void (*freeNode) (void *));
+ void lst_insertafter (LIST * l, /*@keep@*/ void *node, void *after);
+ void *lst_deletenext (/*@only@*/ LIST * l, void *node);
+ /*@dependent@*/ void *lst_first (LIST * l);
+ /*@dependent@*/ void *lst_next (void *prev);
+-void lst_mergesort (LIST * l, int (*cmp_func) ());
++void lst_mergesort (LIST * l, int (*cmp_func) (void*, void*));
+ 
+ #endif
+--- a/src/ViennaRNA/subopt/subopt.c
++++ b/src/ViennaRNA/subopt/subopt.c
+@@ -628,7 +628,7 @@
+        * fprintf(stderr, "maxlevel: %d\n", maxlevel);
+        */
+ 
+-      lst_kill(env->Stack, free_state_node);
++      lst_kill(env->Stack, (void*)free_state_node);
+ 
+       cb(NULL, 0, data);   /* NULL (last time to call callback function */
+ 


=====================================
debian/patches/missing_include_header.patch
=====================================
@@ -0,0 +1,19 @@
+Description: adding missing inclusion of parent directory in the cflags
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2025-09-20
+
+--- a/src/ViennaRNA/Makefile.am
++++ b/src/ViennaRNA/Makefile.am
+@@ -2,9 +2,9 @@
+ 
+ include $(top_srcdir)/silent_rules.mk
+ 
+-AM_CFLAGS = $(RNA_CFLAGS) $(PTHREAD_CFLAGS)
++AM_CFLAGS = $(RNA_CFLAGS) -I../ $(PTHREAD_CFLAGS)
+ AM_CXXFLAGS = $(RNA_CXXFLAGS) $(PTHREAD_CFLAGS)
+-AM_CPPFLAGS = $(RNA_CPPFLAGS) -I$(top_srcdir)/src ${JSON_INC}
++AM_CPPFLAGS = $(RNA_CPPFLAGS) -I../ -I$(top_srcdir)/src ${JSON_INC}
+ AM_LDFLAGS = $(RNA_LDFLAGS) $(PTHREAD_LIBS)
+ 
+ SUBDIRS = static @NAVIEW_DIR@


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
 g2.patch
 use_debian_packaged_dlib.patch
 python3.11.patch
+gcc-15.patch
+missing_include_header.patch



View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/257a580c08535ede00731037473def992ca3d1b8...fe625cf3ae31c49e93ce258e224664dad5cde83b

-- 
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/257a580c08535ede00731037473def992ca3d1b8...fe625cf3ae31c49e93ce258e224664dad5cde83b
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