[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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