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 <[email protected]> Tue, 15 Oct 2024 21:02:47 +0200 + -- Pierre Gruet <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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