[med-svn] [Git][med-team/ghmm][master] 5 commits: buildError.patch: unfuzz.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ghmm


Commits:
8c2250a8 by Étienne Mollier at 2024-07-16T21:52:04+02:00
buildError.patch: unfuzz.

- - - - -
fb8774c8 by Étienne Mollier at 2024-07-16T21:52:50+02:00
d/control: add myself to uploaders.

- - - - -
28174ed0 by Étienne Mollier at 2024-07-16T21:53:10+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
f7e557dd by Étienne Mollier at 2024-07-16T22:05:11+02:00
gcc-14.patch: new: fix a pointer declaration in tests/mcmc.c.

Closes: #1074994

- - - - -
32dff19b by Étienne Mollier at 2024-07-16T22:06:39+02:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/buildError.patch
- + debian/patches/gcc-14.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+ghmm (0.9~rc3-8) unstable; urgency=medium
+
+  * buildError.patch: unfuzz.
+  * d/control: add myself to uploaders.
+  * d/control: declare compliance to standards version 4.7.0.
+  * gcc-14.patch: new: fix a pointer declaration in tests/mcmc.c.
+    (Closes: #1074994)
+
+ -- Étienne Mollier <emollier at debian.org>  Tue, 16 Jul 2024 22:05:51 +0200
+
 ghmm (0.9~rc3-7) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: ghmm
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
@@ -13,7 +14,7 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
                liblapacke-dev,
                zlib1g-dev,
                swig
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/ghmm
 Vcs-Git: https://salsa.debian.org/med-team/ghmm.git
 Homepage: https://sourceforge.net/p/ghmm/wiki/Home/


=====================================
debian/patches/buildError.patch
=====================================
@@ -2,11 +2,9 @@ Author: Steffen Möller
 Last-Update: 2018-05-23 20:24:29 +0200
 Desctiption: Fix format security issue
 
-Index: ghmm-0.9~rc3/ghmm/xmlwriter.c
-===================================================================
---- ghmm-0.9~rc3.orig/ghmm/xmlwriter.c
-+++ ghmm-0.9~rc3/ghmm/xmlwriter.c
-@@ -353,7 +353,7 @@ static int writeDiscreteStateContents(xm
+--- ghmm.orig/ghmm/xmlwriter.c
++++ ghmm/ghmm/xmlwriter.c
+@@ -354,7 +354,7 @@
      bgId = f->model.d[moNo]->background_id[sNo];
      if (bgId != GHMM_kNoBackgroundDistribution) {
         if (f->model.d[moNo]->bp->name[bgId]) { 


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,32 @@
+Description: fix pointer indirection level in tests/mcmc.c.
+ Attempts to build ghmm with gcc 14 end up with the following error:
+ .
+  mcmc.c: In function ‘main’:
+  mcmc.c:148:15: error: initialization of ‘int *’ from incompatible pointer type ‘int **’ [-Wincompatible-pointer-types]
+    148 |   int * Q =   ghmm_dmodel_cfbgibbs(mo, my_output,
+        |               ^~~~~~~~~~~~~~~~~~~~
+  mcmc.c:150:108: error: passing argument 4 of ‘ghmm_dmodel_viterbi_logp’ makes pointer from integer without a cast [-Wint-conversion]
+    150 |   printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0]));
+        |                                                                                                           ~^~~
+        |                                                                                                            |
+        |                                                                                                            int
+ .
+ This looks to be caused by a missing '*' in Q declaration.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1074994
+Forwarded: no
+Last-Update: 2024-07-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ghmm.orig/tests/mcmc.c
++++ ghmm/tests/mcmc.c
+@@ -145,7 +145,7 @@
+   double *pPi = NULL;
+   init_priors(mo, &pA, &pB, &pPi);
+   int iter = 100;
+-  int * Q =   ghmm_dmodel_cfbgibbs(mo, my_output,
++  int **Q =   ghmm_dmodel_cfbgibbs(mo, my_output,
+                         pA, pB, pPi,2, iter, 0);
+   printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0]));
+   printf("likelihood mcmc%f \n", ghmm_dmodel_likelihood(mo, my_output));


=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ python3_syntax.patch
 # setuptools.patch
 fix-test-mcmc.patch
 python3.12.patch
+gcc-14.patch



View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/673a4806277ac65f8325823eca5d33df5a089578...32dff19b2af1930afcb2d166b458d5f2786fd6c7

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