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 <[email protected]> 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 <[email protected]> -Uploaders: Steffen Moeller <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, + Étienne Mollier <[email protected]> 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 <[email protected]> +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 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/673a4806277ac65f8325823eca5d33df5a089578...32dff19b2af1930afcb2d166b458d5f2786fd6c7 You're receiving this email because of your account on salsa.debian.org.
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