[med-svn] [Git][med-team/psortb][master] 4 commits: add_missing_header.patch: supplement to finish fixing ftbfs.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / psortb


Commits:
a9d6e0bb by Étienne Mollier at 2024-05-26T09:28:47+02:00
add_missing_header.patch: supplement to finish fixing ftbfs.

- - - - -
55ccf8d2 by Étienne Mollier at 2024-05-26T09:31:36+02:00
d/control: add myself to uploaders.

- - - - -
8516432f by Étienne Mollier at 2024-05-26T09:31:55+02:00
d/control: migrate to pkgconf.

- - - - -
a2a335af by Étienne Mollier at 2024-05-26T09:51:31+02:00
ready to upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/patches/add_missing_header.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,16 @@
-psortb (3.0.6+dfsg-4) UNRELEASED; urgency=medium
+psortb (3.0.6+dfsg-4) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Add missing header file
     Closes: #1070459
   * Standards-Version: 4.7.0 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Mon, 06 May 2024 15:57:40 +0200
+  [ Étienne Mollier ]
+  * add_missing_header.patch: supplement to finish fixing ftbfs.
+  * d/control: add myself to uploaders.
+  * d/control: migrate to pkgconf.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 26 May 2024 09:32:14 +0200
 
 psortb (3.0.6+dfsg-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: psortb
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Testsuite: autopkgtest-pkg-perl
 Priority: optional
@@ -12,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
                libhmmer2-dev,
                libsvmloc-dev,
                libmodhmm-dev,
-               pkg-config,
+               pkgconf,
                pftools,
 Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/psortb


=====================================
debian/patches/add_missing_header.patch
=====================================
@@ -1,13 +1,37 @@
-Description: Add missing header file
+Description: Add missing header files
+ The patch also complements the funcs.h header file so the Perl XS file
+ knows what find_helices is.  For the record, it is defined in
+ libmodhmm-dev, there is probably some much needed cleanup to do).
+
 Bug-Debian: https://bugs.debian.org/1070459
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 May 2024 15:57:40 +0200
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Last-Update: 2024-05-06
 
---- a/bio-tools-psort-modhmm/binding.c
-+++ b/bio-tools-psort-modhmm/binding.c
+--- psortb.orig/bio-tools-psort-modhmm/binding.c
++++ psortb/bio-tools-psort-modhmm/binding.c
 @@ -1,4 +1,5 @@
  #include <stdio.h>
 +#include <stdlib.h>
  
  #include "modhmm0.92b/structs.h"
  
+--- psortb.orig/bio-tools-psort-modhmm/modhmm0.92b/funcs.h
++++ psortb/bio-tools-psort-modhmm/modhmm0.92b/funcs.h
+@@ -300,3 +300,6 @@
+ void dump_subst_mtx(int a_size, double *mtx);
+ void dump_multi_modules(struct hmm_multi_s *hmmp);
+ void dump_weights(double *total_weights, int nr_seqs);
++
++/* hmmsearch */
++int find_helices(char* seq, char* hmmfilename, char* repfilename, char* path);
+--- psortb.orig/bio-tools-psort-modhmm/modhmm.xs
++++ psortb/bio-tools-psort-modhmm/modhmm.xs
+@@ -2,6 +2,7 @@
+ #include "perl.h"
+ #include "XSUB.h"
+ #include "modhmm0.92b/structs.h"
++#include "modhmm0.92b/funcs.h"
+ 
+ MODULE = Bio::Tools::PSort::ModHMM	PACKAGE = Bio::Tools::PSort::ModHMM
+ 



View it on GitLab: https://salsa.debian.org/med-team/psortb/-/compare/d94c46799a5a6906708478730f02bda5be3b7df2...a2a335afecd76c98ece34d6116691529723d032c

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