[med-svn] [Git][med-team/ivar][master] 7 commits: initialize changelog.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ivar


Commits:
897f6266 by Étienne Mollier at 2022-07-12T22:38:50+02:00
initialize changelog.

- - - - -
c86f5989 by Étienne Mollier at 2022-07-12T23:05:54+02:00
Add gcc-12.patch: fix ftbfs with gcc-12.

Closes: #1012952

- - - - -
0d8d520a by Étienne Mollier at 2022-07-12T23:06:32+02:00
update changelog

- - - - -
7caed869 by Étienne Mollier at 2022-07-12T23:06:51+02:00
routine-update: Standards-Version: 4.6.1

- - - - -
6abb2e66 by Étienne Mollier at 2022-07-12T23:08:23+02:00
routine-update: Ready to upload to unstable

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21970eb8 by Étienne Mollier at 2022-07-12T23:10:27+02:00
d/s/lintian-overrides: update to new lintian semantics.

- - - - -
80b59937 by Étienne Mollier at 2022-07-12T23:12:13+02:00
update changelog

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc-12.patch
- debian/patches/series
- debian/source/lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+ivar (1.3.1+dfsg-5) unstable; urgency=medium
+
+  * Add gcc-12.patch: fix ftbfs with gcc-12. (Closes: #1012952)
+  * Standards-Version: 4.6.1 (routine-update)
+  * d/s/lintian-overrides: update to new lintian semantics.
+
+ -- Étienne Mollier <emollier at debian.org>  Tue, 12 Jul 2022 23:11:44 +0200
+
 ivar (1.3.1+dfsg-4) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libhts-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/ivar
 Vcs-Git: https://salsa.debian.org/med-team/ivar.git
 Homepage: https://github.com/andersen-lab/ivar


=====================================
debian/patches/gcc-12.patch
=====================================
@@ -0,0 +1,31 @@
+Description: fix ftbfs with gcc-12.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012952
+Forwarded: no
+Last-Update: 2022-07-12
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ivar.orig/src/call_consensus_pileup.h
++++ ivar/src/call_consensus_pileup.h
+@@ -5,6 +5,7 @@
+ #include<vector>
+ #include<algorithm>
+ #include<string>
++#include<string.h>
+ #include<regex>
+ #include<libgen.h>
+ 
+--- ivar.orig/src/ivar.cpp
++++ ivar/src/ivar.cpp
+@@ -482,9 +482,9 @@
+       res = common_variants(g_args.prefix, g_args.min_threshold, files, nfiles);
+       // Free files, nfiles
+       for (int i = 0; i < nfiles; ++i) {
+-	free(files[i]);
++        free(files[i]);
+       }
+-      delete files;
++      delete[] files;
+     } else {
+       res = common_variants(g_args.prefix, g_args.min_threshold, argv + optind, argc - optind);
+     }


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ forward-build-options.patch
 gcc-11.patch
 gcc-11_2.patch
 privacy-breach.patch
+gcc-12.patch


=====================================
debian/source/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
 # False positive
-ivar source: source-is-missing docs/html/menu.js line 26 is 695 characters long (>512)
+ivar source: source-is-missing [docs/*]



View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/c799ef2cba472c9cf8686b30f2e8f6dab3f8d5ce...80b59937b69d8f20c6415dac8c7f744dec7185b7

-- 
View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/c799ef2cba472c9cf8686b30f2e8f6dab3f8d5ce...80b59937b69d8f20c6415dac8c7f744dec7185b7
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