[Debian-med-packaging] Bug#984067: fixed in ivar 1.3.1+dfsg-2

[Gianfranco Costamagna]

control: reopen -1
control: notfixed -1 1.3.1+dfsg-2


Hello, for some reasons now gcc-11 complains about a test failure:

g++  -g -O2 -ffile-prefix-map=/ivar-1.3.1+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror  -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o  -lhts -lz -lpthread
test_primer_trim_edge_cases.cpp: In function ‘main’:
test_primer_trim_edge_cases.cpp:75:18: error: ‘t.nlength’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   75 |     replace_cigar(aln, t.nlength, t.cigar);
      |                  ^
test_primer_trim_edge_cases.cpp:32:10: note: ‘t.nlength’ was declared here
   32 |   cigar_ t;
      |          ^
test_primer_trim_edge_cases.cpp:75:18: error: ‘t.cigar’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   75 |     replace_cigar(aln, t.nlength, t.cigar);
      |                  ^
test_primer_trim_edge_cases.cpp:32:10: note: ‘t.cigar’ was declared here
   32 |   cigar_ t;
      |          ^
lto1: all warnings being treated as errors
make[5]: *** [/tmp/ccpHmbdO.mk:2: /tmp/ccQWRY1X.ltrans0.ltrans.o] Error 1


this trivial patch looks like doing the trick

Description: Fix another gcc-11 build failure due to uninitialized variable
Author: Gianfranco Costamagna <locutusofborg at debian.org>
Bug-Debian: https://bugs.debian.org/984067
Forwarded:
Last-Update: 2021-09-22

--- ivar-1.3.1+dfsg.orig/tests/test_primer_trim_edge_cases.cpp
+++ ivar-1.3.1+dfsg/tests/test_primer_trim_edge_cases.cpp
@@ -29,7 +29,12 @@ int main(){
   hts_itr_t *iter = NULL;
   iter  = sam_itr_querys(idx, header, region_.c_str());
   bam1_t *aln = bam_init1();
-  cigar_ t;
+  cigar_ t = {
+    NULL,
+    false,
+    0,
+    0
+  };
   uint32_t *cigar;
   int primer_ctr = 0;
   int ctr = 0;

(taken from another test*.cpp file)

Gianfranco

> Done: Étienne Mollier <emollier at debian.org>
> 
> We believe that the bug you reported is fixed in the latest version of
> ivar, which is due to be installed in the Debian FTP archive.
> 
> A summary of the changes between this version and the previous one is
> attached.
> 
> Thank you for reporting the bug, which will now be closed.  If you
> have further comments please address them to 984067 at bugs.debian.org,
> and the maintainer will reopen the bug report if appropriate.
> 
> Debian distribution maintenance software
> pp.
> Étienne Mollier <emollier at debian.org> (supplier of updated ivar package)
> 
> (This message was generated automatically at their request; if you
> believe that there is a problem with it please contact the archive
> administrators by mailing ftpmaster at ftp-master.debian.org)
> 
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
> 
> Format: 1.8
> Date: Thu, 16 Sep 2021 22:22:30 +0200
> Source: ivar
> Architecture: source
> Version: 1.3.1+dfsg-2
> Distribution: unstable
> Urgency: medium
> Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Changed-By: Étienne Mollier <emollier at debian.org>
> Closes: 984067
> Changes:
>  ivar (1.3.1+dfsg-2) unstable; urgency=medium
>  .
>    * add forward-build-options.patch; build ivar with hardened build options
>    * add gcc-11.patch; fixes ftbfs with Gcc 11  (Closes: #984067)
>    * d/salsa-ci.yml: allow reproducible build test to fail, for the moment
>    * update d/s/lintian-overrides to match the new lintian semantics against the
>      false positive
>    * add privacy-breach.patch to point to the local diagram in cookbook.html,
>      instead of the github page
> Checksums-Sha1:
>  95b9fd79f7b7a78a1f4f399f3814838c0a736100 2090 ivar_1.3.1+dfsg-2.dsc
>  429ed8df0c78a138a323500afe331fa6457c9b0b 45332 ivar_1.3.1+dfsg-2.debian.tar.xz
>  834b1aaca42256116cbc2fe22c4e0111913585d6 6694 ivar_1.3.1+dfsg-2_amd64.buildinfo
> Checksums-Sha256:
>  b45c4f19a0d0ee3141cf18d35f1a2877aa20b268bc358f612e7e329baf58984a 2090 ivar_1.3.1+dfsg-2.dsc
>  18181d2fd9d2b90837cbc48ad79661e4a37e263267204ad20b37e537a691ad99 45332 ivar_1.3.1+dfsg-2.debian.tar.xz
>  7089d3a571b330a8a8291b17427a48ba1bf944d8087d35579333c5b7db8656db 6694 ivar_1.3.1+dfsg-2_amd64.buildinfo
> Files:
>  02fdcdde32dc41805245ac179842fe8b 2090 science optional ivar_1.3.1+dfsg-2.dsc
>  ebfd25824e275dac07cd6b2a0a071f53 45332 science optional ivar_1.3.1+dfsg-2.debian.tar.xz
>  286428a33a3c358d61230624fe3404b5 6694 science optional ivar_1.3.1+dfsg-2_amd64.buildinfo
> 
> -----BEGIN PGP SIGNATURE-----