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 <locutusofb...@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 <emoll...@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 984...@bugs.debian.org,
> and the maintainer will reopen the bug report if appropriate.
>
> Debian distribution maintenance software
> pp.
> Étienne Mollier <emoll...@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 ftpmas...@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-packag...@lists.alioth.debian.org>
> Changed-By: Étienne Mollier <emoll...@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-----
