Your message dated Fri, 25 Nov 2022 10:40:25 +0000
with message-id <e1oyw89-000gku...@fasolo.debian.org>
and subject line Bug#1023230: fixed in t-coffee
13.45.0.4846264+really13.41.0.28bdc39+dfsg-1
has caused the Debian Bug report #1023230,
regarding t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest:
test times out after 2:47 hours
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1023230: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1023230
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: t-coffee, libbio-tools-run-alignment-tcoffee-perl
Control: found -1 t-coffee/13.45.0.4846264+dfsg-1
Control: found -1 libbio-tools-run-alignment-tcoffee-perl/1.7.4-3
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of t-coffee the autopkgtest of
libbio-tools-run-alignment-tcoffee-perl fails in testing on all
architectures but amd64 and i386 when that autopkgtest is run with the
binary packages of t-coffee from unstable. It passes when run with only
packages from testing. In tabular form:
pass fail
t-coffee from testing 13.45.0.4846264+dfsg-1
libbio-tools-run-alignment-tcoffee-perl from testing 1.7.4-3
all others from testing from testing
I copied some of the output at the bottom of this report. There's
nothing there, it just waits for the timeout after 2:47h.
Currently this regression is blocking the migration of t-coffee to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=t-coffee
https://ci.debian.net/data/autopkgtest/testing/arm64/libb/libbio-tools-run-alignment-tcoffee-perl/27686780/log.gz
autopkgtest [11:59:24]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true; . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.l1eqkc21/downtmp/build.05l/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autodep8-perl-build-deps-artifacts";
export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autodep8-perl-build-deps-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=4; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;cd "$buildtree"; exec
/tmp/autopkgtest-lxc.l1eqkc21/downtmp/wrapper.sh
--script-pid-file=/tmp/autopkgtest_script_pid
--stderr=/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autodep8-perl-build-deps-stderr
--stdout=/tmp/autopkgtest-lxc.l1eqkc21/downtmp/autodep8-perl-build-deps-stdout
-- bash -ec '/usr/share/pkg-perl-autopkgtest/runner build-deps' ;"
(kind: test)
autopkgtest [11:59:24]: test autodep8-perl-build-deps
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: t-coffee
Source-Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
t-coffee, 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 1023...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated t-coffee 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: Fri, 25 Nov 2022 11:13:19 +0100
Source: t-coffee
Architecture: source
Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1022570 1023230
Changes:
t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) unstable;
urgency=medium
.
[ Étienne Mollier ]
* d/t/run-unit-test: don't meddle with user's home.
* d/rules: build with -fsigned-char.
This fixes infinite loops on CPU architectures defaulting to the char
type being unsigned, such as on arm*, ppc* and s390*. (Closes: #1023230)
* d/control: add myself to uploaders.
.
[ Andreas Tille ]
* Revert version bump to latest upstream version until
https://github.com/cbcrg/tcoffee/issues/56
is closed.
Closes: #1022570
* Keep updated patches in debian/patches dir with suffix .13.45.0.4846264
to ease upgrading to the new version once it is ready
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