Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours

[Paul Gevers]

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-ci at 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

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