Bug#1023230: [Debian-med-packaging] Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours
Hi all, gregor herrmann, on 2022-11-01: > On Tue, 01 Nov 2022 09:12:43 +0900, Charles Plessy wrote: > > I think that t-coffee never worked on ARM. It built, but never worked. > > The simplest would be to distribute it only on amd64. > > See https://bugs.debian.org/631249 The program hogging CPU cycles on arm, ppc64el and s390x seemed symptomatic of the code assuming the type char is always signed. If I build t-coffee with -fsigned-char in the CFLAGS, it solves the issue on all those architectures for me. > Also https://bugs.debian.org/1022570 might be relevant. This is another problem in t-coffee, the aformentioned change is sufficient to fix the perl module. That being said, this also needs to be fixed. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. signature.asc Description: PGP signature
Processed: Re: Bug#1023230: [Debian-med-packaging] Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours
Processing control commands: > reassign -1 t-coffee 13.45.0.4846264+dfsg-1 Bug #1023230 [src:t-coffee, src:libbio-tools-run-alignment-tcoffee-perl] t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours Bug reassigned from package 'src:t-coffee, src:libbio-tools-run-alignment-tcoffee-perl' to 't-coffee'. No longer marked as found in versions libbio-tools-run-alignment-tcoffee-perl/1.7.4-3 and t-coffee/13.45.0.4846264+dfsg-1. Ignoring request to alter fixed versions of bug #1023230 to the same values previously set Bug #1023230 [t-coffee] t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours Marked as found in versions t-coffee/13.45.0.4846264+dfsg-1. -- 1023230: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1023230 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#1023230: [Debian-med-packaging] Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours
Control: reassign -1 t-coffee 13.45.0.4846264+dfsg-1 On Tue, 01 Nov 2022 09:12:43 +0900, Charles Plessy wrote: > Le Mon, Oct 31, 2022 at 09:27:47PM +0100, Paul Gevers a écrit : > > > > 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 > > I think that t-coffee never worked on ARM. It built, but never worked. > The simplest would be to distribute it only on amd64. > See https://bugs.debian.org/631249 Also https://bugs.debian.org/1022570 might be relevant. Reassigning to (only) t-coffee. Cheers, gregor -- .''`. https://info.comodo.priv.at -- Debian Developer https://www.debian.org : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D 85FA BB3A 6801 8649 AA06 `. `' Member VIBE!AT & SPI Inc. -- Supporter Free Software Foundation Europe `- NP: Rolling Stones: Letitrock signature.asc Description: Digital Signature
Bug#1023230: [Debian-med-packaging] Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours
Le Mon, Oct 31, 2022 at 09:27:47PM +0100, Paul Gevers a écrit : > > 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 Hi all, I think that t-coffee never worked on ARM. It built, but never worked. The simplest would be to distribute it only on amd64. See https://bugs.debian.org/631249 Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from work, https://mastodon.technology/@charles_plessy Tooting from home, https://framapiaf.org/@charles_plessy
Bug#1023230: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: test times out after 2:47 hours
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: passfail t-coffee from testing13.45.0.4846264+dfsg-1 libbio-tools-run-alignment-tcoffee-perl from testing1.7.4-3 all othersfrom testingfrom 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
