[Debian-med-packaging] Bug#1025249: wtdbg2: flaky autopkgtest: Segmentation fault

[Andreas Tille]

Hi Paul,

Am Thu, Dec 01, 2022 at 01:54:09PM +0100 schrieb Paul Gevers:
> https://ci.debian.net/data/autopkgtest/stable/ppc64el/w/wtdbg2/28644876/log.gz
> 
> [Sat Nov 26 06:40:02 2022] masked 154 repeat-like nodes by local subgraph
> analysis
> [Sat Nov 26 06:40:02 2022] generating edges
> /tmp/autopkgtest-lxc.t8xpx53w/downtmp/build.dY0/src/debian/tests/run-unit-test:
> line 23:  1447 Segmentation fault      wtdbg2 -x rs -g 4.6m -i
> pacbio_filtered.fastq -t 16 -fo dbg
> 
> 
> https://ci.debian.net/data/autopkgtest/testing/ppc64el/w/wtdbg2/27771576/log.gz
> 
> [Thu Nov  3 00:50:18 2022] sorting regs ...  Done
> [Thu Nov  3 00:50:19 2022] generating intervals ... /tmp/autopkgtest-lxc.wcfl1vkh/downtmp/build.kT7/src/debian/tests/run-unit-test:
> line 23:  1310 Segmentation fault      wtdbg2 -x rs -g 4.6m -i
> pacbio_filtered.fastq -t 16 -fo dbg

OK, I excluded ppc64el.
 
> https://ci.debian.net/data/autopkgtest/testing/arm64/w/wtdbg2/26361496/log.gz
> 
> [Fri Sep 23 22:33:59 2022] masked 154 repeat-like nodes by local subgraph
> analysis
> [Fri Sep 23 22:33:59 2022] generating edges
> /tmp/autopkgtest-lxc.7iunliwg/downtmp/build.Yi1/src/debian/tests/run-unit-test:
> line 23:  2686 Segmentation fault      wtdbg2 -x rs -g 4.6m -i
> pacbio_filtered.fastq -t 16 -fo dbg

I decided to restrict the package to amd64 only since this is the
architecture which is most probably used and tested by upstream.

BTW, the autopkgtest for riscv64 does not have "Segmentation fault"
but

  https://ci.debian.net/data/autopkgtest/unstable/riscv64/w/wtdbg2/27987776/log.gz

has:

1 contigs 2500 edges 0 basesautopkgtest [14:18:48]: 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.a93se6k6/downtmp/build.2Wn/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.a93se6k6/downtmp/run-unit-test-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.a93se6k6/downtmp/run-unit-test-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.a93se6k6/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.a93se6k6/downtmp/autopkgtest_tmp"; export ADTTMP="$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"; chmod +x /tmp/autopkgtest-lxc.a93se6k6/downtmp/build.2Wn/src/debian/tests/run-unit-test; exec /tmp/autopkgtest-lxc.a93se6k6/downtmp/wrapper.sh --script-pid-file=/tmp/autopkgtest_script_pid --stderr=/tmp/autopkgtest-lxc.a93se6k6/downtmp/run-unit-test-stderr --stdout=/tmp/autopkgtest-lxc.a93se6k6/downtmp/run-unit-test-stdout -- /tmp/autopkgtest-lxc.a93se6k6/downtmp/build.2Wn/src/debian/tests/run-unit-test ;" (kind: test)


This does not make the testing itself better, but I wanted to mention
this in case the debci setup needs to adjust some timeouts.

Kind regards
    Andreas.

-- 
http://fam-tille.de