Re: migration to htslib ecosystem 1.18

Hi Étienne,

Am Wed, Nov 08, 2023 at 09:44:22AM +0100 schrieb Étienne Mollier:
> > I'd like to rewrite bcftools autopkgtest according to the model of
> > samtools.  However, we need a new binary package bcftools-test which I
> > rather delay util the set of packages has migrated to testing.
> 
> Great, thanks for bumping all these!  :)

No problem.  I also dived into the rdepends of libhts3 and stubled
upon kallisto which has a new upstream version.  I tried to upgrade
to this but there is a cmake issue[1]:

CMake Error at src/CMakeLists.txt:20 (ExternalProject_Get_Property):
  Unknown CMake command "ExternalProject_Get_Property".
-- Configuring incomplete, errors occurred!

I guess it is connected to the internal code copy of bifrost which
I just packaged[2] (will try a short autopkgtest before uploading
to new)


We probably also need to talk to debci people since the upload of
htslib has triggered a failing test for jellyfish on arm64[3].  When
looking at the log[4] it ends with

...
182s [ RUN      ] CooperativePool/CooperativePoolTest.Ints/9
10051s autopkgtest [06:02:56]: ERROR: timed out on command "su -s /bin/bash debci -c set -e; exec /tmp/autopkgtest-lxc.xayqrapq/downtmp/wrapper.sh --artifacts=/tmp/autopkgtest-lxc.xayqrapq/downtmp/run-unit-test-artifacts --chdir=/tmp/autopkgtest-lxc.xayqrapq/downtmp/build.N8X/src --env=DEB_BUILD_OPTIONS=parallel=4 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest-lxc.xayqrapq/downtmp/run-unit-test-stderr --stdout=/tmp/autopkgtest-lxc.xayqrapq/downtmp/run-unit-test-stdout --tmp=/tmp/autopkgtest-lxc.xayqrapq/downtmp/autopkgtest_tmp --make-executable=/tmp/autopkgtest-lxc.xayqrapq/downtmp/build.N8X/src/debian/tests/run-unit-test -- /tmp/autopkgtest-lxc.xayqrapq/downtmp/build.N8X/src/debian/tests/run-unit-test" 


These timeout thingies are really hard to debug.  Maybe we should simply
shorten the jellyfish test suite to avoid this.  For instance droping
the `/usr/lib/jellyfish/bin/test_all` call at the end makes the test
more sensible (also in terms of not stressing debci infrastructure to
much?

What do you think?

Kind regards
    Andreas.


[1] https://salsa.debian.org/med-team/kallisto/-/jobs/4901979#L1704
[2] https://salsa.debian.org/med-team/bifrost
[3] https://tracker.debian.org/pkg/htslib
[4] https://ci.debian.net/data/autopkgtest/testing/arm64/j/jellyfish/39674223/log.gz

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