Your message dated Mon, 28 Sep 2026 03:19:20 +0000
with message-id <[email protected]>
and subject line Bug#1144817: fixed in ncbi-entrez-direct 24.0.20250523+dfsg-3
has caused the Debian Bug report #1144817,
regarding ncbi-entrez-direct: autopkgtest fails under incus-lxc: run-unit-test
FAIL non-zero exit status 1
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.
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--
1144817: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1144817
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-entrez-direct
Version: 24.0.20250523+dfsg-2
Severity: important
Justification: fails autopkgtest on Debian CI infrastructure
Tags: forky sid
User: [email protected]
Usertags: lxc
Hi,
Debian CI is switching away from lxc containers in favor of incus Containers.
This is motivated by security concerns from us; incus is based on lxc, but
orchestrates containers substantially different: containers are not privileged
(so root in the container is not uid 0 outside of it, and incus imposes a
stricter isolation from the host system.
ncbi-entrez-direct passes its tests under lxc, but fails under incus.
The relevant part of the failure is (hopefully):
> [93m[1mTest 12: word-at-a-time[0m
> a
> about
> again
> all
> almost
> also
> although
> always
> among
> an
> [92m[1mPassed[0m
>
> [93m[1mTest 13: xml2tbl[0m
> >Feature AF068625.2
> 1 200 source
> organism Mus musculus
> mol_type mRNA
> db_xref taxon:10090
> chromosome 12
> map 4.0 cM
> 1 200 gene
> gene Dnmt3a
> [92m[1mPassed[0m
>
> [93m[1mTest 14: xtract[0m
>
> [0m[31m[1m[7m ERROR: [0m[31m[1m Input data from both stdin and file
> 'sample_query.xml', mode is 'prw-------'[0m
> autopkgtest [21:01:16]: test run-unit-test: -----------------------]
> autopkgtest [21:01:16]: test run-unit-test: - - - - - - - - - - results - -
> - - - - - - - -
> run-unit-test FAIL non-zero exit status 1
The full autokpgtest logs are available at:
https://ci.debian.net/experiments/8/regressions/
(please beware of pagination)
Common types of failure and suggested fixes are being documented at:
https://wiki.debian.org/ContinuousIntegration/LxcToIncus
Note that for the time being, ncbi-entrez-direct is still being tested under
lxc to
avoid disturbing its testing migration test results.
If you decide to add the `isolation-machine` restriction to get this package
tested under qemu, please mention that explicitly when closing this bug (it's
fine to do that only in the package changelog entry that closes the bug) so
that we can configure your package for qemu on ci.debian.net.
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--- End Message ---
--- Begin Message ---
Source: ncbi-entrez-direct
Source-Version: 24.0.20250523+dfsg-3
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ncbi-entrez-direct, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-entrez-direct 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 [email protected])
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Hash: SHA512
Format: 1.8
Date: Sun, 27 Sep 2026 22:58:29 -0400
Source: ncbi-entrez-direct
Architecture: source
Version: 24.0.20250523+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1144817
Changes:
ncbi-entrez-direct (24.0.20250523+dfsg-3) unstable; urgency=medium
.
* debian/tests/run-unit-test: Avoid nominal xtract input ambiguity when
overall standard input comes from a pipe or socket (as in Debian's new
Incus test beds) by hooking xtract's standard input up to /dev/null.
(Closes: #1144817.)
* Standards-Version: 4.7.4 (routine-update)
* Remove Priority field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Add missing ${misc:Static-Built-Using} to Static-Built-Using on
ncbi-entrez-direct.
* Remove redundant dependency from weaker field.
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