[Debian-med-packaging] Bug#1144817: ncbi-entrez-direct: autopkgtest fails under incus-lxc: run-unit-test FAIL non-zero exit status 1

[Antonio Terceiro]

Source: ncbi-entrez-direct
Version: 24.0.20250523+dfsg-2
Severity: important
Justification: fails autopkgtest on Debian CI infrastructure
Tags: forky sid
User: debian-ci at lists.debian.org
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):

> Test 12: word-at-a-time
> a
> about
> again
> all
> almost
> also
> although
> always
> among
> an
> Passed
> 
> Test 13: xml2tbl
> >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
> Passed
> 
> Test 14: xtract
> 
>  ERROR:  Input data from both stdin and file 'sample_query.xml', mode is 'prw-------'
> 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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