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):
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.

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 1144817@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Aaron M. Ucko <ucko@debian.org> (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 ftpmaster@ftp-master.debian.org)
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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <ucko@debian.org>
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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 64ac7fa6d46666feeb64deaf39afc33c63c116e0 54340 ncbi-entrez-direct_24.0.20250523+dfsg-3.debian.tar.xz
Checksums-Sha256:
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 c0e2cef5488aeb893a45e183d767556cfe87b56d36fadb408e227d9babbf5c3b 54340 ncbi-entrez-direct_24.0.20250523+dfsg-3.debian.tar.xz
Files:
 f58ea487f736249abe8d3ce0ed73d2e1 2800 science optional ncbi-entrez-direct_24.0.20250523+dfsg-3.dsc
 df3216dd0ed3490238edd5a14ee5e029 54340 science optional ncbi-entrez-direct_24.0.20250523+dfsg-3.debian.tar.xz
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Hello,

Unfortunately it still fails under incus-lxc while passing under plain
lxc, in a very similar (if not the same) way.

----------------8<----------------8<----------------8<-----------------
 35s Test 14: xtract
 35s
 35s  ERROR:  Input data from both stdin and file 'sample_query.xml', mode is 'prw-------'
----------------8<----------------8<----------------8<-----------------

Compare:

lxc       (pass): https://ci.debian.net/packages/n/ncbi-entrez-direct/testing/amd64/76260427/
incus-lxc (fail): https://ci.debian.net/packages/n/ncbi-entrez-direct/testing/amd64/76260428/

Hi, Antonio.

AFAICT, you accidentally retested the previous version:

 > 14s autopkgtest [21:54:20]: testing package ncbi-entrez-direct
version 24.0.20250523+dfsg-2

Per https://qa.debian.org/excuses.php?package=ncbi-entrez-direct, -3 hit
some unidentified migration delay.  Please wait for it to migrate or
retest against unstable.

I've reconfirmed locally that

   printf '' | bash .../run-unit-test

fails with the error in question when run-unit-test is from -2 but
succeeds with -3's version.

Ack, in that case I will just trut you and switch the package  away from
lxc. Thanks.