This bug was fixed in the package unattended-upgrades -
1.1ubuntu1.18.04.4

---------------
unattended-upgrades (1.1ubuntu1.18.04.4) bionic; urgency=medium

  * Redirect stderr output in upgrade-between-snapshots, too, otherwise it
    breaks the test sometimes (LP: #1781446)

unattended-upgrades (1.1ubuntu1.18.04.3) bionic; urgency=medium

  * Redirect stderr output in upgrade-all-security, otherwise it breaks the
    test (LP: #1781446)

unattended-upgrades (1.1ubuntu1.18.04.2) bionic; urgency=medium

  [ Balint Reczey ]
  * Clear cache when autoremoval is invalid for a package set marked for
    removal and clear cache after failed commits to return from a possibly
    invalid state (LP: #1779157)
  * Don't start or gracefully stop upgrade on battery (LP: #1773033)
  * Skip updates on metered connections (Closes: #855570) (LP: #1781183)
  * Add debian/tests/upgrade-all-security to install all current security 
updates.
    On development releases this tests latest stable, on stable releases it 
tests
    the release itself.
  * Speed up unattended-upgrade (Closes: #892028, #899366) (LP: #1396787)
    - Adjust candidates only for packages to be possibly installed
    - Filter out packages cheaper when they are not from allowed origins
    - Collect autoremovable packages, too, when looking for upgradable ones
    - Measure time of running with --dry-run in autopkgtests
  * Skip starting init.d script in debhelper-generated postinst part
    (LP: #1778800)

  [ Ivan Kurnosov ]
  * Fixed is_pkgname_in_blacklist to be side-effect free. (LP: #1781176)
    Otherwise 'is_pkgname_in_blacklist' mutates the 'pkgs_kept_back' and
    'unattended-upgrades' treats the package as a blacklisted candidate

 -- Balint Reczey <rbal...@ubuntu.com>  Fri, 13 Jul 2018 10:36:23 +0200

** Changed in: unattended-upgrades (Ubuntu Bionic)
       Status: Fix Committed => Fix Released

-- 
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Ubuntu.
https://bugs.launchpad.net/bugs/1781446

Title:
  Autopkgtest upgrade-all-security is failing due to apt printing to
  stderr in Bionic

Status in unattended-upgrades package in Ubuntu:
  Fix Released
Status in unattended-upgrades source package in Bionic:
  Fix Released

Bug description:
  [Impact] 
   * The following error can be seen in autopkgtest, holding back u-u from 
migration:
  
https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-bionic/bionic/amd64/u/unattended-upgrades/20180712_151033_c44d8@/log.gz
 :
  ...
  Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.36.11-2) ...
  W: APT had planned for dpkg to do more than it reported back (2370 vs 2372).
     Affected packages: fuse:amd64
  Reading package lists...
  ...
  autopkgtest [14:17:33]: test upgrade-all-security:  - - - - - - - - - - 
results - - - - - - - - - -
  upgrade-all-security FAIL stderr: W: APT had planned for dpkg to do more than 
it reported back (2370 vs 2372).
  autopkgtest [14:17:34]: test upgrade-all-security:  - - - - - - - - - - 
stderr - - - - - - - - - -
  W: APT had planned for dpkg to do more than it reported back (2370 vs 2372).
     Affected packages: fuse:amd64
  autopkgtest [14:17:34]: test upgrade-between-snapshots: preparing testbed
  ...

  [Test Case]

   * upgrade-all-security autopkgtest

  [Regression Potential]

   * Valid errors manifesting themselves only as output from stderr may
  not fail the autopkgtest.

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