Cron job removes packages althought a package manager could be running

(Adrian your X problem is probably due to the NVIDIA binary driver not loading. It would be interesting to know whether you ever did a manual install of the driver or used a 3rd party tool to install the driver along with what your Xorg.0.log says when it fails to start X along with the output of dmesg but all of this should really be a separate dedicated bug and not here)

Thank you for your bug. Could you run "sudo apt-get dist-upgrade" and copy the log to a comment?

The failed upgrade had been recovered with an apt-get update; apt-get dist-upgrade. I *think* what may have happened is that I started the automatic upgrade early in the morning and went to work, by about 10pm it had finally downloaded all the DEBs and got to the point where the update manager starts asking questions about "do you accept the license of sun java" or "adobe flash" or whatever third party apps. *HOWEVER*, I'd gone to bed and so it sat at this prompt from 10pm until about 11am the next day.

...meanwhile, the automatic midnight/daily equivalent of "apt-get update; apt-get -d dist-upgrade; apt-get autoclean" had downloaded some replacement DEBs for ones that the (still running) update manager was expecting. When I hit "ok" for the installer it could no longer find the DEBs because they'd been cleaned out of the local spool directory.

Current status of the machine is that it is running, and in GNOME (failsafe). Beryl compiz is no longer working (it was working under feisty).

ajft@fafnir:~$ sudo apt-get -u dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

update-manager was not used here. It seems to be a

Accepted inoto gutsy-proposed, please test.

apt (0.7.9ubuntu1) hardy; urgency=low

  * merged from http://bzr.debian.org/apt/apt/debian-sid/, remaining
    changes:
    - mirror download method (pending merge with debian)
    - no pdiff download by default (unsuitable for ubuntu)
    - no recommends-by-default yet
    - add "Original-Maintainer" field to tagfile
    - show warning on apt-get source if the package is maintained
      in a VCS (pedinging merge with debian)
    - use ubuntu-archive keyring instead of debians one
    - support metapackages section for autoremoval
    - debian maintainer field change
    - send ubuntu string in user-agent

  * Changes from the debian-sid bzr branch (but not uploaded to debian
    yet):

  [ Otavio Salvador ]
  * Applied patch from Mike O'Connor <email address hidden> to add a manpage to
    apt-mark, closes: #430207.
  * Applied patch from Andrei Popescu <email address hidden> to add a
    note about some frontends in apt.8 manpage, closes: #438545.
  * Applied patch from Aurelien Jarno <email address hidden> to avoid CPU
    getting crazy when /dev/null is redirected to stdin (which breaks
    buildds), closes: #452858.
  * Applied patch from Aurelien Jarno <email address hidden> to fix building
    with newest dpkg-shlibdeps changing the packaging building order,
    closes: #452862.

  [ Program translations ]
    - Basque updated. Closes: #453088

  [ Michael Vogt ]
  * debian/rules
    - fix https install location
  * methods/gpgv.cc:
    - remove cruft code that caused timestamp/I-M-S issues
  * ftparchive/contents.cc:
    - fix error output
  * methods/mirror.{cc,h}:
    - only update mirror list on IndexFile updates
  * apt-pkg/acquire-item.{cc,h}:
    - make the authentication download code more robust against
      servers/proxies with broken If-Range implementations

  [ Chris Cheney ]
  * ftparchive/contents.cc:
    - support lzma data members
  * ftparchive/multicompress.cc:
    - support lzma output

apt (0.7.9) unstable; urgency=low

  [ Christian Perrier ]
  * Add several languages to LINGUAS and, therefore, really ship the relevant
    translation:
    Arabic, Dzongkha, Khmer, Marathi, Nepali, Thai
    Thanks to Theppitak Karoonboonyanan for checking this out. Closes: #448321

  [ Program translations ]
    - Korean updated. Closes: #448430
    - Galician updated. Closes: #448497
    - Swedish updated.

  [ Otavio Salvador ]
  * Fix configure script to check for CURL library and headers presense.
  * Applied patch from Brian M. Carlson <email address hidden>
    to add backward support for arches that lacks pselect support,
    closes: #448406.
  * Umount CD-ROM when calling apt-cdrom ident, except when called with
    -m, closes: #448521.

apt (0.7.8) unstable; urgency=low

  * Applied patch from Daniel Leidert <email address hidden> to fix
    APT::Acquire::Translation "none" support, closes: #437523.
  * Applied patch from Daniel Burrows <email address hidden> to add support
    for the Homepage field (ABI break), closes: #447970.
  * Applied patch from Frans Pop <email address hidden> to fix a trailing
    space after cd label, closes: #448187.

apt (0.7.7) unstable; urgency=low

  [ Michael Vogt ]
  * apt-inst/contr...

This has been in gutsy-proposed for about half a year now, without any verification. Can someone please test this?

I was able to verify the fix for this bug report using apt package version 0.7.6ubuntu14.1 and the test case provided.

Copied to gutsy-updates, thank you!