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I noticed that my system (Elementary OS, based on Ubuntu 14.04) is trying to remove working packages through auto-remove. Running auto-remove makes system unusable, reinstalling packages do nothing, rebuilding package-cache do the same. This problem appears right after first reboot after installing and updating system; right after I update my system using apt-get update + apt-get upgrade. GUI updater works fine, without any problems and creating list of auto-remove packages.

Here are the packages it removes. Any ideas about could be wrong with system?

dnsmasq-base exuberant-ctags firefox-locale-sv gir1.2-gnomebluetooth-1.0
  gir1.2-peas-1.0 gnome-bluetooth gnome-user-share indicator-bluetooth
  indicator-keyboard indicator-power iputils-arping libatkmm-1.6-1
  libbonoboui2-0 libbonoboui2-common libcairomm-1.0-1 libgail18 libglade2-0
  libglibmm-2.4-1c2a libgnome-menu2 libgnomecanvas2-0 libgnomecanvas2-common
  libgnomeui-0 libgnomeui-common libgtksourceview-3.0-1
  libgtksourceview-3.0-common libgtkspell3-3-0 libmbim-glib0 libmm-glib0
  libmnl0 libnetfilter-conntrack3 libnl-route-3-200 libnm-glib-vpn1
  libpangomm-1.4-1 libqmi-glib0 libruby1.9.1 libscratchcore0
  libsigc++-2.0-0c2a libt1-5 libtimezonemap1 libunique-1.0-0 libunique-3.0-0
  libvala-0.24-0 libwnck-common libwnck22 libyaml-0-2 linux-headers-3.13.0-32
  linux-headers-3.13.0-32-generic linux-image-3.13.0-32-generic
  linux-image-extra-3.13.0-32-generic mobile-broadband-provider-info
  modemmanager network-manager network-manager-gnome network-manager-pptp
  network-manager-pptp-gnome obexd-client pptp-linux python-pycurl ruby
  ruby1.9.1 thunderbird-locale-sv thunderbird-locale-sv-se usb-modeswitch
  usb-modeswitch-data
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    Maybe you have encountered some bug, the elementaryOS version that is based on Ubuntu 14.04 is still in beta testing. The GUI updater is just a frontend that calls the apt package manager. Have you tried to get help at elementaryOS site and Google plus community?
    – zloster
    Mar 13, 2015 at 22:35
  • I think I'm the only one with this problem.
    – user423645
    Mar 15, 2015 at 18:58

1 Answer 1

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In Debian and derivatives the auto-remove option only suggests packages that have been installed as a dependency of another package. If the depending package is removed, those packages are marked as auto-removable.

You don't have to run apt-get auto-remove and the system will inform you happily about those packages for eternity. You can instead set them to be installed manually -- just run apt-get install <package> [<package>]

But your specific issue might stem from the fact that updating an unstable distribution might change dependencies and apt-get upgrade does not account for that. Try running 

apt-get dist-upgrade

which handles the upgrade process more intelligently (but also more intrusively.) Read the man page of apt-get to get the full picture.

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