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I downloaded a Debian wheezy netinstall iso file, and just made a very minimal installation with no Display manager or desktop environment.

I was using the terminal for testing purpose. I later installed cinnamon from Linux Mint backport repos. It worked fine.

Then, to have a display manager, I choose to install lightdm. I used the command

sudo apt-get install lightdm

The installation was successful, but when I restarted, Gnome 3 was also installed. How do I remove gnome3 and all its dependencies without affecting the system ?

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to remove a package use

apt-get remove gnome-session

Then apt-get can remove dependency that have been automatically installed and are not needed anymore with the autoremove command:

apt-get autoremove
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If anyone else stumbles upon this question after searching "remove gnome 3" like I did, the following should help you.

Directly from Debian's wiki:

aptitude purge dpkg --get-selections | grep gnome | cut -f 1
aptitude -f install
aptitude purge `dpkg --get-selections | grep deinstall | cut -f 1
aptitude -f install
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Just run:

sudo apt-get remove gnome-shell

in terminal.

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Clean all gnome3 with this command (copy & paste):

apt-get remove alacarte baobab caribou caribou-antler cheese cheese-common empathy empathy-common eog eog-dbg eog-dev eog-plugins evince evince-common evince-dbg evolution evolution-common evolution-data-server evolution-data-server-common evolution-webcal file-roller gcalctool gconf-editor gdm3 gedit gedit-common gedit-plugins gkbd-capplet gnome gnome-accessibility-themes gnome-applets gnome-applets-data gnome-backgrounds gnome-bluetooth gnome-color-manager gnome-common gnome-contacts gnome-control-center gnome-control-center-data gnome-core gnome-desktop3-data gnome-dictionary gnome-disk-utility gnome-documents gnome-font-viewer gnome-icon-theme gnome-icon-theme-extras gnome-icon-theme-symbolic gnome-js-common gnome-mag gnome-media gnome-menus gnome-mime-data gnome-nettool gnome-online-accounts gnome-orca gnome-packagekit gnome-packagekit-data gnome-panel gnome-panel-data gnome-power-manager gnome-screensaver gnome-session gnome-session-bin gnome-session-common gnome-session-fallback gnome-settings-daemon gnome-shell gnome-shell-common gnome-shell-extensions gnome-menus gnome-system-log gnome-system-monitor gnome-terminal gnome-terminal-data gnome-themes-standard gnome-themes-standard-data gnome-tweak-tool gnome-user-guide gnome-user-share gnome-video-effects gucharmap hamster-applet libreoffice-evolution libreoffice-gnome libreoffice-gtk mousetweaks metacity metacity-common metacity-themes nautilus nautilus-data nautilus-open-terminal nautilus-sendto-empathy notification-daemon python-gnome2 python-gnomedesktop python-nautilus rhythmbox rhythmbox-data rygel sound-juicer task-gnome-desktop tomboy totem totem-common vinagre vino yelp yelp-xsl zenity zenity-common

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Have you tried to determine what all of these packages depend on, and then remove that? – Ignacio Vazquez-Abrams Aug 9 '13 at 10:49
Normaly, this is done by apt-get. Running apt-get autoremove will remove uneeded dependency. – Rémi Nov 1 '13 at 12:08

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