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I am running the latest version of Elementary OS (Loki I believe) and have uninstalled the Pantheon Mail through the App Center as I want to use a different mail client. However I am still getting notifications from Pantheon Mail and when I click on them it opens the Pantheon Mail app (with a low res image of the app logo on the dock).

Any help/solutions to this would be greatly appreciated, thanks!

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I used sudo apt purge to remove mine and have no problems, but I never signed in to an account. If it was not a clean uninstall perhaps reinstalling and ensuring your accounts are disconnected before removing the program may help.

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    So I couldn't figure out how to remove my account so I removed it in ~/.local/share/pantheon-mail and then did sudo apt purge. Hopefully this will solve the problem. Cheers. – E.Hazledine Nov 2 '17 at 21:01
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On elementary OS, some apps run in the background to be able to receive mail, send notifications, play music, etc. When you update or uninstall an app, anything that's currently running will actually continue to run the old version since it's pointing at the existing app in memory. To ensure something stops running, you need to completely stop the app.

The easiest way to stop any old or uninstalled versions of apps is to restart your device. For Mail, you can also choose the "Quit" option in the menu.

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ps aux look for pantheon mail

username+ 17814  0.3  3.4 2732984 137244 ?      SLl  07:15   2:26 pantheon-mail

note it's PID (in my case: 17814) after that: kill 17814

then:

sudo apt purge pantheon-mail

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