Until Slack releases a new version with an updated Electron, you can use
this workaround that worked for me:
sudo touch /usr/lib/libunity-electron_notification_fix
See the full details in:
https://github.com/electron/electron/issues/465#issuecomment-206582829
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https://bugs.launchpad.net/bugs/1547448
Title:
Ubuntu 16.04: Notifications of some apps displayed in a classic window
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