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gksu has been removed from Debian and other GNU/Linux distributions for
maintenance and security reasons (see
<https://jeremy.bicha.net/2018/03/21/gksu-is-dead/>), so I'd rather
focus on any other tools having similar problems. That being said, you
should be able to work around the gksu issue by setting (or unsetting)
XDG_RUNTIME_DIR in gksu's subsidiary environment before invoking Emacs
(not that I recommend using gksu at all...).