In /etc/eos-script-lib-yad.conf.pacnew was this text:
EOS_ROOTER configures the command for acquiring elevated privileges
when running in terminal.
Supported values:
“su -c”
“pkexec bash -c”
“sudo bash -c”
“/usr/bin/su -c”
“/usr/bin/pkexec bash -c”
“/usr/bin/sudo bash -c”
export EOS_ROOTER=“su -c”
And that was missing in /etc/eos-script-lib-yad.conf , so I added it there. Thanks to @ringo for helping me 
