Simulating ENTER keypress in bash script

echo -ne '\n' | <yourfinecommandhere>

or taking advantage of the implicit newline that echo generates (thanks Marcin)

echo | <yourfinecommandhere>

Now we can simply use the --sk option:

--sk, --skip-keypress Don’t wait for a keypress after each test

i.e. sudo rkhunter --sk --checkall

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