Can you please elaborate

Have you installed packages, if so which ones?

Rather sounds as if you have built machinekit from sources, if you have 
somewhere to try running 'sudo make setuid' ?
In which case you presumably have not completed the building properly.

The whole latency-test issue rather suggests you are operating under the 
misapprehension that you can do software stepping on an x86 with rt-preempt 
kernel.
You can't.

The reason there is no base thread reading by default in latency-test, is 
that the various hardware step generation methods used ( BBB PRU, 
DE0-NANO-Soc, Mesa boards)
do not require a base thread.

The rtai kernel based Linuxcnc distro you were pointed to earlier is where 
you need to go if you want to run a machine off the parport with software 
stepgen.

On Saturday, 18 November 2017 17:35:44 UTC, Jeff Washburn wrote:
>
> I have loaded Machinekit on an Intel Core i5 3400 series and on Debian 
> Stretch. Flavor is rt-preempt. When I run Latency Test, I get the subject 
> message in the linuxcnc.log file as it is starting up. When I run 
> latency-test in root, then I get a mesage saying the rtapi_app is not root. 
> Thus, lack of root privilege stops rtapi_app.
>
> How do I give rtapi_app root privilege? Somebody might suggest 'sudo make 
> setuid' running from /src. I've tried it and get an error: 'no rule to make 
> target 'setuid''. I am guessing that make operates with setuid, which I 
> don't have.
>

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