Out of interest, are you using the CLI from NPM, or GitHub?
Those modules are built-in, and this usually happens if the CLI hasn't been able to work out what type of board is connected (it queries process.env when it connects) so it doesn't know that the libraries are actually built in.
There was a bug in the order in which the CLI did things that messed this up, but I thought that was fixed - it's entirely possible I haven't updated it in NPM though, and I'll try and do that today.
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