When creating a package, I would like a way to tell R that
a function with a period in its name is not a method.

I'm writing a package now with a modified version of qr.R.
R CMD check gives warnings:

* checking S3 generic/method consistency ... WARNING
qr:
  function(x, ...)
qr.R:
  function(qr, complete, pivot)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.

* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'QR.Auxiliaries':
  ‘qr.R’

The \usage entries for S3 methods should use the \method markup and
not their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

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