Update checkS3methods to ignore deprecated/defunct functions

[hturner]

This task is to update tools::checkS3methods(), so that ignores functions where there is a call to .Deprecated() or .Defunct() in the body of a function.

This will enable a more elegant approach to fixing packages that have functions that look like S3 methods, as discussed on the CRAN Cookbook repo. This approach has the support of Kurt Hornik from the CRAN team.

tools::checkS3methods() is a pure R function, but it is a long function! So part of the task will be working through the code to understand how it could be adapted to only check functions that are not deprecated or defunct, then working on the code to implement the change.