In my function declarations and roxygen2 comments, I have hard-wrapped all lines to less than 80 characters. Roxygen2 appears to be expanding my function definitions to violate this, causing R-devel to complain about my over 90 character length lines.
For instance, I declare my function in my .R file with hard-wrapped arguments,
This is a bit tricky to fix because currently we're generating the usage from the function formals, not from the source code. It might be possible to use a srcref to get to the original function, but you'd still need to do some munging since in your example you probably wouldn't want such extreme indenting in the usage statement.
When I have got some time, I will see if I can plug formatR into roxygen2 as an optional feature to reformat code in usage and examples. The current implementation in Rd2roxygen is mostly for my personal use.