I have no idea if this is related to your problem (which I hope has been resolved since ...), but I had a similar problem, and it turned out that it was due to bad interactions with my awkward agreements about names
As a rule, I wrote functions with a name plot.XXX()where it XXXdescribes what needs to be done. Roxygen interpreted them as general function definitions for the S3 object system. XXXthen it was considered as a (not exportable) class with a function plot()and, accordingly, wrote a NAMESPACE file, which I did not expect. I suppose the same thing will happen for str.XXX(), summary.XXX()etc., or for XXX.data.frame(), etc. I did not have any of them, but that would make sense if that happened.
, ... S3/S4/S5!