The author writes that the software wasn't the focus of the manuscript and that the reviewers should not have commented on the software at all but that it actua

The author writes that the software wasn't the focus of the manuscript and that the reviewers should not have commented on the software at all but that it actually not true. If you look at the preprint manuscript, you'll find that the software is prominently advertised in the abstract of the paper. In this situation, it is perfectly reasonable for the reviewer to comment on the implementation of the software. And as much as I like Julia, I think he is right when he says that an R package would be more useful.