I thought that maybe the really long delay in approving this package came from the fact that it wasn't associated with a doi of a paper?

Since this isn't possible at the moment, I've added some statistics explanations to the vignette, which will hopefully improve the utility of the package.

I also removed the 'hello.R' file that is auto-generated by RStudio.


Here is my response to the comment:

  1. Thanks, we see:

The Title field should be in title case. Current version is: 'Pairwise association of functional annotations' In title case that is: 'Pairwise Association of Functional Annotations'


  1. Is there some reference about the method you can add in the Description field in the form Authors (year) ?

As I stated in point #3 in 11-11-2019: we do not have a doi to include. This will be updated as soon as we do have one. In fact, we wanted to get it on CRAN before submitting it to a journal, so the reviewers could test the package.


We have addressed the following issues in the earlier submission:

1.Please shorten the title to a maximum of 65 characters. Acronyms can be used on their own in the title as long as they are explained in the description field.

This has been done.

  1. Please never name your variables T or F. F.i.: visualisation.R

Oops-- we had tried to make sure that they were TRUE and FALSE before submission, but we missed two instances of this!


We have addressed the following issues in the earlier submission:

  1. the [email protected] field should be a call to person(), or combine such calls: c(person(...), person(...), ...)

DONE-- see description

  1. Please explain all acronyms (e.g. GO) in your Description text to avoid misunderstandings.

DONE-- see description

If there are references describing the (theoretical background of) methods in your package, please add these in the Description field of your DESCRIPTION file in the form authors (year) authors (year) authors (year, ISBN:...) with no space after 'doi:', 'arXiv:' and angle brackets for auto-linking

  1. Although we submitted an extended abstract to a conference, this does not yet have a doi because it is currently in the process of being peer reviewed. We will add the doi as soon we have it.


New submission. Other than that, no ERRORS, WARNINGS, or NOTES detected on Mac, Windows, Ubuntu Linux, or Fedora Linux (via rhub).

An extended abstract associated with this package has been submitted to RECOMB2020.

ezer/PAFway documentation built on Dec. 11, 2019, 12:10 a.m.