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Question: How to solve "WARNING: Add non-empty \value" with roxygen tags
0
11 months ago by
Cardiff, UK
Paul Brennan0 wrote:

Hello,

I am developing a package to automate the drawing of protein schematics. I don't think a similar package exists in R or Bioconductor and I hope I haven't missed someone else's package. The github repo is here: https://github.com/brennanpincardiff/drawProteins. I'm working to raise it to Bioconductor standards.

When I BiocCheck the package, it gives me a:

WARNING: Add non-empty \value sections to the following man pages: five_rel_list.Rd

This is a WARNING than another has encountered but I can't find an roxygen2 tag solution. I could manually add some Latex to my .Rd files but I'm using roxygen2 tags to make my documentation so that seems like a bad solution.

With that context: How do I add a roxygen2 tag to create a \value in my Rd file?

Here is a copy of the code that generates the .Rd file for the data file with the name five_rel_list.

#' Features of five human Rel A proteins
#'
#' Uniprot on 15 August 2017
#'
#' @format Large List of 5 elements - one element for each protein
#'
#' @source Uniprot {http://www.uniprot.org}
#' Accession numbers Q04206 Q01201 Q04864 P19838 Q00653
"five_rel_list"

The #' is the roxygen2 comment lines. The @ code generates the Latex.

Best wishes,

Paul

----

Dr Paul Brennan

Cardiff University

BrennanP@cardiff.ac.uk

http://rforbiochemists.blogspot.co.uk/

modified 11 months ago by Lluís Revilla Sancho400 • written 11 months ago by Paul Brennan0
3
11 months ago by
European Union
Lluís Revilla Sancho400 wrote:

The warning tells you need to have the value field in the .Rd files. Using roxygen2 you need to use @return which in the .Rd files is converted into the \value field:

#' Features of five human Rel A proteins
#'
#' Uniprot on 15 August 2017
#'
#' @return Large List of 5 elements - one element for each protein
#' @source Uniprot {http://www.uniprot.org}
#' Accession numbers Q04206 Q01201 Q04864 P19838 Q00653

Thanks for the prompt, helpful and correct response. One less warning.

In my case it is a repeat of the @format tag... You left out the @format tag is that OK?

Thanks again,

Paul

1

I removed the @format tag because what you seemed to describe is what it returns, but if you are describing the structure of the dataset you can use it in addition to @return. Although I am not sure if forcing to have a @return is  strictly followed in the review of packages as it seems more addressed to software packages.

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