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Question: How to solve "WARNING: Add non-empty \value" with roxygen tags
0
gravatar for Paul Brennan
14 days 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
#'
#' List of features from five human NFkappaB proteins downloaded from
#' 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. 

Thanks in advance for your help. 

Best wishes, 

Paul

----

Dr Paul Brennan

Cardiff University

BrennanP@cardiff.ac.uk

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

ADD COMMENTlink modified 14 days ago by Lluís R300 • written 14 days ago by Paul Brennan0
2
gravatar for Lluís R
14 days ago by
Lluís R300
European Union
Lluís R300 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
#'
#' List of features from five human NFkappaB proteins downloaded from
#' 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

 

ADD COMMENTlink written 14 days ago by Lluís R300

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

ADD REPLYlink written 14 days ago by Paul Brennan0
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.

ADD REPLYlink written 14 days ago by Lluís R300
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