[R] [Rd] S4 Method Rd Warning

[Dario Strbenac]

Thanks for this. I was thinking the spaces rule only applied within the \alias{} statements. I'm not sure why I thought this.

---- Original message ----
>Date: Mon, 30 Aug 2010 18:43:35 +0100 (BST)
>From: Prof Brian Ripley <ripley at stats.ox.ac.uk>  
>Subject: Re: [Rd] S4 Method Rd Warning  
>To: Duncan Murdoch <murdoch.duncan at gmail.com>
>Cc: D.Strbenac at garvan.org.au
>
>On Mon, 30 Aug 2010, Duncan Murdoch wrote:
>
>> On 30/08/2010 1:00 AM, Dario Strbenac wrote:
>>> Hello,
>>> 
>>> I am using R 2.11.0. I have a curious problem where I get a warning in R 
>>> CMD check which is seemingly not relevant to my Rd file.
>>> 
>>
>> 2.11.0 isn't the current release, and there have been fixes to this stuff 
>> since 2.11.1 was released.  Could you try 2.11.1-patched or the devel version 
>> of 2.12.0 and see if you still get the warnings?
>
>But there are incorrect spaces at e.g. {GRanges, BSgenome}.  Classes 
>in signatures are comma-separated, not comma+space separated.
>
>If we've changed it, we are now accepting errorneous files AFAICS.
>
>>
>> Duncan Murdoch
>>> The warning says :
>>> 
>>> * checking Rd \usage sections ... WARNING
>>> Bad \usage lines found in documentation object 'enrichmentCalc':
>>>     <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, 
>>> organism, seqLen=NULL, ...)
>>>     <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, 
>>> organism, seqLen=NULL, do.warn=FALSE)
>>>     <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, 
>>> organism, seqLen=NULL)
>>> 
>>> Functions with \usage entries need to have the appropriate \alias entries,
>>> and all their arguments documented.
>>> The \usage entries must correspond to syntactically valid R code.
>>> See the chapter 'Writing R documentation files' in manual 'Writing R
>>> Extensions'.
>>> 
>>> But, I have documented all the arguments, and I have all the aliases. What 
>>> else could it be warning me about ?
>>> 
>>> The Rd file contents are :
>>> 
>>> \name{enrichmentCalc}
>>> \alias{enrichmentCalc}
>>> \alias{enrichmentCalc,GenomeDataList,BSgenome-method}
>>> \alias{enrichmentCalc,GenomeData,BSgenome-method}
>>> \alias{enrichmentCalc,GRanges,BSgenome-method}
>>> 
>>> \title{Calculate sequencing enrichment}
>>> \description{A description}
>>> \usage{
>>>   \S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, 
>>> seqLen=NULL, ...)
>>>   \S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, 
>>> seqLen=NULL, do.warn=FALSE)
>>>   \S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL)
>>> }
>>> \arguments{
>>>   \item{rs}{jjj}
>>>   \item{organism}{ghi}
>>>   \item{seqLen}{def}
>>>   \item{do.warn}{abc}
>>>   \item{...}{xyz}
>>> }
>>> \details{
>>>   Details.
>>> }
>>> \value{
>>>  Text here.
>>> }
>>> \author{A Person}
>>> \examples{
>>>  #See the manual
>>> }
>>> 
>>> Thanks,
>>>        Dario.
>>> 
>>> --------------------------------------
>>> Dario Strbenac
>>> Research Assistant
>>> Cancer Epigenetics
>>> Garvan Institute of Medical Research
>>> Darlinghurst NSW 2010
>>> Australia
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>-- 
>Brian D. Ripley,                  ripley at stats.ox.ac.uk
>Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>University of Oxford,             Tel:  +44 1865 272861 (self)
>1 South Parks Road,                     +44 1865 272866 (PA)
>Oxford OX1 3TG, UK                Fax:  +44 1865 272595


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia