From murdoch.duncan at gmail.com  Mon Aug 30 17:48:31 2010
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Mon, 30 Aug 2010 11:48:31 -0400
Subject: [Rd] S4 Method Rd Warning
In-Reply-To: <20100830150002.BIN17749@gimr.garvan.unsw.edu.au>
References: <20100830150002.BIN17749@gimr.garvan.unsw.edu.au>
Message-ID: <4C7BD2CF.7070001@gmail.com>

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?

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
>



[Rd] S4 Method Rd Warning
Duncan Murdoch