From D.Strbenac at garvan.org.au  Mon Aug 30 07:00:02 2010
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Mon, 30 Aug 2010 15:00:02 +1000 (EST)
Subject: [Rd] S4 Method Rd Warning
Message-ID: <20100830150002.BIN17749@gimr.garvan.unsw.edu.au>

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.

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



[Rd] S4 Method Rd Warning
Dario Strbenac