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
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