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
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