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
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 >
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