[Bioc-devel] documentation help

[Martin Morgan]

On 03/09/2011 08:21 AM, Stefano Berri wrote:
> Hi Greg
> 
> Thanks a lot for your help.
> I think I am almost there, still have a warnings I cannot solve
> 
> Documentation file
> +++++++++++++++++++++
> \name{gcNorm}
> \docType{methods}
> \alias{gcNorm}
> \alias{CNAnorm}
> \alias{gcNorm-methods}
> \alias{gcNorm, CNAnorm-method}

Hi Stefano --

no ' ' between 'gcNorm,' and 'CNAnorm'.

Martin

> 
> ....
> 
> \usage{
> \S4method{gcNorm}{CNAnorm}(object, excludeFromGCNorm = character(0),
>      maxNumPoints = 10000)
> } 
> 
> ...
> 
> ++++++++++++++++++++++
> 
> code
> 
> ++++++++++++++++++++++
> 
> setGeneric("gcNorm", function(object, ...){standardGeneric("gcNorm")})
> 
> setMethod(f = "gcNorm", signature = "CNAnorm", definition = .gcNorm)
> 
> .gcNorm <- function(object, excludeFromGCNorm = character(0), maxNumPoints =
> 10000){
> # all the code
> }
> 
> ++++++++++++++++++++++
> 
> running R CMD CHECK
> 
> * checking Rd \usage sections ... WARNING
> Objects in \usage without \alias in documentation object 'gcNorm':
>   \S4method{gcNorm}{CNAnorm}
> 
> 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.
> 
> 
> Any help is really appreciated
> 
> thanks
> 
> Stefano
> 
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