Re: [Rd] [Bioc-devel] promptClass

From: cstrato <cstrato_at_aon.at>
Date: Sun, 27 May 2007 13:15:52 +0200

Dear Martin

Thank you for sending the fast fix to the problem.

Best regards
Christian

Martin Morgan wrote:
> promptClass fails to identify methods associated with the class. Here
> is a fix:
>
> Index: promptClass.R
> ===================================================================
> --- promptClass.R (revision 41719)
> +++ promptClass.R (working copy)
> @@ -165,7 +165,7 @@
> if (nmeths > 0) {
> .meths.body <- " \\describe{"
> for (i in 1:nmeths) {
> - .sigmat <- sigsList(methnms[i], where)
> + .sigmat <- sigsList(methnms[i], where=whereClass)
> for (j in seq_along(.sigmat)) {
> if (!all(is.na(match(.sigmat[[j]],clName)))) {
> methn.i <- escape(methnms[i])
> Index: RMethodUtils.R
> ===================================================================
> --- RMethodUtils.R (revision 41719)
> +++ RMethodUtils.R (working copy)
> @@ -621,7 +621,7 @@
> getMethodsMetaData <-
> ## get the methods meta-data for function f on database where
> function(f, where = topenv(parent.frame())) {
> - mname <- mlistMetaName(f, where)
> + mname <- mlistMetaName(f, getPackageName(where))
> if(exists(mname, where = where, inherits = missing(where)))
> get(mname, where)
> else
>
> Seth Falcon <sfalcon_at_fhcrc.org> writes:
>
>
>> cstrato <cstrato_at_aon.at> writes:
>>
>>
>>> Dear all,
>>>
>>> What is the best way to write the docs for S4 classes?
>>>
>>> Concretely, is it possible to include the methods in the class
>>> documentation?
>>> For example, the documentation for class "AffyBatch" contains all methods.
>>> However, when I do:
>>> promptClass("AffyBatch")
>>> the relevant output of file "AffyBatch-class.Rd" is:
>>> \section{Methods}{
>>> No methods defined with class "AffyBatch" in the signature.
>>> }
>>>
>> promptClass used to provide more useful output. You might want to
>> report the issue on one of the R lists.
>>
>>
>>> Since PromptClass() contains a parameter "where" is it possible to use
>>> it, and how?
>>>
>> I'm not sure that is relevant here.
>>
>> One thing that can be useful here is showMethods(classes="AffyBatch").
>> The problem with static documentation for methods is that what methods
>> are available can change based on what packages are attached.
>>
>> If showMethods or a wrapper for it could be convinced to output a link
>> to a help file, then it might actually be a good way to go...
>>
>> + seth
>>
>> --
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>> http://bioconductor.org
>>
>> _______________________________________________
>> Bioc-devel_at_stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Sun 27 May 2007 - 11:18:47 GMT

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