From cstrato at aon.at  Sun May 27 13:15:52 2007
From: cstrato at aon.at (cstrato)
Date: Sun, 27 May 2007 13:15:52 +0200
Subject: [Rd] [Bioc-devel] promptClass
In-Reply-To: <6phfy5ivpsk.fsf@gopher4.fhcrc.org>
References: <46586BDB.5000700@aon.at> <m2bqg7cbos.fsf@ziti.local>
	<6phfy5ivpsk.fsf@gopher4.fhcrc.org>
Message-ID: <46596868.7030509@aon.at>

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
>>     
>
>



[Rd] [Bioc-devel] promptClass
cstrato