From mtmorgan at fhcrc.org  Sun May 27 06:44:27 2007
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Sat, 26 May 2007 21:44:27 -0700
Subject: [Rd] [Bioc-devel] promptClass
In-Reply-To: <m2bqg7cbos.fsf@ziti.local> (Seth Falcon's message of "Sat, 26
	May 2007 18:11:47 -0700")
References: <46586BDB.5000700@aon.at> <m2bqg7cbos.fsf@ziti.local>
Message-ID: <6phfy5ivpsk.fsf@gopher4.fhcrc.org>

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

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org



[Rd] [Bioc-devel] promptClass
Martin Morgan