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 <[EMAIL PROTECTED]> writes:
> cstrato <[EMAIL PROTECTED]> 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
>
> _______________________________________________
> [EMAIL PROTECTED] mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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