[Bioc-devel] promptClass

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

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