Re: [Rd] [Bioc-devel] promptClass

From: Martin Maechler <>
Date: Mon, 28 May 2007 12:52:47 +0200

>>>>> "MartinMo" == Martin Morgan <> >>>>> on Sat, 26 May 2007 21:44:27 -0700 writes:

    MartinMo> promptClass fails to identify methods associated     MartinMo> with the class. Here is a fix:

Thank you, Martin;
I've applied your patch to my working copy of R-devel, and I can confirm it solves the problem for class "AffyBatch" (from bioconductor package 'affy').

However it does not seem to fix the problem in my case:


which still produces a sparseMatrix-class.Rd file which contains

No methods defined with class "sparseMatrix" in the signature. }

so there's at least another bug there.
One difference: "sparseMatrix" is a virtual class, "AffyBatch" not, but then showMethods(classes = "..") works for both.

I'd be glad if you have time to find another patch ;-) :-)

Martin Maechler     

>> cstrato <> 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
>> _______________________________________________
>> mailing list

    MartinMo> -- Martin Morgan Bioconductor / Computational     MartinMo> Biology

    MartinMo> ______________________________________________
    MartinMo> mailing list     MartinMo> mailing list Received on Mon 28 May 2007 - 10:55:02 GMT

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