[Rd] [Bioc-devel] promptClass

Martin Maechler maechler at stat.math.ethz.ch
Mon May 28 12:52:47 CEST 2007

>>>>> "MartinMo" == Martin Morgan <mtmorgan at fhcrc.org>
>>>>>     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

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 <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

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

    MartinMo> ______________________________________________
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