R devel - May 2003 - Documenting S4 classes; debugging them

1.  I'm putting together my first package that uses S4 classes and
objects.  I'd like to document them, but I'm not sure what the
documentation should look like, and package.skeleton doesn't produce
any at all for the classes or methods.

Are there any good examples to follow?

2.  How do I do the equivalent of debug(foo), when foo is an anonymous
function being used as a method?  

Duncan Murdoch

I was a little stumped with documenting S4 classes too when writing the 
`gpclib' package.  There are the promptClass() and promptMethods() which 
provide a bare-bones Rd file for a particular class.

-roger

Duncan Murdoch wrote:
> 1.  I'm putting together my first package that uses S4 classes and
> objects.  I'd like to document them, but I'm not sure what the
> documentation should look like, and package.skeleton doesn't produce
> any at all for the classes or methods.
> 
> Are there any good examples to follow?
> 
> 2.  How do I do the equivalent of debug(foo), when foo is an anonymous
> function being used as a method?  
> 
> Duncan Murdoch
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> 
>

Duncan Murdoch wrote:
> 
> 1.  I'm putting together my first package that uses S4 classes and
> objects.  I'd like to document them, but I'm not sure what the
> documentation should look like, and package.skeleton doesn't produce
> any at all for the classes or methods.
Hmm, sounds as if it should.

Meanwhile, promptClass and promptMethods generate skeleton
documentation.

> 
> Are there any good examples to follow?
The bioconductor packages (e.g, Biobase) have some examples.
> 
> 2.  How do I do the equivalent of debug(foo), when foo is an anonymous
> function being used as a method?
The S4-style trace() function allows you to insert debugging functions
(or any expressions) into functions; it has a `signature' argument that
causes the debugging to be inserted into the method with the
corresponding signature.

Usually either `browser' or `recover' are suitable functions to insert.

My canonical piece of debugging code is along the lines of:

   trace("f", signature = "numeric", browser, exit =
browser)

If you are really attached to debug(), you can insert an extra level of
function call; i.e., instead of:

  fNumeric <- function(x)x+1
  setMethod("f", "numeric", fNumeric)

and then the call to trace, do
  setMethod("f", "numeric", function(x)fNumeric(x))
  debug(fNumeric)

But trace() is more flexible, though requiring a bit more typing.

John
> 
> Duncan Murdoch
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
-- 
John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
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My previous post should have had this subject heading - my apologies.

Gordon
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