Re: [Rd] validity testing as part of '@<-'

From: Martin Morgan <>
Date: Sat 23 Sep 2006 - 00:06:47 GMT

While on the topic... validObject might check that the object (and its slots) is actually the new S4:

> validObject(a)

[1] TRUE
> isS4(a)

> sessionInfo()

R version 2.4.0 beta (2006-09-22 r39490) x86_64-unknown-linux-gnu


attached base packages:

[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "base"     

Thomas Lumley <> writes:

> On Fri, 22 Sep 2006, Parlamis Franklin wrote:
>> all those points are good ones, i just wonder what happens to S4
>> "guarantees" when invalid objects are allowed to exist. one of the
>> advantages of methods, as i understand, is that they can be written
>> with absolute confidence about what is being passed to them, and thus
>> do not need to contemplate a bunch of different possibilities (and as
>> a result can be terse and stylized). it seems if you really want
>> bulletproof code, you have to make validObject the first call in any
>> method definition to which an object with a validity method is being
>> passed (and which relies on receiving a valid object). i am not sure
>> whether the time spent in those validObject calls is less than the
>> time that might be spent in enforcing validity checks on all possible
>> object mutations.
> I think the contract is that new() guarantees an object is valid, and that
> programmers must guarantee that object mutation maintains validity.
> validObject() is available as a tool to help programmers fulfill their
> side of the bargain, but its use is not required. Given this contract it
> is not necessary for methods to check that the objects they are given are
> valid.
> Since validObject() isn't guaranteed to be true when changes are in
> progress, it is not easy to identify a necessary and sufficient set of
> places to call validObject() to ensure validity automatically.
> The other consequence of validObject() not being compulsory is that it can
> be slow -- it can check properties that are expensive to verify but are
> cheap to maintain. For example, you could have a data object where
> validObject() did a lot of range checks and consistency checks between
> variables. Redoing these checks would be appropriate for a [<- method,
> which changes the values, but not for a [ method that just extracts a
> subset.
> -thomas
> ______________________________________________
> mailing list

Martin T. Morgan
Bioconductor / Computational Biology

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Received on Sat Sep 23 10:08:55 2006

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