R help - Jul 2007 - initalizing and checking validity of S4 classes

Dear useRs and wizaRds,

I am currently developing a set of functions using S4 classes. On the way I
encountered the problem exemplified with the code below. For some reason the
'validity' method does not seem to work, i.e. does not check for errors
in the specification of the slots of the defined class. Any hints?

My understanding of the whole S4 system was that validity checks are made
*after* class initialization. Is that correct?

Thanks a lot in advance!

PS. Session info:

R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250

attached base packages:
[1] "stats"     "graphics"  "grDevices"
"utils"     "datasets"  "methods"
[7] "base"     
> 



-b-e-g-i-n--r--c-o-d-e-

setClass( "someclass", representation(v="numeric",
l="character"),
    prototype( v=numeric(0),
	l=character(0) )
    )

setMethod("initialize", "someclass",
function(.Object, v=numeric(0), l=character(0))
{
    # strip the vector names
    cv <- v
    cl <- l
    names(cv) <- NULL
    names(cl) <- NULL
    rval <- .Object
    rval@v <- cv
    rval@l <- cl
    rval
} )

# at this point this should be OK
o <- new("someclass", v=1:2, l=letters[1:3])
o

# check validity
f <- function(object)
{
    rval <- NULL
    if( length(object@v) != length(object@l) )
	rval <- c( rval, "lengths dont match")
    if( is.null(rval) ) return(TRUE)
    else return(rval)
}
 
# this should return error description
f(o)


# define the validity method
setValidity( "someclass", f)

# this should return an error
new("someclass", v=1:2, l=letters[1:3])

# but it doesn't...

-e-n-d--r--c-o-d-e-




____________________________________
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
Room 1428
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/


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Hi Michal --

Add validObject to your initialize method:
> setMethod("initialize", "someclass",
+ function(.Object, v=numeric(0), l=character(0))
+ {
+     # strip the vector names
+     cv <- v
+     cl <- l
+     names(cv) <- NULL
+     names(cl) <- NULL
+     rval <- .Object
+     rval at v <- cv
+     rval at l <- cl
+     validObject(rval)
+     rval
+ } )
[1] "initialize"
> new("someclass", v=1:2, l=letters[1:3])
Error in validObject(rval) : 
  invalid class "someclass" object: lengths dont match

Note that without initialize, we have:
> setClass("A",
+          representation=representation(
+            v="numeric", l="character"))
[1] "A"
> setValidity("A", f)
Slots:
                          
Name:          v         l
Class:   numeric character
> new("A", v=1:2, l=letters[1:3])            
Error in validObject(.Object) : 
  invalid class "A" object: lengths dont match
 
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject. (2) Responsibility for object
validity is ambiguous -- does it belong with 'new',
'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).

Martin

"Bojanowski, M.J.  (Michal)" <M.J.Bojanowski at uu.nl> writes:
> Dear useRs and wizaRds,
>
> I am currently developing a set of functions using S4 classes. On the way I
encountered the problem exemplified with the code below. For some reason the
'validity' method does not seem to work, i.e. does not check for errors
in the specification of the slots of the defined class. Any hints?
>
> My understanding of the whole S4 system was that validity checks are made
*after* class initialization. Is that correct?
>
> Thanks a lot in advance!
>
> PS. Session info:
>
> R version 2.5.1 (2007-06-27) 
> i386-pc-mingw32 
>
> locale:
>
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices"
"utils"     "datasets"  "methods"
> [7] "base"     
>> 
>
>
>
>
> -b-e-g-i-n--r--c-o-d-e-
>
> setClass( "someclass", representation(v="numeric",
l="character"),
>     prototype( v=numeric(0),
> 	l=character(0) )
>     )
>
> setMethod("initialize", "someclass",
> function(.Object, v=numeric(0), l=character(0))
> {
>     # strip the vector names
>     cv <- v
>     cl <- l
>     names(cv) <- NULL
>     names(cl) <- NULL
>     rval <- .Object
>     rval at v <- cv
>     rval at l <- cl
>     rval
> } )
>
> # at this point this should be OK
> o <- new("someclass", v=1:2, l=letters[1:3])
> o
>
> # check validity
> f <- function(object)
> {
>     rval <- NULL
>     if( length(object at v) != length(object at l) )
> 	rval <- c( rval, "lengths dont match")
>     if( is.null(rval) ) return(TRUE)
>     else return(rval)
> }
>  
> # this should return error description
> f(o)
>
>
> # define the validity method
> setValidity( "someclass", f)
>
> # this should return an error
> new("someclass", v=1:2, l=letters[1:3])
>
> # but it doesn't...
>
> -e-n-d--r--c-o-d-e-
>
>
>
>
> ____________________________________
> Michal Bojanowski
> ICS / Department of Sociology
> Utrecht University
> Heidelberglaan 2; 3584 CS Utrecht
> Room 1428
> m.j.bojanowski at uu dot nl
> http://www.fss.uu.nl/soc/bojanowski/
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org

Dear Martin and Seth,

Thanks a million for explanations and suggestions. I find myself still in the
process of learning S4 system. Can you possibly suggest some material that I
could use in this "process"?

Anything apart from "Programming with data" book? I also know the
notes written
by John Chambers and I also have Fritz Leisch's slides from the first UseR!,
all three available on the Web. Do you have any suggestions in that matter?

Thanks a lot in advance!

Best, Michal
> Martin Morgan <mtmorgan at fhcrc.org> writes:
> 
> > Hi Michal --
> >
> > Add validObject to your initialize method:
> 
> Actually, a call to valid object is part of the default initialization
> method which has been masked.  A different solution, which might have
> some other benefits is to delegate back to the default method using
> callNextMethod.  So you could do:
> 
> setMethod("initialize", "someclass",
> function(.Object, v=numeric(0), l=character(0))
> {
>     # strip the vector names
> 
>     cv <- v
>     cl <- l
>     names(cv) <- NULL
>     names(cl) <- NULL
>     callNextMethod(.Object=.Object, v=cv, l=cl)
> } )
> 
> 
> > Here are two interpretations of this. (1) using 'initialize'
means
> > that you are taking control of the initialization process, and hence
> > know when you need to call validObject.
> 
> Yes.  Anytime you specialize a method you must take responsibility for
> any less specific methods.  In this case, the default 'initialize'
> does object validation.  So if you want validation, you either need to
> do it directly or invoke the default method.
> 
> > (2) Responsibility for object
> > validity is ambiguous -- does it belong with 'new',
'initialize', or a
> > 'constructor' that the programmer might write? This is
particularly
> > problematic with R's copy semantics, where creating transiently
> > invalid objects seems to be almost necessary (e.g., callNextMethod()
> > in 'initialize' might initialize the inherited slots of the
object,
> > but the object itself is of the derived class and could well be
> > invalid 'invalid' after the base class has finished with
initialize).
> 
> This is a good point.  It suggests that, at least, one must initialize
> all non-inherited slots to valid values _before_ calling the next
> method.
> 
> + seth


:
::
::: Note that my e-mail address has changed to m.j.bojanowski at uu dot nl
::: Please update you address books accordingly. Thank you!
::
:


____________________________________
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
The Netherlands
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/


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