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Problem with initialize of S4 classes

3 messages · cstrato, Martin Morgan

cstrato
# 
Dear all

Below is the code for "scriptPreFilter.R" which gives the following result:
 > source("scriptPreFilter.R")
 > prefltr <- new("PreFilter", mad=c(0.5,0.01))
[1] "------initialize:PreFilter------"
[1] "------initialize:Filter------"
 > str(prefltr)
Formal class 'PreFilter' [package ".GlobalEnv"] with 2 slots
  ..@ mad       :List of 2
  .. ..$ cutoff : num 0.5
  .. ..$ epsilon: num 0.01
  ..@ numfilters: num 1

It seems that everything is ok, the results are as expected.

However, my problem is that copying the identical code to my package 
results in an error:
 > prefltr <- new("PreFilter", mad=c(0.5,0.01))
[1] "------setValidity:Filter------"
Error in validObject(.Object) :
  invalid class "PreFilter" object: invalid object for slot "mad" in 
class "PreFilter": got class "numeric", should be or extend class "list"

The following code avoids the error and gives the result:
 > prefltr <- new("PreFilter", mad=list(0.5,0.01))
[1] "------setValidity:Filter------"
[1] "------setValidity:PreFilter------"
 > str(prefltr)
Formal class 'PreFilter' [package "xps"] with 11 slots
  ..@ mad        :List of 2
  .. ..$ : num 0.5
  .. ..$ : num 0.01
  ..@ numfilters : num 0

This is only partly correct, e.g. numfilters is 0.

Only the following code gives the correct result:
 > prefltr <- new("PreFilter")
 > madFilter(prefltr) <- c(0.5,0.01)
 > str(prefltr)
Formal class 'PreFilter' [package "xps"] with 11 slots
  ..@ mad        :List of 2
  .. ..$ cutoff : num 0.5
  .. ..$ epsilon: num 0.01
  ..@ numfilters : num 1

As you see, the loading "scriptPreFilter.R" calls method initialize but 
not setValidity.
In contrast, loading my package as library calls setValidity but not 
initialize.

My question is:
- Why can the identical code behave differently when put in a package?
- How can I ensure, that initialize gets also called in my package?

 > sessionInfo()
R version 2.6.1 (2007-11-26)
i386-apple-darwin8.10.1

locale:
C

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

other attached packages:
[1] xps_0.4.0

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Best regards and Merry Christmas
Christian
_._._._._._._._._._._._._._._._
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a       A.u.s.t.r.i.a
e.m.a.i.l:    cstrato at aon.at
_._._._._._._._._._._._._._._._


------- BEGIN: scriptPreFilter.R ---------
setClass("Filter",
   representation(numfilters = "numeric"),
   prototype(numfilters = 0)
)

setClass("PreFilter",
   representation(mad = "list"),
   contains=c("Filter"),
   prototype(mad = list())
)

setGeneric("madFilter",   function(object) standardGeneric("madFilter"))
setGeneric("madFilter<-", function(object, value) 
standardGeneric("madFilter<-"))

"initialize.Filter" <- function(.Object, ...)
{
   print("------initialize:Filter------")
   .Object <- callNextMethod(.Object, ...)
   .Object
}
setMethod("initialize", "Filter", initialize.Filter)

setValidity("Filter",
   function(object) {
      print("------setValidity:Filter------")
      msg <- NULL
      if (is.null(msg)) TRUE else msg
   }
)

"initialize.PreFilter" <- function(.Object, mad = list(), ...)
{
   print("------initialize:PreFilter------")
   .Object at numfilters <- 0
   if (length(mad)) madFilter(.Object) <- unlist(mad)
   .Object <- callNextMethod(.Object, ...)
   .Object
}
setMethod("initialize", "PreFilter", initialize.PreFilter)

setValidity("PreFilter",
   function(object) {
      print("------setValidity:PreFilter------")
      msg <- NULL
      if (is.null(msg)) TRUE else msg
   }
)

setMethod("madFilter", signature(object="PreFilter"),
   function(object) object at mad
)

setReplaceMethod("madFilter", signature(object="PreFilter", 
value="numeric"),
   function(object, value) {
      if (length(value) == 1) {
         value[2] <- 0.01
      } else if (length(value) != 2) {
         stop(paste(sQuote("mad"), "must have <cutoff,epsilon>"))
      }#if

      if (length(object at mad) == 0) {
         object at numfilters <- object at numfilters + 1
      }#if
      object at mad <- list(cutoff  = as.double(value[1]),
                         epsilon = as.double(value[2]))
      return(object)
   }
)
------- END: scriptPreFilter.R ---------
Martin Morgan
# 
Hi Christian --

Does your package have a name space, but not export 'initialize'?
Calling 'new' will then go directly to the default constructors,
generating the error. A different solution would be to define a
constructor in your package

PreFilter <- function(...) {
    new("PreFilter", ...)
}

so that your user would not have to know about the details of calling
new, you could provide helpful arguments to your constructor, and
'pre-processing' of arguments can be done (in the constructor) before
calling 'new' (I find this helpful, to avoid have to be too careful
when constructing initialize methods that deal with both the class and
classes derived from the class).

Martin

cstrato <cstrato at aon.at> writes:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
      #
    

  


  

      
Dear Martin

Thank you for your comments!

You are correct, I have a name space but did not export "initialize",
since I thought that a user will never need to use it.

I will also try your suggestion to define a constructor in my package,
this seems to me to be a great idea.

Merry Christmas
Christian

        
Martin Morgan wrote: