[Rd] Bug in str or issue with class management in my package?

[Ulrike Grömping]

Martin,

thank you, you've pointed me in the right direction! I just wasn't aware
that a slot must not be unassigned (everything but str worked so far, and
even str works in R 2.3.1). 

Actually, looking up the help for function new, I see that the solution is
much easier, because my class relimplmbooteval extends the class relimplm of
the object ausgabe. Therefore, I can simply write 
          obj <- new("relimplmbooteval", ausgabe)
which copies all slots from ausgabe to the right place in the new obj.

Regards, Ulrike


Martin Morgan wrote:
> 
> Ulrike,
> 
> booteval.relimp has the statement
> 
>     ausgabe <- calc.relimp(empcov, type = type, diff = diff, 
>         rank = rank, rela = rela, always = always, groups = groups, 
>         groupnames = groupnames)
>     class(ausgabe) <- "relimplmbooteval"
> 
> This changes the name of the class of ausgabe, without changing its
> structure. I'm guessing that prior to this call ausgabe did not have a
> slot "pmvd.lower". Here's the simpler version:
> 
>>setClass("A", representation=representation(x="numeric"))
> [1] "A"
>> setClass("B", contains="A", representation=representation(y="numeric"))
> [1] "B"
>> a <- new("A")
>> class(a) <- "B"
>> str(a)
> Error in FUN(c("y", "x")[[1L]], ...) : no slot of name "y" for this object
> of class "B"
> 
> and some behavior which is somehow weird:
> 
>> slot(a, "y")
> Error in slot(a, "y") : no slot of name "y" for this object of class "B"
>> slot(a, "y") <- 10 # 'creates' the slot!
>> slot(a, "y")
> [1] 10
> 
> Probably what you want to do is to create a 'setAs' method
> 
> setAs('relimplm', 'relimplmbooteval',
>       function(from) {
>           <your code here, e.g.,>
>       })
> 
> and use
> 
>     ausgabe <- as(ausgabe, "relimplmbooteval")
> 
> I'm not really sure what <your code here> should look like; my first
> stab was
> 
>           obj <- new("relimplmbooteval")
>           slots <- slotNames(from)
>           for (slt in slots)
>               slot(obj, slt) <- slot(from, slt)
>           obj
> 
> which would not be very memory efficient (each slot assignment copies
> the entire object) but is perhaps fine for your needs.
> 
> Hope that helps
> 
> Martin
> 
> Ulrike Grömping <groemp at tfh-berlin.de> writes:
> 
>> Dear developeRs,
>>
>> with R 2.4.1 (and also 2.4.0), the function str() fails on objects of
>> class
>> relimplmbooteval, if there are unused slots, which is very often the
>> case. I
>> am not sure whether this is a bug in str() or a correct behavior of str()
>> that unmasks some sloppiness in my usage of S4 classes (that I am not
>> aware
>> of)?
>>
>> Reproducible example (package relaimpo needed):
>>
>> The program 
>>
>> require(relaimpo)
>> bte<-booteval.relimp(boot.relimp(swiss,b=100))
>> str(bte)
>>
>> yields the error message
>>
>> Errorr in FUN(c("lmg.lower", "lmg.upper", "lmg.rank.lower",
>> "lmg.rank.upper",  : 
>>         no slot named "pmvd.lower" for this object of class
>> "relimplmbooteval"
>> (back-translated from German).
>>
>> Regards, Ulrike
>> -- 
>> View this message in context:
>> http://www.nabble.com/Bug-in-str-or-issue-with-class-management-in-my-package--tf3453429.html#a9633559
>> Sent from the R devel mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 

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