If a class is derived from a superclass using 'contains', then coercion of
an object from the class to the superclass fails to preserve the 'package'
attribute of class of the object.
This occurs only when the derived class has no additional slots.
This is a problem because the 'new' function relies on the exact identity
of the class, including the package attribute.
This can clearly be worked around by the introduction of dummy slots, but it
took me some time to track down.
> setClass("baseClass",representation(a="numeric"))
[1] "baseClass"
> setClass("fancyClass",contains="baseClass")
[1] "fancyClass"
>
setClass("fancyClassExtraSlots",representation(b="numeric"),contains="baseCl
ass")
[1] "fancyClassExtraSlots"
>
>
> aFP <- new("fancyClass",a=2)
> aFP2 <- new("fancyClassExtraSlots",a=2,b=3)
>
> aBP <- new("baseClass",a=1)
> aBPcast <- as(aFP,"baseClass")
> aBPcast2 <- as(aFP2,"baseClass")
> # all the baseClass objects have the right class
> sapply(list(aBP,aBPcast,aBPcast2),class)
[1] "baseClass" "baseClass" "baseClass"
> # however the object cast from a fancy class with no slots has a different
package attribute
> sapply(list(aBP,aBPcast,aBPcast2),function(x)attr(class(x),"package"))
[[1]]
[1] ".GlobalEnv"
[[2]]
NULL
[[3]]
[1] ".GlobalEnv"
> new("baseClass",aBP) # works
An object of class "baseClass"
Slot "a":
[1] 1
> new("baseClass",aBPcast) # fails. Note the error message!
Error in initialize(value, ...) : Initialize method returned an object of
class "baseClass" instead of the required class "baseClass"
> new("baseClass",aBPcast2) # works
An object of class "baseClass"
Slot "a":
[1] 2
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 1
minor 9.0
year 2004
month 04
day 12
language R
Jonathan Swinton, Statistical Scientist, Computational Biology, Pathway
Analysis, Global Sciences and Information, x29400, 19F44 Mereside Alderley
Park.
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