Dear S4 experts, Since I was reminded that I posted a similar question some time ago, I am attaching a modified version of my demo package, which allows me to track what happens during initialization of the following similar subclasses: SubSubClassA <- SubClassB <- BaseClass SubSubClassB <- SubClassB <- BaseClass
First, I need to create SubClassA: > library(myclasspkg)> subA <- new("SubClassA",filename="OutSubA",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",mytitle="TitleSubA")
Then, I create both subclasses, SubSubClassA and SubSubClassB, either
with a virtual BaseClass or with a non-virtual BaseClass:
1. new("SubSubClassA"): BaseClass is VIRTUAL
> subsubA <-
new("SubSubClassA",filename="MyFileName",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassA------"
[1] "------initialize:SubClassB------"
[1] "------initialize:BaseClass------"
[1] "------setValidity:BaseClass------"
[1] "------setValidity:SubClassB------"
[1] "------setValidity:SubSubClassA------"
As far as I understand the S4 classes, this is the correct initialization
workflow that I expect. The resulting object "subsubA" is correct.
However, when BaseClass is not virtual, I get the following unexpected
initialization workflow:
2. new("SubSubClassA"): BaseClass is NOT VIRTUAL
> subsubA <-
new("SubSubClassA",filename="MyFileName",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassA------"
[1] "------initialize:SubClassB------"
[1] "------initialize:BaseClass------"
[1] "------setValidity:BaseClass------" (called but NOT executed!)
[1] "------initialize:BaseClass------" (2.initialization, why?)
[1] "------setValidity:BaseClass------"
[1] "------setValidity:SubClassB------"
[1] "------setValidity:SubSubClassA------"
The first call to setValidity is not executed, and BaseClass is
initialized twice, the second time in a completely wrong way, which
normally results in an error. Interestingly, the resulting object
"subsubA" is still correct.
The results are completely different for SubSubClassB:
3. new("SubSubClassB"): BaseClass is VIRTUAL
> subsubB <-
new("SubSubClassB",filename="MyFileNameB",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassB------" [1] "------initialize:SubClassB------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------initialize:SubClassB------" [1] "------initialize:BaseClass------" [1] "------initialize:SubClassA------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------setValidity:SubClassA------" [1] "------setValidity:BaseClass------" [1] "------setValidity:SubClassB------"Error in validObject(.Object) : invalid class "SubClassB" object: 'filename' is missing
For some unknown reason SubClassA is initialized and BaseClass is
initialized three times. SetValidity is called until an error occurs.
Things get more weird when BaseClass is not virtal:
4. new("SubSubClassB"): BaseClass is NOT VIRTUAL
> subsubB <-
new("SubSubClassB",filename="MyFileNameB",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassB------" [1] "------initialize:SubClassB------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------initialize:SubClassB------" [1] "------initialize:BaseClass------" [1] "------initialize:SubClassA------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------setValidity:SubClassA------" [1] "------setValidity:BaseClass------" [1] "------initialize:BaseClass------" [1] "------setValidity:BaseClass------" [1] "------setValidity:SubClassB------"Error in validObject(.Object) : invalid class "SubClassB" object: 'filename' is missing
It seems that initialization occurs in an endless cycle until an
error occurs.
Finally, let us look what happens when I follow the usual convention
where callNextMethod() is called first:
5. new("SubSubClassA"): callNextMethod() as 1.command; BaseClass is VIRTUAL
> subsubA <-
new("SubSubClassA",filename="MyFileName",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassA------"
[1] "------initialize:SubClassB------"
[1] "------initialize:BaseClass------"
The object "subsubA" is created correctly, however, setValidity()
is never called.
The same is true for SubSubClassB:
6. new("SubSubClassB"): callNextMethod() as 1.command; BaseClass is VIRTUAL
> subsubB <-
new("SubSubClassB",filename="MyFileNameB",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassB------" [1] "------initialize:SubClassB------" [1] "------initialize:BaseClass------" The object "subsubB" is for the first time created correctly, however, once again setValidity() is never called. Maybe, I am misunderstanding an important part of creating S4 classes. I would be really greatful, if the S4 experts could explain me what happens here and what might be wrong with my demo package. As a side note, when studying the code of the S4 packages "Biobase", "affy" and "oligo", I made the observation, that none of these packages calls "initialize" and "setValidity" for all classes and sub-classes. Thank you very much in advance. Best regards Christian
myclasspkg_0.1.1.tar.gz
Description: GNU Zip compressed data
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