R devel - Mar 2007 - Problem with S4 inheritance: unexpected re-initialization?

Dear all,

To explain my problem I am attaching a demonstration package
"myclasspkg":
I have the following two S4 classes with similar inheritance:
   SubSubClassA <- SubClassB <- BaseClass
   SubSubClassB <- SubClassB <- BaseClass

In R I am calling the following functions:
 > library(myclasspkg)
 > subA <- 
new("SubClassA",filename="OutSubA",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",mytitle="TitleSubA")
 > subsubA <- 
new("SubSubClassA",filename="MyFileName",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
 > subsubB <- 
new("SubSubClassB",filename="MyFileNameB",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)

Creating subsubA works fine and gives the correct result:
 > subsubA <- 
new("SubSubClassA",filename="MyFileName",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassA------"
[1] "SubSubClassA:init:class(.Object) =  SubSubClassA"
[1] "------initialize:SubClassB------"
[1] "SubClassB:init:class(.Object) =  SubSubClassA"
[1] "------initialize:BaseClass------"
[1] "BaseClass:init:class(.Object) =  SubSubClassA"
[1] "------pathFile------"
[1] "BaseClass:init:dirfile =  
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName"
[1] "------setValidity:BaseClass------"
[1] "BaseClass:val:class(object) =  SubClassB"
[1] "BaseClass:val:dirfile =  
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName"
[1] "BaseClass:val:filedir = 
/Volumes/CoreData/CRAN/Workspaces/rclasspkg"
[1] "------setValidity:SubClassB------"
[1] "SubClassB:val:class(object) =  SubClassB"
[1] "SubClassB:val:filename =  MyFileName"
[1] "BaseClass:val:dirfile =  
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName"
[1] "------setValidity:SubSubClassA------"
[1] "SubSubClassA:val:class(.Object) =  SubSubClassA"

In contrast, when trying to create subsubB, it seems that setValidity
re-initializes SubClassB:
 > subsubB <- 
new("SubSubClassB",filename="MyFileNameB",filedir="/Volumes/CoreData/CRAN/Workspaces/rclasspkg",subA=subA)
[1] "------initialize:SubSubClassB------"
[1] "SubSubClassB:init:class(.Object) =  SubSubClassB"
[1] "SubSubClassB:init:subsubnameB =  subsubNameB"
[1] "------initialize:SubClassB------"
[1] "SubClassB:init:class(.Object) =  SubSubClassB"
[1] "------initialize:BaseClass------"
[1] "BaseClass:init:class(.Object) =  SubSubClassB"
[1] "------pathFile------"
[1] "BaseClass:init:dirfile =  
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileNameB"
[1] "------setValidity:BaseClass------"
[1] "------initialize:SubClassB------"
[1] "SubClassB:init:class(.Object) =  SubClassB"
[1] "------initialize:BaseClass------"
[1] "BaseClass:init:class(.Object) =  SubClassB"
[1] "------pathFile------"
Error in if (dirname(filename) != ".") { :
        argument is of length zero

Can someone tell me why the first case works fine, but the second case not?
Probably, I am making some mistake, but since two weeks I am unable to 
find it.
Thank you in advance.

P.S.: I am running R-2.5.0 on Intel-Mac OS 10.4.8.

Best regards
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
_._._._._._._._._._._._._._._._

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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

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