R devel - Mar 2011 - WARNING Undocumented S4 methods 'initialize' - why?

Dear all,

I am just writing the documentation file for S4 class 'QualTreeSet' and 
get the following warning with R CMD check:

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
   generic 'initialize' and siglist 'QualTreeSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.

All my S4 classes have a method 'initialize' and R CMD check has never 
complained. Thus, do you have any idea why I get suddenly this warning 
for method 'initialize'?


Here is the code for 'QualTreeSet':

setClass("QualTreeSet",
    representation(qualtype = "character",
                   qualopt  = "character"
    ),
    contains=c("ProcesSet"),
    prototype(qualtype = "rlm",
              qualopt  = "raw"
    )
)#QualTreeSet

setMethod("initialize", "QualTreeSet",
    function(.Object,
             qualtype = "rlm",
             qualopt  = "raw",
             ...)
    {
       if (qualtype == "") qualtype <- "rlm";
       if (qualopt  == "") qualopt  <- "raw";

       .Object <- callNextMethod(.Object,
                                 qualtype = qualtype,
                                 qualopt  = qualopt,
                                 ...);
       .Object at qualtype = qualtype;
       .Object at qualopt  = qualopt;
       .Object;
    }
)#initialize


However, here is my code for a similar class 'ExprTreeSet' (which is the
class from where I have copied the code):

setClass("ExprTreeSet",
    representation(exprtype = "character",
                   normtype = "character"
    ),
    contains=c("ProcesSet"),
    prototype(exprtype = "none",
              normtype = "none"
    )
)#ExprTreeSet

setMethod("initialize", "ExprTreeSet",
    function(.Object,
             exprtype = "none",
             normtype = "none",
             ...)
    {
       if (exprtype == "") exprtype <- "none";
       if (normtype == "") normtype <- "none";

       .Object <- callNextMethod(.Object,
                                 exprtype = exprtype,
                                 normtype = normtype,
                                 ...);
       .Object at exprtype = exprtype;
       .Object at normtype = normtype;
       .Object;
    }
)#initialize

In this case R CMD check does not complain, so why does it in the case 
of 'QualTreeSet'?

Here is my:
 > sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

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

other attached packages:
[1] xps_1.11.4

Thank you in advance
Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.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
_._._._._._._._._._._._._._._._._._

Dear all,

Meanwhile I found my mistake.
I forgot to add class QualTreeSet to 'initialize-methods.Rd'.
However, I am not sure if I should make 'initialize' public at all.

Best regards
Christian

On 3/11/11 9:58 PM, cstrato wrote:
> Dear all,
>
> I am just writing the documentation file for S4 class 'QualTreeSet'
and
> get the following warning with R CMD check:
>
> * checking for missing documentation entries ... WARNING
> Undocumented S4 methods:
> generic 'initialize' and siglist 'QualTreeSet'
> All user-level objects in a package (including S4 classes and methods)
> should have documentation entries.
> See the chapter 'Writing R documentation files' in manual
'Writing R
> Extensions'.
>
> All my S4 classes have a method 'initialize' and R CMD check has
never
> complained. Thus, do you have any idea why I get suddenly this warning
> for method 'initialize'?
>
>
> Here is the code for 'QualTreeSet':
>
> setClass("QualTreeSet",
> representation(qualtype = "character",
> qualopt = "character"
> ),
> contains=c("ProcesSet"),
> prototype(qualtype = "rlm",
> qualopt = "raw"
> )
> )#QualTreeSet
>
> setMethod("initialize", "QualTreeSet",
> function(.Object,
> qualtype = "rlm",
> qualopt = "raw",
> ...)
> {
> if (qualtype == "") qualtype <- "rlm";
> if (qualopt == "") qualopt <- "raw";
>
> .Object <- callNextMethod(.Object,
> qualtype = qualtype,
> qualopt = qualopt,
> ...);
> .Object at qualtype = qualtype;
> .Object at qualopt = qualopt;
> .Object;
> }
> )#initialize
>
>
> However, here is my code for a similar class 'ExprTreeSet' (which
is the
> class from where I have copied the code):
>
> setClass("ExprTreeSet",
> representation(exprtype = "character",
> normtype = "character"
> ),
> contains=c("ProcesSet"),
> prototype(exprtype = "none",
> normtype = "none"
> )
> )#ExprTreeSet
>
> setMethod("initialize", "ExprTreeSet",
> function(.Object,
> exprtype = "none",
> normtype = "none",
> ...)
> {
> if (exprtype == "") exprtype <- "none";
> if (normtype == "") normtype <- "none";
>
> .Object <- callNextMethod(.Object,
> exprtype = exprtype,
> normtype = normtype,
> ...);
> .Object at exprtype = exprtype;
> .Object at normtype = normtype;
> .Object;
> }
> )#initialize
>
> In this case R CMD check does not complain, so why does it in the case
> of 'QualTreeSet'?
>
> Here is my:
>  > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] xps_1.11.4
>
> Thank you in advance
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.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
> _._._._._._._._._._._._._._._._._._
>
>