[R-pkg-devel] How to get rid of R CMD check warning/note for new S4 classes

Dear David,

A follow-up if you don't mind: one slot of my actual S4 object contains either NULL or a grid::frameGrob object. As you may know, frameGrob objects inherit from multiple S3 classes: "frame" "gTree" "grob" ?"gDesc".

Based upon my understanding of the documentation, I need to define my S4 class as follows using a setOldClass call for the S3 classes that are used in the setClassUnion call.

----
? setOldClass(c('frame','gTree','grob','gDesc'))
? setClassUnion('myFrame', c('frame','gTree','grob','gDesc','NULL'))
? 
? 
? setClass('myClass',
? ? where = .GlobalEnv, 
? ? slots = c(
????? grid.frame = 'myFrame',
? ? ),
? ? prototype = list(
? ? ? grid.frame = NULL,
? ? )
? )
----

This causes `R CMD check` to complain about "frame" "gTree" "grob"  "gDesc"
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  "frame" "gTree" "grob"  "gDesc"
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.

Including \alias{frame-class}, \alias{grob-class}, \alias{gTree-class}, \alias{gDesc-class} in my S4 class .Rd files prevents the WARNING to be reported, but this does not feel right, since these are classes from the grid package. Any suggestions?

Sebastien


-----------------------

From: David Kepplinger <david.kepplinger at gmail.com>
Sent: Tuesday, February 9, 2021 19:11
To: Sebastien Bihorel <Sebastien.Bihorel at cognigencorp.com>
Cc: r-package-devel at r-project.org <r-package-devel at r-project.org>
Subject: Re: [R-pkg-devel] How to get rid of R CMD check warning/note for new S4 classes 
?
Dear Sabastien,

Your second approach is correct, but as the warning suggests, you have to document the S4 class "character or NULL". The documentation at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-S4-classes-and-methods should get you started.

Best,
David

Hi 

I posted the following message on Jan 2nd and got no response... Assuming that my timing was off (everybody was probably still on vacation or recovering from New Year's celebration), I am taking the liberty to post it again, hoping that I'll reach a larger audience today.

------

I am creating a few S4 classes for a package. These classes include slots set to classes obtained using setClassUnion (some common across the new S4 classes). The code is functional but `R CMD check` keeps on reporting notes or warnings whatever I try. I am pulling my hair on this one and would really appreciate some insight on what I am doing wrong. 


Below are some simplified versions of a real function, which each gives different note/warning:

* Option 1 returns a note

createyNewClass <- function(){
? setClassUnion("character or NULL",c("character","NULL"),where = .GlobalEnv)
? setClass('newS4Classe',
? ? where = .GlobalEnv, 
? ? slots = c(type = 'character or NULL'),
? ? prototype = list(type = NULL)
? )
}

R CMD check
...
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: class "NULL" is defined (with package slot "methods") but no metadata object found to revise superClass information---not exported?? Making a copy in package ".GlobalEnv"
Warning: class "character" is defined (with package slot "methods") but no metadata object found to revise superClass information---not exported?? Making a copy in package ".GlobalEnv"
...

* Option 2: returns a WARNING

createyNewClass <- function(){
? setClassUnion("character or NULL",c("character","NULL"))
? setClass('newS4Classe',
? ? slots = c(type = 'character or NULL'),
? ? prototype = list(type = NULL)
? )
}

R CMD check:
...
* checking for missing documentation entries ... WARNING 
Undocumented S4 classes: 
? ?"character or numeric"
All user-level objects in a package (including S4 classes and methods) 
should have documentation entries.
...

Bit of information: I am running the R CMD check with R 3.6.1 (sorry, I cannot update on my corporate machine :( )

Thanks in advance for your help
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David Kepplinger, PhD
https://www.dkepplinger.org