Still problems with R CMD check: undocumented S4 classes - class

Question

I read the long list of questions posted in stackoverlow and other websites about problems with R CMD check and missing documentation. However, I still did not find the correct information to make Roxygen2 to generate the correct .RD file to solve the WARNING in R CMD check.
The WARNING is generated when documenting an S4 class.
I generated a package "TMP" just composed by a S4 class XPSCoreLine
This is my Roxygen header and the R code:
#' #title class XPSCoreLine
#' #description definition of the coreLine class for the XPS Core-Line spectra
#'
#' #slot RegionToFit the portion of the spectrum to fit
#' #slot Baseline the Baseline applied to subtract background
#' #slot Components the fitting components
#' #slot Fit the best fit
#' #slot Boundaries the values of the RegionToFit edges
#' #slot RSF the relative seisitivity factor associated to the element spectrum
#' #slot Shift the energy correction shift if charging present
#' #slot units the adopted units: kinetic/binding energy, counts/counts_per_second
#' #slot Flags logical
#' #slot Info information regarding the spectrum acquisition
#' #slot Symbol symbol of the element associated to the spectrum
#'
#' #aliases XPSCoreLine
#' #keywords XPSCoreLine
#' #name XPSCoreLine
#' #rdname XPSCoreLine
#' #docType class
#'
#' #examples
#' \dontrun{
#' test <- new("XPSCoreLine", Info="test", units=c("Binding [eV]", "Counts"))
#' }
#' #exportClass XPSCoreLine
#'
setClass("XPSCoreLine",
representation(
RegionToFit="list",
Baseline="list",
Components="list",
Fit="list",
Boundaries="list",
RSF="numeric",
Shift="numeric",
units="character",
Flags="logical",
Info="character",
Symbol="character"
),
prototype(
RegionToFit=list(),
Baseline=list(),
Components=list(),
Fit=list(),
RSF=0,
Shift=0,
Boundaries=list(),
units=c("Binding Energy [eV]","Intensity [cps]"),
Flags=c(TRUE, FALSE, FALSE),
Info="",
Symbol=""
),
contains = "list"
)
This generates the following .../man/XPSCoreLine.RD:
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/XPSClass.r
\docType{class}
\name{XPSCoreLine}
\alias{XPSCoreLine}
\title{class XPSCoreLine}
\description{
definition of the coreLine class for the XPS Core-Line spectra
}
\section{Slots}{
\describe{
\item{\code{RegionToFit}}{the portion of the spectrum to fit}
\item{\code{Baseline}}{the Baseline applied to subtract background}
\item{\code{Components}}{the fitting components}
\item{\code{Fit}}{the best fit}
\item{\code{Boundaries}}{the values of the RegionToFit edges}
\item{\code{RSF}}{the relative seisitivity factor associated to the element spectrum}
\item{\code{Shift}}{the energy correction shift if charging present}
\item{\code{units}}{the adopted units: kinetic/binding energy, counts/counts_per_second}
\item{\code{Flags}}{logical}
\item{\code{Info}}{information regarding the spectrum acquisition}
\item{\code{Symbol}}{symbol of the element associated to the spectrum}
}}
\examples{
\dontrun{
test <- new("XPSCoreLine", Info="test", units=c("Binding [eV]", "Counts"))
}
}
\keyword{XPSCoreLine}
The NAMESPACE contains:
# Generated by roxygen2: do not edit by hand
exportClasses(XPSCoreLine)
In RStudio the command check_man applied to the package "TMP" just composed by the S4class XPSCoreLine defined above:
> check_man("~/R/tmp/")
ℹ Updating TMP documentation
ℹ Loading TMP
ℹ Checking documentation...
✔ No issues detected
However running devtools::check using the command check("~/R/tmp/", document=TRUE)
I'm unable to get rid of the WARNING
checking for missing documentation entries ... WARNING
Undocumented S4 classes:
‘XPSCoreLine’
Undocumented S4 methods:
generic 'hasBoundaries' and siglist 'XPSCoreLine'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Is there anybody which can suggest a solution?
Thanks in advance
G. Speranza

Answer 1

Following a private mail exchange with Hadley Wickman, the roxygen maintainer, he kindly answered my request suggesting to remove
#' #aliases XPSCoreLine
#' #keywords XPSCoreLine
#' #name XPSCoreLine
#' #rdname XPSCoreLine
#' #docType class
and replace
#' #exportClass XPSCoreLine
with
#' #export
"Otherwise you've effectively disabled all the S4 stuff that roxygen2 does for you."
This makes R CMD check to recognize the S4 class 'XPSCoreLine'. I then got a second error from R CMD check:
❯ checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'XPSCoreLine-class':
Slots for class 'XPSCoreLine'
Code: .Data Baseline Boundaries Components Fit Flags Info RSF
RegionToFit Shift Symbol units
Docs: Baseline Boundaries Components Fit Flags Info RSF RegionToFit
Shift Symbol units
The slot .Data is implicitly introduced in the S4 class. It is not included in the representation and in the prototype. I included it in the roxygen header then the correct code for the 'XPSCoreLine' class is:
#' #title class XPSCoreLine
#' #description definition of the coreLine class for the XPS Core-Line spectra
#'
#' #slot .Data contains the X, Y spectral data
#' #slot RegionToFit the portion of the spectrum to fit
#' #slot Baseline the Baseline applied to subtract background
#' #slot Components the fitting components
#' #slot Fit the best fit
#' #slot Boundaries the values of the RegionToFit edges
#' #slot RSF the relative seisitivity factor associated to the element spectrum
#' #slot Shift the energy correction shift if charging present
#' #slot units the adopted units: kinetic/binding energy, counts/counts_per_second
#' #slot Flags logical
#' #slot Info information regarding the spectrum acquisition
#' #slot Symbol symbol of the element associated to the spectrum
#'
#' #examples
#' \dontrun{
#' test <- new("XPSCoreLine", Info="test", units=c("Binding [eV]", "Counts"))
#' }
#' #export
#'
setClass("XPSCoreLine",
representation(
RegionToFit="list",
Baseline="list",
Components="list",
Fit="list",
Boundaries="list",
RSF="numeric",
Shift="numeric",
units="character",
Flags="logical",
Info="character",
Symbol="character"
),
prototype(
RegionToFit=list(),
Baseline=list(),
Components=list(),
Fit=list(),
RSF=0,
Shift=0,
Boundaries=list(),
units=c("Binding Energy [eV]","Intensity [cps]"),
Flags=c(TRUE, FALSE, FALSE),
Info="",
Symbol=""
),
contains = "list"
)
This removes the last R CMD check warning...