[R-pkg-devel] check --as-cran error on Rd file

[Charles Geyer]

blurfle$ cat sped.Rcheck/00check.log
* using log directory ‘/home/geyer/Software/sped/package/sped.Rcheck’
* using R Under development (unstable) (2020-03-10 r77920)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘sped/DESCRIPTION’ ... OK
* this is package ‘sped’ version ‘0.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Charles J. Geyer <charlie using stat.umn.edu>’

New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘sped’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ...
OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Variables with usage in documentation object 'alberta' but not in code:
  ‘alberta’

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘foo.R’
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 1 NOTE
blurfle$

I do not get this warning when --as-cran is omitted.  I have never seen the
warning before.  The Rd file is

blurfle$ cat sped/man/alberta.Rd
\name{alberta}
\docType{data}
\alias{alberta}
\title{Pedigree Data on Equus przewalskii in Alberta}
\description{
  Pedigree of Asian wild horse (also called Mongolian wild horse)
  \emph{Equus przewalskii} individuals living in Alberta, Canada in 1988.
}
\usage{alberta}
\format{
A matrix with 69 rows giving (individual, father, mother) triplets.
The column labels are \code{ind}, \code{pa}, and \code{ma}.
The names (which are numbers) are studbook numbers.
There are 82 individuals in this pedigree in all.
There are \eqn{82 - 69 = 13} founders.
}
\examples{
library(sped)
data(alberta)
}
\keyword{datasets}
blurfle$

And this is AFAICS what Section 2.1.2 of Writing R Extensions (R-devel
version) says it should be.

So what is this warning about?

-- 
Charles Geyer
Professor, School of Statistics
Resident Fellow, Minnesota Center for Philosophy of Science
University of Minnesota
charlie using stat.umn.edu

	[[alternative HTML version deleted]]