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

[Duncan Murdoch]

On 11/03/2020 11:44 a.m., Charles Geyer wrote:
> 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?

The manual says "The \usage entry is always bar or (for packages which 
do not use lazy-loading of data) data(bar). (In particular, only 
document a single data object per Rd file.)".  So maybe you aren't using 
lazy loading?

Duncan Murdoch