Some documentation not appearing in CRAN PDF

[John Ramey]

Dario Strbenac wrote:

I installed the newest version of sparsediscrim, but in the reference manual on the CRAN website, http://cran.r-project.org/web/packages/sparsediscrim/sparsediscrim.pdf there's no documented function dlda. But in R, if I do ?dlda it is documented. I thought I'd point it out in case it confuses other users.

I confirmed that this is the case for versions 0.1 and 0.2 on CRAN.

My guess is that this is related to exporting S3 generics. Check the devtools and roxygen2 docs.

[John Ramey]

Based on Hadley's SO answer, I updated the Roxygen directives.

Afterwards, I ran:

document('.', clean=TRUE)
install()

Although ?mdeb functions correctly, mdeb is still not showing up in package's help index. Same for other classifiers.

!> sessionInfo()
 R version 3.0.3 (2014-03-06)
 Platform: x86_64-apple-darwin12.5.0 (64-bit)

 locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

 other attached packages:
 [1] sparsediscrim_0.2 roxygen2_3.1.0    devtools_1.4.1

 loaded via a namespace (and not attached):
  [1] bdsmatrix_1.3-1  brew_1.0-6       codetools_0.2-8  compiler_3.0.3
  [5] corpcor_1.6.6    digest_0.6.4     evaluate_0.5.3   httr_0.3
  [9] memoise_0.1      mvtnorm_0.9-9997 parallel_3.0.3   Rcpp_0.11.1
 [13] RCurl_1.95-4.1   stringr_0.6.2    tools_3.0.3      whisker_0.3-2

Relevant packages:

• roxygen2: version 3.1.0
• devtools: version 1.4.1

[Kevin Ushey]

Discovered the problem:

You use @keyword internal on one of the methods that ends up belonging to the same .Rd file, e.g. print.mdeb has

#' Outputs the summary for a MDEB classifier object.
#'
#' Summarizes the trained mdeb classifier in a nice manner.
#'
#' @keywords internal
#' @param x object to print
#' @param ... unused
#' @rdname mdeb
#' @export

But then, the mdeb.Rd file generated has the \keyword{internal} bit added, and everything in there gets set as internal, so nothing mdeb-related gets indexed.

[Kevin Ushey]

@hadley, this behaviour is a bit surprising -- should the rd vignette be updated to state that keywords apply to the .Rd file, not the function?

Or is there some smarter way roxygen2 could handle this?

[John Ramey]

Thanks for helping, @kevinushey. Damn copy/pasta error. Never noticed it.

[Hadley Wickham]

@kevinushey all roxygen tags apply to a file, not a function :/