[R-pkg-devel] possible solution to package-documentation-alias problem

[Roy Mendelssohn - NOAA Federal]

Thanks Dan.  Also see:

https://r-pkgs.org/man.html#sec-man-package-doc

My understanding is that literally thousands of packages are broken in the same way.

-Roy

> On Aug 19, 2023, at 5:54 AM, Daniel Kelley <kelley using dal.ca> wrote:
> 
> # Preamble
> 
> This email is to tell other developers what I did to address an issue with
> documenting a package.  I'm not sure that I am correct in my approach --
> comments would definitely be appreciated -- but at least this email is fairly
> concrete about the changes I made. To be honest, I don't know how to test
> whether my changes are suitable, since no problem is reported in local builds or
> in remote windows checks, and no problem is listed on the CRAN tests page.
> 
> # The problem
> 
> Today I received multiple emails from K. Hornik, telling me about problems with
> the package-level documentation for several CRAN packages that I maintain. Here
> is a key part of that email:
> 
>    You have file 'oce/man/oce.Rd' with \docType{package}, likely intended as a
>    package overview help file, but without the appropriate PKGNAME-package
>    \alias as per "Documenting packages" in R-exts.
> 
> # Possible solution
> 
> As a test (using the 'plan' package, which is much smaller and thus ought to
> give faster test results), I changed my Roxygen2 block
> 
>    #' @name plan
>    #' @docType package
>    #' @author Dan Kelley
>    NULL
> 
> to read
> 
>    #' @name plan
>    #' @docType package
>    #' @author Dan Kelley
>    #' @keywords internal
>    "_PACKAGE"
>    ## usethis namespace: start
>    ## usethis namespace: end
>    NULL
> 
> Note that the two ## comments are likely not required, but I included them
> because I saw them at
> 
> https://github.com/jonesor/mpmsim/commit/e8d0f0d657ffa24c25ddd3165c7ddcad16322e3d
> 
> which I found to be quite a helpful resource.
> 
> # Local testing
> 
> After rebuilding locally, I can now do
> 
>    package?plan
> 
> and get the expected documentation for the package as a whole.
> 
> # CRAN submission
> 
> I submitted the update to CRAN, and it has appeared as a tarball.  It has not
> yet appeared in built-up packages sources, but perhaps the fact that I didn't
> get any warnings from CRAN suggests that the flaw has been addressed.
> 
> # Conclusions
> 
> If I am right, a simple fix is all that will be required for many packages.
> However, I don't know of any way to know if this fix follows recommended
> procedures.  There appear to be multiple ways of addressing the issue.
> 
> Perhaps other developers will have better solutions than the one I've outlined
> above.  Or, if I happen to have done something right, then perhaps this email
> will be of some use to other developers.
> 
> Dan Kelley / Department of Oceanography / Dalhousie University / Canada
> 
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**********************
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**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
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