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

3 messages · Dan Kelley, Roy Mendelssohn - NOAA Federal, Duncan Murdoch

Original
Dan Kelley
# 
# 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
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
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
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 at noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
Duncan Murdoch
# 
When you get a note from CRAN, remember that it ignores Roxygen comments 
completely.  It's just looking at the files that Roxygen produces.  So 
you should look at the .Rd files when you get a complaint about them.

Your previous code would have produced a file named plan.Rd, and that 
file didn't include the "plan-package" alias that was requested.  The 
new version does, so things are now fine.  I think that up until a few 
years ago, the old version would have worked, but this news item from 
2019 hints at the change:

"Using @docType package no longer automatically adds -name. Instead 
document _PACKAGE to get all the defaults for package documentation, or 
use @name to override the default file name."

Duncan Murdoch
On 19/08/2023 8:54 a.m., Daniel Kelley wrote: