[R-pkg-devel] NOTE about lack of prebuilt manual

[Viechtbauer, Wolfgang (NP)]

Hi Michael,

I assume you are getting this note because you are using mathjaxr. I am also getting this and others have reported the same:

https://github.com/wviechtb/mathjaxr/issues/15

(my response on the forum was a bit premature, since this note eventually did show up for me as well).

This appears to be related to this change (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):

- tools::checkRd() (used by R CMD check) detects more problems with ⁠\Sexpr⁠-based dynamic content, including bad nesting of ⁠\Sexpr⁠s and invalid arguments.

which was made in R version 4.4.0. I have submitted an updated metafor version in the meantime despite this note and it was accepted without any problems. Also, while I am getting this note locally, this note does not show up on the CRAN check results:

https://cran.r-project.org/web/checks/check_results_metafor.html

The manual is also available on the CRAN website:

https://cran.r-project.org/package=metafor

and also in the build directory of the tarball (https://cran.r-project.org/src/contrib/metafor_4.6-0.tar.gz).

So, unless CRAN states otherwise, I would suggest to submit the updated versions, burn some incense, pray twenty vectorized hail Rs, and hope for the best.

Best,
Wolfgang

> -----Original Message-----
> From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf Of Uwe
> Ligges
> Sent: Monday, July 8, 2024 16:40
> To: Iris Simmons <ikwsimmo using gmail.com>; Michael Dewey <lists using dewey.myzen.co.uk>
> Cc: List r-package-devel <r-package-devel using r-project.org>
> Subject: Re: [R-pkg-devel] NOTE about lack of prebuilt manual
>
> On 08.07.2024 16:08, Iris Simmons wrote:
> > This is something I'd run into recently as well.
> >
> > The R devs changed the default from building the manual to not building the
> > manual. Now if you want (or need) to build the manual, you should add
>
> Well, not really, we still build manuals unless file(s) containing
> install/render-stage \Sexpr{}  are present (as in this case).
>
> Best,
> Uwe Ligges
>
> > BuildManual: TRUE
> >
> > to your DESCRIPTION.
> >
> > On Mon, Jul 8, 2024, 10:05 Michael Dewey <lists using dewey.myzen.co.uk> wrote:
> >
> >> Short version
> >>
> >> I have recently tried to update two of my CRAN packages and I am getting
> >> the NOTE from R CMD check --as-cran
> >>
> >> Package has help file(s) containing install/render-stage \Sexpr{}
> >> expressions but no prebuilt PDF manual.
> >>
> >> (It comes on one line in the check.log)
> >>
> >> What am I doing wrong?
> >>
> >> ===================
> >>
> >> More details
> >>
> >> Both packages have lived successfuly on CRAN for some time but my recent
> >> attempts to update lead to the NOTE shown above. I notice that the
> >> version currently on CRAN do have in the tarball a directory called
> >> build which amongst other thing does contain the package manual. However
> >> when I build the updated versions the tarball still contains a build
> >> directory but without the manual.
> >>
> >> I am using 4.4.1 under Windows 10. I open a command line and do
> >> everything from there with R CMD, I do not use any helper package. The
> >> help files do not explicitly contain any instance of \Sexpr{} but they
> >> do contain macros. Both of them use mathjaxr and Rdpack and one also has
> >> some macros written by me. They have been like that for some while. The
> >> Rd files are hand-written, I do not use any package to generate
> >> documentation.
> >>
> >> I notice that R CMD build has an option to turn off the manual but I do
> >> not set that and there does not seem to be a turn on option. I have
> >> looked at the NEWS for R4.4.0 and 4.4.1 but withou enlightenment. The
> >> versions on CRAN were probably generated with R 4.3.3 judgin by the date
> >> when I made them.
> >>
> >> I know it is only a NOTE but I would like to know why it is happening.
> >>
> >> I hope that is enough detail to be helpful but I can expand on any
> >> unclear areas.
> >>
> >> --
> >> Michael