From trevor@|@d@v|@ @end|ng |rom gm@||@com  Mon Mar 11 16:59:31 2024
From: trevor@|@d@v|@ @end|ng |rom gm@||@com (Trevor Davis)
Date: Mon, 11 Mar 2024 08:59:31 -0700
Subject: [Rd] Vignettes with long compute time
In-Reply-To: <d2a753$lln78o@ironport10.mayo.edu>
References: <d2a753$lln78o@ironport10.mayo.edu>
Message-ID: <CAMigB8GOmZWSY-OQPPmhA4eb1AzwopFM1tGOiyDJDue4Rm=TGA@mail.gmail.com>

> Is there a way to include the compiled version of a vignette in the doc
directory but mark
it to NOT be rerun by CRAN?

Some developers "precompute" their vignettes so CRAN has nothing left to
run: https://ropensci.org/blog/2019/12/08/precompute-vignettes/

> Beth Atkinson and I are splitting out many of the vignettes from the
survival
package into a separate package survivalVignettes.

An alternative some authors use is to temporarily use a special
`.Rbuildignore` file to omit large vignettes when building the CRAN package
but don't use that file for the normal development version (so that all the
vignettes are available in the `{pkgdown}` website and for users who
install using alternative channels like `remotes::install_github()`).

Trevor

On Mon, Mar 11, 2024 at 8:44?AM Therneau, Terry M., Ph.D. via R-devel <
r-devel at r-project.org> wrote:

> Is there a way to include the compiled version of a vignette in the doc
> directory but mark
> it to NOT be rerun by CRAN?   I think I remember that this is possible,
> but have forgotton
> how.   (It might even be a false memory.)
>
> Terry T.
>
> Background:  Beth Atkinson and I are splitting out many of the vignettes
> from the survival
> package into a separate package survivalVignettes.  There are a few reasons
>
>   1. Some vignettes use packages outside of the base + recommended set;
> psueodovalues for
> instance are normally used as input to a subsequent GEE model.    Since
> survival is itself
> a recommended package, it can't legally host the pseudo.Rnw vignette.
>   2. The set of vignettes for survival is large, and likely to get
> larger.    It makes
> sense to slim down the size of the package itself.
>   3. It allows us to use Rmd.  (Again, survival can't use anything outside
> of base +
> recommended).
>   4. We have a couple of 'optional' vignettes that talk about edge cases,
> useful to some
> people but not worth the size cost of cluttering up the main package.
>
> The current submission fails due to one vignette in group 4 which takes a
> looong time to
> run.  This vignette in particular is talking about compute time, and
> illustrates a cases
> where an O(n^2) case arises.   As sentence that warns the use "of you do
> this it will take
> hours to run" is a perfect case for a pdf that should not be recreated by
> R CMD check.
>
> --
> Terry M Therneau, PhD
> Department of Quantitative Health Sciences
> Mayo Clinic
> therneau at mayo.edu
>
> "TERR-ree THUR-noh"
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] Vignettes with long compute time
Trevor Davis