[Bioc-devel] Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

[Dan Tenenbaum]

----- Original Message -----
> From: "lcollado" <lcollado at jhu.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Thursday, October 29, 2015 2:09:57 PM
> Subject: [Bioc-devel] Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

> Hi,
> I'm planning on switching some vignettes to BiocStyle (html version).
> Is there any particular reason why the html vignette for BiocStyle is
> outside of the /vignettes directory? I see it at
> /inst/rmarkdown/templates/html_document/skeleton/skeleton.Rmd with
> /vignettes/HtmlStyle.Rmd linking to it. I didn't know that you could
> write such links, thanks! But does it help with speeding up the
> building or testing steps if the vignette is outside of /vignettes?
> BiocCheck has its vignette at /vignettes/BiocCheck.Rmd so I know that
> such a setup is not necessary.

I will let the BiocStyle maintainers answer this one.

> Currently, one of my vignettes takes a few min to render, which is why
> I followed ggbio's setup: fake empty vignettes + real ones and a
> Makefile making sure the correct vignette gets built. I thought that
> this trick saved time in R CMD check.
> I looked at "Writing R Extensions" and I think that such a trick only
> saves time when you run R CMD check on the source directory instead of
> the tarball created by R CMD build. So unless I'm forgetting
> something, this trick doesn't seem necessary at all given that
> Bioconductor runs build and then check (with --no-vignettes) on the
> tarball. Right?
> I guess that it was useful for me before when I would run lots of
> checks directly on the source code directory instead of building and
> checking.

Yes, these tricks don't save any time on the build system because although the build system runs
R CMD build on a directory, that directory is newly created every day so no cached files persist between builds. And then as you point out, R CMD check is run with the --no-vignettes option, and runs on a tarball anyway.

Dan


> Thanks,
> Leo
> 
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