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

----- 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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Hi Leonardo,

thank you for considering using BiocStyle for your vignettes! Please read
below.

On Thu, Oct 29, 2015 at 10:17 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- 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.

There is no specific reason for this other than convenience: at some point
I had the idea of providing a template for BiocStyle::html_document and
figured out that the package vignette itself could serve that purpose. So
to avoid redundancy I put the vignette in the templates directory which is
discovered by RStudio/rmarkdown, and link to it from the  vignettes
directory in order to build it as the package vignette as well. The other
way round wouldn't probably work as the vignette source gets copied to
/inst/doc upon installation. I don't see any obvious reason how this
approach could affect performance in any way, either positively or
negatively.

Cheers,
Andrzej
Awesome, thanks for the replies and clarifications!
Hi Leonardo,

thank you for considering using BiocStyle for your vignettes! Please read
below.

On Thu, Oct 29, 2015 at 10:17 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- 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.

There is no specific reason for this other than convenience: at some point I
had the idea of providing a template for BiocStyle::html_document and
figured out that the package vignette itself could serve that purpose. So to
avoid redundancy I put the vignette in the templates directory which is
discovered by RStudio/rmarkdown, and link to it from the  vignettes
directory in order to build it as the package vignette as well. The other
way round wouldn't probably work as the vignette source gets copied to
/inst/doc upon installation. I don't see any obvious reason how this
approach could affect performance in any way, either positively or
negatively.

Cheers,
Andrzej