[Bioc-devel] BiocStyle markdown, pdf and html

[Peter Humburg]

There was some related discussion of this here:
https://github.com/yihui/knitr/issues/1051.
The conclusion was that this wouldn't be too difficult but there was little
enthusiasm from R core.

Cheers,
Peter

On Sat, 27 Feb 2016 at 11:44 Henrik Bengtsson <henrik.bengtsson at gmail.com>
wrote:

> On Feb 26, 2016 09:23, "Andrzej Oleś" <andrzej.oles at gmail.com> wrote:
> >
> > Hi Kasper,
> >
> > 1. It actually does, see BiocStyle::pdf_document.
> > 2. I think you might be right that R doesn't support that yet, but maybe
> > this could be circumvented through a Makefile.
> >
> > Cheers,
> > Andrzej
> >
> > On Fri, Feb 26, 2016 at 5:33 PM, Kasper Daniel Hansen <
> > kasperdanielhansen at gmail.com> wrote:
> >
> > > 1. It would be great if BiocStyle supported PDF generation from R
> markdown.
> > > 2. Would it be worth considering (if possible) generation of both PDF
> and
> > > HTML from a vignette.  We could probably do that through a Makefile,
> but
> > > I'm unsure if R supports two output files for a single input (probably
> not,
> > > come to think of it).
>
> Just adding a few comments about multiple vignette product files per
> vignette:
>
> I'd like to separate package vignettes from non-package vignettes.
> When we do the latter, there's really nothing preventing a vignette
> being compiled into multiple output files / file formats.  There's
> also no restriction in what the output format should be.
>
> When it comes to package vignettes it's a bit different.  I assume
> this is what you're think of.  The files generated from package
> vignette sources are termed "vignette products" in R / the tools
> package.  The only recognized/accepted output formats are PDF and
> HTML.  See tools:::find_vignette_product().  This function is used by
> tools::buildVignettes(), which is main function that build package
> vignettes.  (BTW, there's also tools::buildVignette() which one use to
> test build single package vignette.)    There is also a direct test in
> tools:::find_vignette_product() that only accepts one vignette product
> per package vignette, cf.
>
>
> https://github.com/wch/r-source/blob/trunk/src/library/tools/R/Vignettes.R#L80-L84
>
> It should be too hard to change this part to allow for multiple output
> files/formats.  What complicates things is the package vignette index.
> In addition to the HTML vignette index page having to be updated also
> the internal data table (a plain matrix) has to be adjusted such that
> it is can represent multiple output files, e.g.
>
> > head(tools::getVignetteInfo("R.rsp"), 2L)
>      Package Dir
> [1,] "R.rsp" "C:/Users/hb/R/win-library/3.3/R.rsp"
> [2,] "R.rsp" "C:/Users/hb/R/win-library/3.3/R.rsp"
>      Topic
> [1,] "Dynamic_document_creation_using_RSP"
> [2,] "RSP_intro"
>      File
> [1,] "Dynamic_document_creation_using_RSP.tex.rsp"
> [2,] "RSP_intro.md.rsp"
>      Title                                 R
> [1,] "Dynamic document creation using RSP" ""
> [2,] "Introductory slides on RSP"          ""
>      PDF
> [1,] "Dynamic_document_creation_using_RSP.pdf"
> [2,] "RSP_intro.html"
>
> The vignette product is in the 'PDF' column, which is a legacy name
> from the Sweave-only time.
>
> Ignoring the HTML vignette index issue (which you can override using
> your own Makefile), I think if you would try trick R CMD build using a
> customized vignette engine (specifically it's "weave" function) that
> outputs multiple products, you would get complains from R CMD check
> (--as-cran?) that there are stray vignette files.
>
> But to summarize, if multiple products per vignette is really needed,
> it wouldn't be that hard to implement.  The challenge would probably
> be convince R core that it's needed(*).
>
> /Henrik
>
> (*) One use case I can imagine is for visually impaired users; I
> pretty sure I've read somewhere (R Journal article?) that when it
> comes to reading equations, the *.tex file is often much more helpful
> than the PDF.  In this case it could be neat if Sweave/knitr source
> vignettes would keep both the (intermediate) *.tex file and the final
> PDF file.
>
> > >
> > > Best,
> > > Kasper
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
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> >
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