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.bengts...@gmail.com> wrote: > On Feb 26, 2016 09:23, "Andrzej Oleś" <andrzej.o...@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 < > > kasperdanielhan...@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@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
