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
