I think it requires Bioc core to make a statement that pandoc will be added to the list of external software that can be assume to exist on the servers.
If it is also expected that users should be able to rebuild all vignettes/documents themselves, then that assumption has to be extended to the users as well. BTW, is there such an assumption on LaTeX-dependent packages today? Installing pandoc is not that hard and lightweight (much smaller than LaTeX), but it does add one more installation. On the other hand, it opens up for doing lots of other neat things. Henrik On Oct 3, 2014 6:40 AM, "James W. MacDonald" <jmac...@uw.edu> wrote: > Hi Gordon, > > Sean Davis has something about this on his blog: > > > http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/ > > Best, > > Jim > > > > On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball <gordon.b...@ki.se> wrote: > > > Hello > > > > Is it possible to use (RStudio's) rmarkdown package as a vignette > > builder for the upcoming release? > > > > ie, with the (at least locally working) configuration > > > > DESCRIPTION > > > > Suggests: knitr, rmarkdown, BiocStyle > > VignetteBuilder: knitr > > > > vignette/vignette.Rmd > > > > --- > > title: ... > > output: BiocStyle::html_document > > vignette: > > > %% \VignetteEngine{knitr::rmarkdown} > > %% \VignetteIndexEntry{...} > > ---- > > > > I couldn't find any explicit reference to markdown vs rmarkdown in the > > package guidelines. The documentation for [BiocStyle] indicates that it > > isn't possible to build package vignettes with the newer rmarkdown - is > > that still correct? > > > > I note that the newer [rmarkdown] is now in CRAN, so presumably can be > > used by the builders - but do they have the non-R dependency (pandoc) > > available? > > > > The rationale for wanting rmarkdown instead markdown is support for a > > few extended features, particularly being able to cite from a bibtex > > file (which as far as I know isn't possible with the older markdown). > > > > Thanks > > > > Gordon Ball > > Computational Medicine Group > > Karolinska Institute > > > > > > > > [BiocStyle]: > > > > > http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html > > > > [rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/ > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[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