----- Original Message ----- > From: "Leo Lahti" <leo.la...@iki.fi> > To: bioc-devel@r-project.org > Sent: Monday, October 6, 2014 7:25:03 AM > Subject: [Bioc-devel] Fwd: Rmarkdown built html vignette not included in > final package tarball > > Hi Sean, thanks again. Even this does not seem to help. The html file > is > not built from Rmd during package build. >
Do you have pandoc installed? Dan > If someone has pointers to functional examples I could try to compare > and > find the explanation. > > best, > Leo > > On Mon, Oct 6, 2014 at 3:33 PM, Sean Davis <sdav...@mail.nih.gov> > wrote: > > > > > > > On Mon, Oct 6, 2014 at 9:25 AM, Leo Lahti <leo.la...@iki.fi> wrote: > > > >> Thanks Sean, in fact I had already bumped into this very useful > >> post. > >> > >> I tried to make the changes you suggested, yet the html file is > >> not built > >> as it should. > >> > >> Any pointers to public code for packages with successful automated > >> builds > >> of html vignettes from Rmd ? > >> > >> The current version of my package vignette is in: > >> > >> https://github.com/microbiome/microbiome/blob/master/vignettes/vignette.Rmd > >> For some reason the html file fails to build during package build > >> as it > >> should. > >> > >> > > Hi, Leo. > > > > This block: > > > > <!-- > > %\VignetteEngine{knitr::rmarkdown} > > %\VignetteIndexEntry{microbiome tutorial} > > %\usepackage[utf8]{inputenc} > > --> > > > > needs to go after the yaml header. > > > > Sean > > > > > > > >> > >> > >> > >> On Mon, Oct 6, 2014 at 3:16 PM, Sean Davis <sdav...@mail.nih.gov> > >> wrote: > >> > >> > Hi, Leo. > >> > > >> > I think you'll need to include the VignetteIndexEntry and > >> > VignetteEngine > >> > as the first lines of your vignette, enclosed in an HTML > >> > comment. > >> You'll > >> > also need to adjust your DESCRIPTION file slightly. Though not > >> > meant > >> to be > >> > authoritative, I put together the details that worked for me > >> > here: > >> > > >> > > >> > > >> http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/ > >> > > >> > Sean > >> > > >> > > >> > On Mon, Oct 6, 2014 at 8:23 AM, Leo Lahti <leo.la...@iki.fi> > >> > wrote: > >> > > >> >> Dear list, > >> >> > >> >> I have built html vignettes from Rmd files > >> >> > >> >> For this I have added the following lines in vignette start: > >> >> > >> >> --- > >> >> title: "my vignette" > >> >> author: "N.N" > >> >> date: "`r Sys.Date()`" > >> >> output: rmarkdown::html_vignette > >> >> vignette: > > >> >> %\VignetteEngine{knitr::rmarkdown} > >> >> %\VignetteIndexEntry{my tutorial} > >> >> %\usepackage[utf8]{inputenc} > >> >> --- > >> >> > >> >> and then run in R: > >> >> rmarkdown::render("vignette.Rmd", "html_document") > >> >> > >> >> However after R CMD check and build, the html vignette is not > >> >> included > >> in > >> >> the package tarball. > >> >> > >> >> How I can ensure that the html vignette will be included in the > >> >> final > >> >> tarball ? Querying the bioc list messages did not lead to > >> >> solution so > >> far. > >> >> > >> >> > >> >> best regards > >> >> Leo Lahti > >> >> > >> >> [[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 > >> > > > > > > [[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
