Hi Sean, thanks again. Even this does not seem to help. The html file is not built from Rmd during package build.
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
