----- Original Message ----- > From: "Leo Lahti" <leo.la...@iki.fi> > To: "Dan Tenenbaum" <dtene...@fhcrc.org> > Cc: bioc-devel@r-project.org > Sent: Monday, October 6, 2014 7:55:07 AM > Subject: Re: [Bioc-devel] Fwd: Rmarkdown built html vignette not included in > final package tarball > > > > > Hi Dan, > > The command "pandoc -v" gives: "pandoc 1.12.4.2" so the version seems > to be ok. I am also able to convert md file to html in R with the > knitr::pandoc command so pandoc seems to work. > > However it might be worth noting that I am using pandoc via a > symbolic link from RStudio binaries > /usr/lib/rstudio/bin/pandoc/pandoc since updating to pandoc >=1.12.3 > otherwise in Ubuntu 14.04 has appeared quite problematic. >
Can you post a link to your package code? If you'd prefer not to, you can send it to me off-list. Dan > Leo > > > > > > > > On Mon, Oct 6, 2014 at 4:35 PM, Dan Tenenbaum < dtene...@fhcrc.org > > wrote: > > > > > ----- 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