----- Original Message ----- > From: "Leo Lahti" <leo.la...@iki.fi> > To: bioc-devel@r-project.org, "Git Svn Bridge" <dtene...@fhcrc.org> > Sent: Monday, October 6, 2014 10:11:55 AM > Subject: Re: Rmarkdown built html vignette not included in final package > tarball > > > Hi Dan, good to hear. I guess you checked that the html file is in > the package after build?
Yes. Dan > For me the build is ok but the html file > does not appear. If you get the html file during build, then the > pandoc linking issue should cause my problems. > > > > > In Ubuntu 14.04 running "sudo apt-get install pandoc" install an > older version of pandoc than is required by R build for knitr > (pandoc>=1.12.3). And upgrading to >=1.12.3 is known to be > problematic in Ubuntu 14.04 (ample discussions on this available in > the web). I have already tried to install it based on various tips > from the web (including direct installations from source, yum > scripts, changing the repository etc) but no success so far. Hence I > was finally using RStudios pandoc since that is sufficiently new and > I got it working with the symbolic linking. Hopefully this pandoc > issue gets solved for the 14.04 LTS later on. > > > Leo > > > > > > > > > > > > > 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. > > > > Not sure what you mean by that. I was able to build your package with > no problem. You might try removing that symlink and installing > pandoc with > > > sudo apt-get install pandoc > > Dan > > > > > > Leo > > > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
