[Bioc-devel] Rmarkdown built html vignette not included in final package tarball

[Leo Lahti]

Hi Dan, good to hear. I guess you checked that the html file is in the
package after build? 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
> >
> >
>

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