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

[Dan Tenenbaum]

----- Original Message -----
> From: "Leo Lahti" <leo.lahti at iki.fi>
> To: bioc-devel at r-project.org, "Git Svn Bridge" <dtenenba at 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
> > 
> > 
> 
>