[R-pkg-devel] LaTeX warnings on debian builds only

[Heather Turner]

Hi Adam,

I suspect these two lines in your YAML header are causing trouble

>   %\usepackage[utf8]{inputenc}
>   %\usepackage[table]{xcolor}

- this is LaTeX code, which you shouldn't need if you're producing an HTML vignette.

Also, with more recent versions of R markdown you should use knitr::rmarkdown rather than knitr::knitr as the vignette engine. For an HTML vignette, I'd expect your vignette field to look like this:

vignette: >
  %\VignetteIndexEntry{DEVis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}

so try updating that block and see if that fixes it.

Best wishes,

Heather


On Fri, Jan 18, 2019, at 3:42 PM, Adam Price wrote:
> Hi,
> 
> I am currently having an issue getting past a warning that's occurring on
> linux based builds for my vignette.  The warning is: "! LaTeX Error: Option
> clash for package xcolor."
> 
> The check results are here:
> *https://win-builder.r-project.org/incoming_pretest/DEVis_1.0.1_20181220_164555/Debian/00check.log
> <https://win-builder.r-project.org/incoming_pretest/DEVis_1.0.1_20181220_164555/Debian/00check.log>*
> 
> Windows and OS X builds work fine, but I don't have access to a debian
> machine that I can reproduce this on.  I currently cannot reproduce this
> issue on my side, and travis-ci checks do not seem to produce this warning
> for linux on ubuntu.  I can only see it currently when submitting an update
> to my package and failing the CRAN auto-checks.
> 
> I have recently changed from PDF vignette to html-based, and am not sure
> why LaTeX packages would even be loading in this case.  I have attempted to
> correct for it based on this post (
> https://github.com/haozhu233/kableExtra/issues/274
> ) which claims the issue is a conflict between kableExtra and xcolor.
> 
> Some relevant sections of code from the vignette might include:
> "
> vignette: |
>   %\VignetteIndexEntry{DEVis}
>   %\usepackage[utf8]{inputenc}
>   %\usepackage[table]{xcolor}
>   %\VignetteEngine{knitr::knitr}
> ---
> 
> ```{r loadData, echo = F, eval = TRUE}
> #load("../data/exampleData.Rda")
> knitr::opts_knit$set(root.dir = '../vignettes/')
> knitr::opts_chunk$set(fig.path='figure/graphics-',
>                  cache.path='cache/graphics-',
>                  fig.align='center',
>                  external=TRUE,
>                  echo=TRUE,
>                  warning=FALSE,
>                  fig.pos='H'
>                 )
>   a4width<- 8.3
>   a4height<- 11.7
> library(kableExtra)
> library(rmarkdown)
> library(knitr)
> options(knitr.table.format = "html")
> options(kableExtra.latex.load_packages = FALSE)
> "
> 
> 
> The full package code can be found here: https://github.com/price0416/DEvis
> 
> I would appreciate any insight anyone can offer into this issue, as I
> cannot update my package until I get to the bottom of this!  Thanks very
> much in advance!
> 
> Best,
> -Adam
> 
> 	[[alternative HTML version deleted]]
> 
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