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

3 messages · Adam Price, Dirk Eddelbuettel, Heather Turner

Original
Adam Price
# 
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
Dirk Eddelbuettel
#
On 18 January 2019 at 10:42, Adam Price wrote:
| 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

You do -- RHub, ie https://builder.r-hub.io.. It's so worth it. Please explore it.

As a community we could do / should do one better and ensure that the
testable resources actually correspond to the testbeds used but that is
something where I can only plead to the galactic overloards.  I do try on
occassion though...

Dirk
Heather Turner
# 
Hi Adam,

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