From Thierry.ONKELINX at inbo.be  Tue Dec  9 11:19:08 2014
From: Thierry.ONKELINX at inbo.be (ONKELINX, Thierry)
Date: Tue, 9 Dec 2014 10:19:08 +0000
Subject: [Rd] UTF8 markdown vignette
In-Reply-To: <5486C91E.90409@gmail.com>
References: <AA818EAD2576BC488B4F623941DA7427F3C7D1D8@inbomail.inbo.be>
	<5486C91E.90409@gmail.com>
Message-ID: <AA818EAD2576BC488B4F623941DA7427F3C7D24C@inbomail.inbo.be>

Dear Duncan,

The UTF-8 characters aren't properly rendered in the pdf version of the vignette.
$?? ????? ?????? ?????? ????? ?? ?? is rendered as $????? ?????????? ???????????? ????? ?????? ? ???????? ????????

The same problem occurs when I use render("vignette.md", output_format = "mypackage::mystyle"), instead of render("vignette.md", output_format = "mypackage::mystyle", encoding = "UTF-8"). The default value of the encoding argument of rmarkdown::render() is encoding = getOption("encoding"), which is "native.enc" on my system.

I'll post the question on an RStudio forum as well.

Best regards,

Thierry

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey


-----Oorspronkelijk bericht-----
Van: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
Verzonden: dinsdag 9 december 2014 11:04
Aan: ONKELINX, Thierry; r-devel at r-project.org
Onderwerp: Re: [Rd] UTF8 markdown vignette

On 09/12/2014, 4:48 AM, ONKELINX, Thierry wrote:
> Dear all,
>
> I'm trying to use a Markdown vignette with UTF-8 encoding. It compiles well when knitting the vignette in RStudio, but it fails to recognize the UTF-8 settings when building the source package. Can someone point out what I'm doing wrong? I tried to put the relevant information below.

You don't describe the symptoms of "failing to recognize", but from the look of it, this is a problem with the knitr::rmarkdown engine or with the devtools packaging, so you should probably ask on an RStudio forum.

Duncan Murdoch

> Best regards,
>
> Thierry
>
> Details:
>
> Using 64-bit R 3.1.2 with encoding = "native.enc" on Windows 7 with Rstudio 0.97.1091.
>
> The source packages is build using the devtools package. The build
> command is R --vanilla CMD build  "myPackage" --no-manual
> --no-resave-data
>
> The DESCRIPTION file has
>
> VignetteBuilder: knitr
> Suggests: knitr
> Imports: rmarkdown
>
> The markdown vignette YAML contains
> vignette: >
>   %\VignetteEngine{knitr::rmarkdown}
>   %\VignetteIndexEntry{The title}
>   \usepackage[utf8]{inputenc}
>
> The custom output style converts the markdown to beamer with the --latex-engine = xelatex flag.
>
> The vignette in tar.gz passes R --vanilla CMD check  --timings
> --as-cran
>
> * checking files in 'vignettes' ... OK
> * checking for unstated dependencies in vignettes ... OK
> * checking package vignettes in 'inst/doc' ... OK
> * checking running R code from vignettes ...
>    'markdown_intro.Rmd' using 'UTF-8' ... OK OK
> * checking re-building of vignette outputs ... [22s] OK
>
>
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality
> Assurance Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
>
> Disclaimer Bezoek onze website / Visit our
> website<https://drupal.inbo.be/nl/disclaimer-mailberichten-van-het-inb
> o>
>
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>

Disclaimer Bezoek onze website / Visit our website<https://drupal.inbo.be/nl/disclaimer-mailberichten-van-het-inbo>


[Rd] UTF8 markdown vignette
ONKELINX, Thierry