On 09/12/2014, 4:38 PM, ONKELINX, Thierry wrote:> Dear Yihui, > > I have created a reproducible example at https://github.com/ThierryO/utf8vignette > > The \usepackage{} line is needed, otherwise R CMD check --as-cran will give a warning. > %\VignetteEncoding{UTF-8} did not solve the problem.I've just taken a look at the sources, and that's only in R-devel, it never got backported to R-patched so it isn't in the release R. You would need to use %\SweaveUTF8 instead. (It was introduced in 3.1.0, and should be kept until at least 3.2.0, but \VignetteEncoding will be preferred in the long run. It should make it into 3.1.3 unless we drop the ball again.) Duncan Murdoch> > I use rmarkdown_0.3.11 > > HTML vignette is not an option as the vignette demonstrates the use of a custom beamer output format. > > 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 > > ________________________________________ > Van: xieyihui at gmail.com [xieyihui at gmail.com] namens Yihui Xie [xie at yihui.name] > Verzonden: dinsdag 9 december 2014 17:13 > Aan: ONKELINX, Thierry > CC: r-devel at r-project.org; Duncan Murdoch; Kurt Hornik > Onderwerp: Re: [Rd] UTF8 markdown vignette > > A few things to clarify: > > 1. You do not necessarily have to keep the \usepackage{} line if you > use %\VignetteEncoding{UTF-8}, because Pandoc will use UTF-8 anyway in > its LaTeX template. > > 2. Perhaps the vignette engine in R has done something clever to > convert utf8 to UTF-8, but I'd recommend %\VignetteEncoding{UTF-8} > instead of %\VignetteEncoding{utf8} to make sure it is a valid > encoding name, e.g. > >> 'utf8' %in% iconvlist() > [1] FALSE >> 'UTF-8' %in% iconvlist() > [1] TRUE >> 'UTF8' %in% iconvlist() > [1] TRUE > > BTW, %\VignetteEncoding is not documented anywhere (Cc'ing Kurt), and > I think it needs to be documented, since the old approach > \usepackage[enc]{inputenc} was basically a hack, which looks really > odd in non-LaTeX vignettes (e.g. HTML vignettes). > > 3. The default `encoding` argument of rmarkdown::render() is not > relevant here, even if its value is native.enc. When R build a > vignette, it tries to detect its encoding and pass it to the vignette > engine, so the default argument value may not be native.enc. > > Lastly, the most important piece of information is missing in this > post: library(rmarkdown); sessionInfo(). There is not a minimal > reproducible example, either. Without these information, I can only > guess blindly. > > BTW, you may also try HTML vignettes instead, which is much much > easier to get right than LaTeX in terms of character encodings. > > Regards, > Yihui > -- > Yihui Xie <xieyihui at gmail.com> > Web: http://yihui.name > > > On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: >> On 09/12/2014, 5:19 AM, ONKELINX, Thierry wrote: >>> Dear Duncan, >>> >>> The UTF-8 characters aren't properly rendered in the pdf version of the vignette. >>> $?? ????? ?????? ?????? ????? ?? ?? is rendered as $????? ?????????? ???????????? ????? ?????? ? ???????? ???????? >> >> That looks as though the UTF-8 characters are being interpreted as >> Latin1 characters (or whatever your native encoding is on Windows) when >> read from the file. >> >> It is quite tricky to work with UTF-8 in R in Windows. I think Sweave >> does it properly, though there may be exceptions. The issue is that >> many character input routines assume characters start out in the native >> encoding. (There's also a translation that happens by default on >> output, but I don't think that's your problem.) So the way to debug >> this is to follow all of the I/O, and see where the misinterpretation >> happens. For vignettes, things are complicated, because R reads the >> file to determine which vignette engine to use, then the vignette engine >> reads it (perhaps more than once). >> >> >>> 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. >>> >> >> It sounds as though the render function needs a way to determine the >> encoding from the file itself. Recent Sweave versions support the >> declaration >> >> %\VignetteEncoding{utf8} >> >> as well as the older >> >> \usepackage[utf8]{inputenc} >> >> that you used. You might want to try that line as well. (You need to >> keep the \usepackage line to tell LaTeX what encoding you're using.) >> >> Duncan Murdoch >> >> >>> I'll post the question on an RStudio forum as well. >>> >>> Best regards, >>> >>> Thierry >>> >>> >>> -----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 > Disclaimer Bezoek onze website / Visit our website<https://drupal.inbo.be/nl/disclaimer-mailberichten-van-het-inbo> >
I took a look at the R source and I realized that the encoding was actually never passed to the vignette engine: https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507 Apparently only the file and quiet arguments are passed to the vignette engine. Did I miss anything? To Thierry: I explicitly asked for library(rmarkdown);sessionInfo(), but you only told me the version of rmarkdown, which is not the only thing I was asking for. It is extremely important in this case to know the versions of other packages as well as your system locale information. Regards, Yihui -- Yihui Xie <xieyihui at gmail.com> Web: http://yihui.name On Tue, Dec 9, 2014 at 3:42 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> On 09/12/2014, 4:38 PM, ONKELINX, Thierry wrote: >> Dear Yihui, >> >> I have created a reproducible example at https://github.com/ThierryO/utf8vignette >> >> The \usepackage{} line is needed, otherwise R CMD check --as-cran will give a warning. >> %\VignetteEncoding{UTF-8} did not solve the problem. > > I've just taken a look at the sources, and that's only in R-devel, it > never got backported to R-patched so it isn't in the release R. You > would need to use > > %\SweaveUTF8 > > instead. (It was introduced in 3.1.0, and should be kept until at least > 3.2.0, but \VignetteEncoding will be preferred in the long run. It > should make it into 3.1.3 unless we drop the ball again.) > > Duncan Murdoch > >> >> I use rmarkdown_0.3.11 >> >> HTML vignette is not an option as the vignette demonstrates the use of a custom beamer output format. >> >> Best regards, >> >> Thierry >> ________________________________________ >> Van: xieyihui at gmail.com [xieyihui at gmail.com] namens Yihui Xie [xie at yihui.name] >> Verzonden: dinsdag 9 december 2014 17:13 >> Aan: ONKELINX, Thierry >> CC: r-devel at r-project.org; Duncan Murdoch; Kurt Hornik >> Onderwerp: Re: [Rd] UTF8 markdown vignette >> >> >> Lastly, the most important piece of information is missing in this >> post: library(rmarkdown); sessionInfo(). There is not a minimal >> reproducible example, either. Without these information, I can only >> guess blindly.
Dear Yihui and Duncan,
Using \%SweaveUTF8 does not solve the problem. The nice thing about it, it that
it no longer requires \usepackage[utf8]{} to make R CMD check --as-cran happy.
To Yihui: here is the sessionInfo().
> library(rmarkdown)
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252
LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rmarkdown_0.3.11
loaded via a namespace (and not attached):
[1] digest_0.6.4 fortunes_1.5-2 htmltools_0.2.6 tools_3.1.2
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: xieyihui at gmail.com [mailto:xieyihui at gmail.com] Namens Yihui Xie
Verzonden: woensdag 10 december 2014 4:37
Aan: Duncan Murdoch
CC: ONKELINX, Thierry; r-devel at r-project.org; Kurt Hornik
Onderwerp: Re: [Rd] UTF8 markdown vignette
I took a look at the R source and I realized that the encoding was actually
never passed to the vignette engine:
https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507
Apparently only the file and quiet arguments are passed to the vignette engine.
Did I miss anything?
To Thierry: I explicitly asked for library(rmarkdown);sessionInfo(), but you
only told me the version of rmarkdown, which is not the only thing I was asking
for. It is extremely important in this case to know the versions of other
packages as well as your system locale information.
Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Web: http://yihui.name
On Tue, Dec 9, 2014 at 3:42 PM, Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:> On 09/12/2014, 4:38 PM, ONKELINX, Thierry wrote:
>> Dear Yihui,
>>
>> I have created a reproducible example at
>> https://github.com/ThierryO/utf8vignette
>>
>> The \usepackage{} line is needed, otherwise R CMD check --as-cran will
give a warning.
>> %\VignetteEncoding{UTF-8} did not solve the problem.
>
> I've just taken a look at the sources, and that's only in R-devel,
it
> never got backported to R-patched so it isn't in the release R. You
> would need to use
>
> %\SweaveUTF8
>
> instead. (It was introduced in 3.1.0, and should be kept until at
> least 3.2.0, but \VignetteEncoding will be preferred in the long run.
> It should make it into 3.1.3 unless we drop the ball again.)
>
> Duncan Murdoch
>
>>
>> I use rmarkdown_0.3.11
>>
>> HTML vignette is not an option as the vignette demonstrates the use of
a custom beamer output format.
>>
>> Best regards,
>>
>> Thierry
>> ________________________________________
>> Van: xieyihui at gmail.com [xieyihui at gmail.com] namens Yihui Xie
>> [xie at yihui.name]
>> Verzonden: dinsdag 9 december 2014 17:13
>> Aan: ONKELINX, Thierry
>> CC: r-devel at r-project.org; Duncan Murdoch; Kurt Hornik
>> Onderwerp: Re: [Rd] UTF8 markdown vignette
>>
>>
>> Lastly, the most important piece of information is missing in this
>> post: library(rmarkdown); sessionInfo(). There is not a minimal
>> reproducible example, either. Without these information, I can only
>> guess blindly.
Disclaimer Bezoek onze website / Visit our
website<https://drupal.inbo.be/nl/disclaimer-mailberichten-van-het-inbo>
On 09/12/2014, 10:36 PM, Yihui Xie wrote:> I took a look at the R source and I realized that the encoding was > actually never passed to the vignette engine: > https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507 > Apparently only the file and quiet arguments are passed to the > vignette engine. Did I miss anything?I think it's actually a little messier than that: sometimes the encoding is passed (e.g. by tools:::.run_one_vignette, used in R CMD check), but not always. Here's what I think should happen instead: When building a vignette in a package, R knows the encoding declared for the package, so it should assume this as the default for the vignette. If nothing is declared, it should assume "native.enc", i.e. whatever is the native encoding on the machine it's running on. For each vignette, at the same time as it determines the vignette engine, it should see whether there is a declared encoding within the vignette. When it calls the engine, it should pass an encoding (and it should be a legal one, e.g. UTF-8, not utf8). Unless I notice something missing when I do this, or someone else tells me something that's missing, I'll try to make the changes above in R-devel and R-patched sometime before 3.1.3 is released. In the meantime, unless declaring a dependence on R >= 3.1.3, vignette engines should determine the encoding themselves whenever they are called without an "encoding" argument. Duncan Murdoch> > To Thierry: I explicitly asked for library(rmarkdown);sessionInfo(), > but you only told me the version of rmarkdown, which is not the only > thing I was asking for. It is extremely important in this case to know > the versions of other packages as well as your system locale > information. > > Regards, > Yihui > -- > Yihui Xie <xieyihui at gmail.com> > Web: http://yihui.name > > > On Tue, Dec 9, 2014 at 3:42 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: >> On 09/12/2014, 4:38 PM, ONKELINX, Thierry wrote: >>> Dear Yihui, >>> >>> I have created a reproducible example at https://github.com/ThierryO/utf8vignette >>> >>> The \usepackage{} line is needed, otherwise R CMD check --as-cran will give a warning. >>> %\VignetteEncoding{UTF-8} did not solve the problem. >> >> I've just taken a look at the sources, and that's only in R-devel, it >> never got backported to R-patched so it isn't in the release R. You >> would need to use >> >> %\SweaveUTF8 >> >> instead. (It was introduced in 3.1.0, and should be kept until at least >> 3.2.0, but \VignetteEncoding will be preferred in the long run. It >> should make it into 3.1.3 unless we drop the ball again.) >> >> Duncan Murdoch >> >>> >>> I use rmarkdown_0.3.11 >>> >>> HTML vignette is not an option as the vignette demonstrates the use of a custom beamer output format. >>> >>> Best regards, >>> >>> Thierry >>> ________________________________________ >>> Van: xieyihui at gmail.com [xieyihui at gmail.com] namens Yihui Xie [xie at yihui.name] >>> Verzonden: dinsdag 9 december 2014 17:13 >>> Aan: ONKELINX, Thierry >>> CC: r-devel at r-project.org; Duncan Murdoch; Kurt Hornik >>> Onderwerp: Re: [Rd] UTF8 markdown vignette >>> >>> >>> Lastly, the most important piece of information is missing in this >>> post: library(rmarkdown); sessionInfo(). There is not a minimal >>> reproducible example, either. Without these information, I can only >>> guess blindly.