Re: [Rd] UTF8 markdown vignette

[Yihui Xie]

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 
Web: http://yihui.name


On Tue, Dec 9, 2014 at 3:42 PM, Duncan Murdoch  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: xieyi...@gmail.com [xieyi...@gmail.com] namens Yihui Xie 
>> [x...@yihui.name]
>> Verzonden: dinsdag 9 december 2014 17:13
>> Aan: ONKELINX, Thierry
>> CC: r-devel@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.

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Re: [Rd] R on the Cydia Store

[Marc Schwartz]

Hi,

I would send an introductory e-mail to:

  r-foundat...@r-project.org 

That will facilitate further discussion on the matter and additional details 
can be requested offline as may be needed.

Be aware that none of the R Foundation members are lawyers. So while we can 
perhaps offer informal and non-binding opinions, you should seek formal legal 
guidance from counsel specifically familiar with open source licensing 
regarding your obligations in that domain.

Finally, it would be helpful and courteous to know at least a primary contact 
full name for your group, as opposed to the Team moniker.

Regards,

Marc


> On Dec 9, 2014, at 5:39 PM, Apps Embedded  wrote:
> 
> Hi,
> 
> Thanks for your first answers.
> 
> So, should we contact the R foundation team members to inform them of our 
> project on the Android platform and on the Cydia Store ?
> If yes, could you give us their email please ? Or should we write to the 
> president of the R foundation for instance ? 
> 
> Best regards.
> 
> Apps Embedded Team.
> 
> 
> 2014-12-09 23:49 GMT+01:00 Marc Schwartz  >:
> 
> > On Dec 9, 2014, at 3:34 PM, Duncan Murdoch  > > wrote:
> >
> > On 09/12/2014, 4:26 PM, Marc Schwartz wrote:
> >>
> >>> On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson  >>> > wrote:
> >>>
> >>> On Dec 9, 2014 6:38 AM, "Apps Embedded"  >>> > wrote:
> 
>  Hi,
> 
>  We have published an Android app called R Console on the Play Store since
>  Décember 2013.
>  https://play.google.com/store/apps/details?id=com.appsopensource.R 
>  
>  https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
>   
>  
> 
>  In the mean time, we have developped its equivalent app for the App 
>  Store.
>  We released it on march 2014. We have been approved from this date by 
>  Apple
>  to publish it world wide.
>  Recently, we learnt that GPL app are not compatible with the App Store
>  distribution licence.
> >>>
> >>> What I would like to write here, would fall under "this is certainly
> >>> not a topic for R devel", so I refrain.
> >>>
> >>> However, I can say that it's likely your problems wouldn't have stopped 
> >>> there;
> >>>
> >>> [R] R on the iPhone/iPad? Not so mucha GPL violation
> >>> https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html 
> >>> 
> >>>
> >>> /Henrik
> >>
> >> Hi,
> >>
> >> I might add that, given the intentions expressed below, in terms of doing 
> >> this on a jailbroken iOS device via Cydia, the concerns raised in the 
> >> Apple iOS SDK, that I referenced in the above linked post from 2010, 
> >> essentially go away.
> >>
> >> They would still be germane, as may now be expressed in the current SDK, 
> >> including the use of the new Swift language, if the OP's intent was to 
> >> pursue this via official AppStore channels and am surprised that it was 
> >> approved by Apple previously given the indicated content and functionality 
> >> of the app.
> >>
> >> The primary intention of jailbreaking an iOS device is, of course, to 
> >> circumvent Apple's restrictions on the software that can be installed by 
> >> using third party distribution channels and in the tools that can be used 
> >> to develop apps.
> >>
> >> That being said, the licensing issues, as Duncan raised in his reply, are 
> >> still germane and permission from the R Foundation should be sought for 
> >> any uses involving R Foundation copyrighted content. That would be 
> >> relevant for both the iOS implementation and the Android implementation.
> >
> > Just to be clear:  everybody already has permission from the R copyright
> > holders to use R within the existing licenses.  There's no need to seek
> > extra permission for that.
> >
> > Trademarks are different...
> >
> > Duncan Murdoch
> 
> 
> Thanks for the clarification Duncan, I was imprecise in my language.
> 
> Regards,
> 
> Marc
> 
> 
> >
> >> Regards,
> >>
> >> Marc Schwartz
> >>
> >> P.S. I echo's Duncan's comment, in that I am also a member of the R 
> >> Foundation, but am not speaking here on it's behalf.
> >>
> >>
> >>>
> 
>  Thus we decided to remove the iOS app from the App Store several days 
>  ago.
> 
>  We are thinking of publishing the same app published under Cydia with a
>  freemium model.
>  Its licence would be GPL v3.
> 
>  What we would like to do under Cydia with R Console is to have the
>  following behavior :
>  - free version will be able to run recommended packages and graphics are
>  not enabled. A small ad banner is present on top of the app.
>  - premium version will be the sa

Re: [Rd] R on the Cydia Store

[Apps Embedded]

Hi,

Thanks for your first answers.

So, should we contact the R foundation team members to inform them of our
project on the Android platform and on the Cydia Store ?
If yes, could you give us their email please ? Or should we write to the
president of the R foundation for instance ?

Best regards.

Apps Embedded Team.


2014-12-09 23:49 GMT+01:00 Marc Schwartz :

>
> > On Dec 9, 2014, at 3:34 PM, Duncan Murdoch 
> wrote:
> >
> > On 09/12/2014, 4:26 PM, Marc Schwartz wrote:
> >>
> >>> On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson 
> wrote:
> >>>
> >>> On Dec 9, 2014 6:38 AM, "Apps Embedded" 
> wrote:
> 
>  Hi,
> 
>  We have published an Android app called R Console on the Play Store
> since
>  Décember 2013.
>  https://play.google.com/store/apps/details?id=com.appsopensource.R
> 
> https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
> 
>  In the mean time, we have developped its equivalent app for the App
> Store.
>  We released it on march 2014. We have been approved from this date by
> Apple
>  to publish it world wide.
>  Recently, we learnt that GPL app are not compatible with the App Store
>  distribution licence.
> >>>
> >>> What I would like to write here, would fall under "this is certainly
> >>> not a topic for R devel", so I refrain.
> >>>
> >>> However, I can say that it's likely your problems wouldn't have
> stopped there;
> >>>
> >>> [R] R on the iPhone/iPad? Not so mucha GPL violation
> >>> https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html
> >>>
> >>> /Henrik
> >>
> >> Hi,
> >>
> >> I might add that, given the intentions expressed below, in terms of
> doing this on a jailbroken iOS device via Cydia, the concerns raised in the
> Apple iOS SDK, that I referenced in the above linked post from 2010,
> essentially go away.
> >>
> >> They would still be germane, as may now be expressed in the current
> SDK, including the use of the new Swift language, if the OP's intent was to
> pursue this via official AppStore channels and am surprised that it was
> approved by Apple previously given the indicated content and functionality
> of the app.
> >>
> >> The primary intention of jailbreaking an iOS device is, of course, to
> circumvent Apple's restrictions on the software that can be installed by
> using third party distribution channels and in the tools that can be used
> to develop apps.
> >>
> >> That being said, the licensing issues, as Duncan raised in his reply,
> are still germane and permission from the R Foundation should be sought for
> any uses involving R Foundation copyrighted content. That would be relevant
> for both the iOS implementation and the Android implementation.
> >
> > Just to be clear:  everybody already has permission from the R copyright
> > holders to use R within the existing licenses.  There's no need to seek
> > extra permission for that.
> >
> > Trademarks are different...
> >
> > Duncan Murdoch
>
>
> Thanks for the clarification Duncan, I was imprecise in my language.
>
> Regards,
>
> Marc
>
>
> >
> >> Regards,
> >>
> >> Marc Schwartz
> >>
> >> P.S. I echo's Duncan's comment, in that I am also a member of the R
> Foundation, but am not speaking here on it's behalf.
> >>
> >>
> >>>
> 
>  Thus we decided to remove the iOS app from the App Store several days
> ago.
> 
>  We are thinking of publishing the same app published under Cydia with
> a
>  freemium model.
>  Its licence would be GPL v3.
> 
>  What we would like to do under Cydia with R Console is to have the
>  following behavior :
>  - free version will be able to run recommended packages and graphics
> are
>  not enabled. A small ad banner is present on top of the app.
>  - premium version will be the same as the free version except the ad
> banner
>  will not be present anymore and 3 compilers will be integrated into
> the app
>  in order to be able to compile and run most of the Cran packages from
>  source.
>  - graphics may be added in a second step.
> 
>  The app will be considered as a bundle of open-source tools. This
> bundle
>  will be under the Gnu General Public Licence version 3. Each
> open-source
>  tool which contributes to the overall bundle will stay in its original
>  licence (R is GPL v2 for instance) but the bundle will be GPL v3.
> 
> 
> > From your point of view, do you see any legal issue with this
> project under
>  Cydia for jailbroken iOS devices?
> > From a trademark point of view, is the name of the apps "R Console
> Free"
>  and "R Console Premium" ok ?
> 
>  Thanks for your help.
> 
>  Apps Embedded Team.
> >>
> >
>
>

[[alternative HTML version deleted]]

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Re: [Rd] R on the Cydia Store

[Marc Schwartz]

> On Dec 9, 2014, at 3:34 PM, Duncan Murdoch  wrote:
> 
> On 09/12/2014, 4:26 PM, Marc Schwartz wrote:
>> 
>>> On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson  wrote:
>>> 
>>> On Dec 9, 2014 6:38 AM, "Apps Embedded"  wrote:
 
 Hi,
 
 We have published an Android app called R Console on the Play Store since
 Décember 2013.
 https://play.google.com/store/apps/details?id=com.appsopensource.R
 https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
 
 In the mean time, we have developped its equivalent app for the App Store.
 We released it on march 2014. We have been approved from this date by Apple
 to publish it world wide.
 Recently, we learnt that GPL app are not compatible with the App Store
 distribution licence.
>>> 
>>> What I would like to write here, would fall under "this is certainly
>>> not a topic for R devel", so I refrain.
>>> 
>>> However, I can say that it's likely your problems wouldn't have stopped 
>>> there;
>>> 
>>> [R] R on the iPhone/iPad? Not so mucha GPL violation
>>> https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html
>>> 
>>> /Henrik
>> 
>> Hi,
>> 
>> I might add that, given the intentions expressed below, in terms of doing 
>> this on a jailbroken iOS device via Cydia, the concerns raised in the Apple 
>> iOS SDK, that I referenced in the above linked post from 2010, essentially 
>> go away. 
>> 
>> They would still be germane, as may now be expressed in the current SDK, 
>> including the use of the new Swift language, if the OP's intent was to 
>> pursue this via official AppStore channels and am surprised that it was 
>> approved by Apple previously given the indicated content and functionality 
>> of the app.
>> 
>> The primary intention of jailbreaking an iOS device is, of course, to 
>> circumvent Apple's restrictions on the software that can be installed by 
>> using third party distribution channels and in the tools that can be used to 
>> develop apps.
>> 
>> That being said, the licensing issues, as Duncan raised in his reply, are 
>> still germane and permission from the R Foundation should be sought for any 
>> uses involving R Foundation copyrighted content. That would be relevant for 
>> both the iOS implementation and the Android implementation.
> 
> Just to be clear:  everybody already has permission from the R copyright
> holders to use R within the existing licenses.  There's no need to seek
> extra permission for that.
> 
> Trademarks are different...
> 
> Duncan Murdoch


Thanks for the clarification Duncan, I was imprecise in my language.

Regards,

Marc


> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>> P.S. I echo's Duncan's comment, in that I am also a member of the R 
>> Foundation, but am not speaking here on it's behalf.
>> 
>> 
>>> 
 
 Thus we decided to remove the iOS app from the App Store several days ago.
 
 We are thinking of publishing the same app published under Cydia with a
 freemium model.
 Its licence would be GPL v3.
 
 What we would like to do under Cydia with R Console is to have the
 following behavior :
 - free version will be able to run recommended packages and graphics are
 not enabled. A small ad banner is present on top of the app.
 - premium version will be the same as the free version except the ad banner
 will not be present anymore and 3 compilers will be integrated into the app
 in order to be able to compile and run most of the Cran packages from
 source.
 - graphics may be added in a second step.
 
 The app will be considered as a bundle of open-source tools. This bundle
 will be under the Gnu General Public Licence version 3. Each open-source
 tool which contributes to the overall bundle will stay in its original
 licence (R is GPL v2 for instance) but the bundle will be GPL v3.
 
 
> From your point of view, do you see any legal issue with this project 
> under
 Cydia for jailbroken iOS devices?
> From a trademark point of view, is the name of the apps "R Console Free"
 and "R Console Premium" ok ?
 
 Thanks for your help.
 
 Apps Embedded Team.
>> 
> 

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Re: [Rd] UTF8 markdown vignette

[Duncan Murdoch]

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.onkel...@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: xieyi...@gmail.com [xieyi...@gmail.com] namens Yihui Xie 
> [x...@yihui.name]
> Verzonden: dinsdag 9 december 2014 17:13
> Aan: ONKELINX, Thierry
> CC: r-devel@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 
> Web: http://yihui.name
> 
> 
> On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch  
> 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.
>>> $£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
>>> äëïöüÿ áéà óúý à èìòù ãñçµ
>>
>> 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
>> encodi

Re: [Rd] UTF8 markdown vignette

[ONKELINX, Thierry]

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 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.onkel...@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: xieyi...@gmail.com [xieyi...@gmail.com] namens Yihui Xie [x...@yihui.name]
Verzonden: dinsdag 9 december 2014 17:13
Aan: ONKELINX, Thierry
CC: r-devel@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 
Web: http://yihui.name


On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch  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.
>> $£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
>> äëïöüÿ áéà óúý à èìòù ãñçµ
>
> 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.dun...@gmail.com]
>> Verzonden: dinsdag 9 december 2014 11:04
>> Aan: ONKELINX, Thierry; r-devel@r-project.org
>> Onderwerp: Re: [Rd] UTF8 markdown v

Re: [Rd] R on the Cydia Store

[Duncan Murdoch]

On 09/12/2014, 4:26 PM, Marc Schwartz wrote:
> 
>> On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson  wrote:
>>
>> On Dec 9, 2014 6:38 AM, "Apps Embedded"  wrote:
>>>
>>> Hi,
>>>
>>> We have published an Android app called R Console on the Play Store since
>>> Décember 2013.
>>> https://play.google.com/store/apps/details?id=com.appsopensource.R
>>> https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
>>>
>>> In the mean time, we have developped its equivalent app for the App Store.
>>> We released it on march 2014. We have been approved from this date by Apple
>>> to publish it world wide.
>>> Recently, we learnt that GPL app are not compatible with the App Store
>>> distribution licence.
>>
>> What I would like to write here, would fall under "this is certainly
>> not a topic for R devel", so I refrain.
>>
>> However, I can say that it's likely your problems wouldn't have stopped 
>> there;
>>
>> [R] R on the iPhone/iPad? Not so mucha GPL violation
>> https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html
>>
>> /Henrik
> 
> Hi,
> 
> I might add that, given the intentions expressed below, in terms of doing 
> this on a jailbroken iOS device via Cydia, the concerns raised in the Apple 
> iOS SDK, that I referenced in the above linked post from 2010, essentially go 
> away. 
> 
> They would still be germane, as may now be expressed in the current SDK, 
> including the use of the new Swift language, if the OP's intent was to pursue 
> this via official AppStore channels and am surprised that it was approved by 
> Apple previously given the indicated content and functionality of the app.
> 
> The primary intention of jailbreaking an iOS device is, of course, to 
> circumvent Apple's restrictions on the software that can be installed by 
> using third party distribution channels and in the tools that can be used to 
> develop apps.
> 
> That being said, the licensing issues, as Duncan raised in his reply, are 
> still germane and permission from the R Foundation should be sought for any 
> uses involving R Foundation copyrighted content. That would be relevant for 
> both the iOS implementation and the Android implementation.

Just to be clear:  everybody already has permission from the R copyright
holders to use R within the existing licenses.  There's no need to seek
extra permission for that.

Trademarks are different...

Duncan Murdoch

> Regards,
> 
> Marc Schwartz
> 
> P.S. I echo's Duncan's comment, in that I am also a member of the R 
> Foundation, but am not speaking here on it's behalf.
> 
> 
>>
>>>
>>> Thus we decided to remove the iOS app from the App Store several days ago.
>>>
>>> We are thinking of publishing the same app published under Cydia with a
>>> freemium model.
>>> Its licence would be GPL v3.
>>>
>>> What we would like to do under Cydia with R Console is to have the
>>> following behavior :
>>> - free version will be able to run recommended packages and graphics are
>>> not enabled. A small ad banner is present on top of the app.
>>> - premium version will be the same as the free version except the ad banner
>>> will not be present anymore and 3 compilers will be integrated into the app
>>> in order to be able to compile and run most of the Cran packages from
>>> source.
>>> - graphics may be added in a second step.
>>>
>>> The app will be considered as a bundle of open-source tools. This bundle
>>> will be under the Gnu General Public Licence version 3. Each open-source
>>> tool which contributes to the overall bundle will stay in its original
>>> licence (R is GPL v2 for instance) but the bundle will be GPL v3.
>>>
>>>
 From your point of view, do you see any legal issue with this project under
>>> Cydia for jailbroken iOS devices?
 From a trademark point of view, is the name of the apps "R Console Free"
>>> and "R Console Premium" ok ?
>>>
>>> Thanks for your help.
>>>
>>> Apps Embedded Team.
>

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Re: [Rd] R on the Cydia Store

[Marc Schwartz]

> On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson  wrote:
> 
> On Dec 9, 2014 6:38 AM, "Apps Embedded"  wrote:
>> 
>> Hi,
>> 
>> We have published an Android app called R Console on the Play Store since
>> Décember 2013.
>> https://play.google.com/store/apps/details?id=com.appsopensource.R
>> https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
>> 
>> In the mean time, we have developped its equivalent app for the App Store.
>> We released it on march 2014. We have been approved from this date by Apple
>> to publish it world wide.
>> Recently, we learnt that GPL app are not compatible with the App Store
>> distribution licence.
> 
> What I would like to write here, would fall under "this is certainly
> not a topic for R devel", so I refrain.
> 
> However, I can say that it's likely your problems wouldn't have stopped there;
> 
> [R] R on the iPhone/iPad? Not so mucha GPL violation
> https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html
> 
> /Henrik

Hi,

I might add that, given the intentions expressed below, in terms of doing this 
on a jailbroken iOS device via Cydia, the concerns raised in the Apple iOS SDK, 
that I referenced in the above linked post from 2010, essentially go away. 

They would still be germane, as may now be expressed in the current SDK, 
including the use of the new Swift language, if the OP's intent was to pursue 
this via official AppStore channels and am surprised that it was approved by 
Apple previously given the indicated content and functionality of the app.

The primary intention of jailbreaking an iOS device is, of course, to 
circumvent Apple's restrictions on the software that can be installed by using 
third party distribution channels and in the tools that can be used to develop 
apps.

That being said, the licensing issues, as Duncan raised in his reply, are still 
germane and permission from the R Foundation should be sought for any uses 
involving R Foundation copyrighted content. That would be relevant for both the 
iOS implementation and the Android implementation.

Regards,

Marc Schwartz

P.S. I echo's Duncan's comment, in that I am also a member of the R Foundation, 
but am not speaking here on it's behalf.


> 
>> 
>> Thus we decided to remove the iOS app from the App Store several days ago.
>> 
>> We are thinking of publishing the same app published under Cydia with a
>> freemium model.
>> Its licence would be GPL v3.
>> 
>> What we would like to do under Cydia with R Console is to have the
>> following behavior :
>> - free version will be able to run recommended packages and graphics are
>> not enabled. A small ad banner is present on top of the app.
>> - premium version will be the same as the free version except the ad banner
>> will not be present anymore and 3 compilers will be integrated into the app
>> in order to be able to compile and run most of the Cran packages from
>> source.
>> - graphics may be added in a second step.
>> 
>> The app will be considered as a bundle of open-source tools. This bundle
>> will be under the Gnu General Public Licence version 3. Each open-source
>> tool which contributes to the overall bundle will stay in its original
>> licence (R is GPL v2 for instance) but the bundle will be GPL v3.
>> 
>> 
>>> From your point of view, do you see any legal issue with this project under
>> Cydia for jailbroken iOS devices?
>>> From a trademark point of view, is the name of the apps "R Console Free"
>> and "R Console Premium" ok ?
>> 
>> Thanks for your help.
>> 
>> Apps Embedded Team.

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Re: [Rd] R on the Cydia Store

[Duncan Murdoch]

On 09/12/2014 9:38 AM, Apps Embedded wrote:

Hi,

We have published an Android app called R Console on the Play Store since
Décember 2013.
https://play.google.com/store/apps/details?id=com.appsopensource.R
https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium

In the mean time, we have developped its equivalent app for the App Store.
We released it on march 2014. We have been approved from this date by Apple
to publish it world wide.
Recently, we learnt that GPL app are not compatible with the App Store
distribution licence.

Thus we decided to remove the iOS app from the App Store several days ago.

We are thinking of publishing the same app published under Cydia with a
freemium model.
Its licence would be GPL v3.

What we would like to do under Cydia with R Console is to have the
following behavior :
- free version will be able to run recommended packages and graphics are
not enabled. A small ad banner is present on top of the app.
- premium version will be the same as the free version except the ad banner
will not be present anymore and 3 compilers will be integrated into the app
in order to be able to compile and run most of the Cran packages from
source.
- graphics may be added in a second step.

The app will be considered as a bundle of open-source tools. This bundle
will be under the Gnu General Public Licence version 3. Each open-source
tool which contributes to the overall bundle will stay in its original
licence (R is GPL v2 for instance) but the bundle will be GPL v3.


You need to be careful with that:  R has a variety of licenses for 
various parts, and I'm not sure all of them are GPL v3 compatible.



>From your point of view, do you see any legal issue with this project under
Cydia for jailbroken iOS devices?
>From a trademark point of view, is the name of the apps "R Console Free"
and "R Console Premium" ok ?


I don't think the R Foundation would object to those names, but you 
could ask them to be sure.  You should get permission if you want to use 
the logo.


Duncan Murdoch
P.S. I am a Foundation member, but I'm not writing in that capacity.



Thanks for your help.

Apps Embedded Team.

[[alternative HTML version deleted]]

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Re: [Rd] UTF8 markdown vignette

[Yihui Xie]

Thanks for the kind words. Actually we have more ambitious plans than
just reverse search :)

Regards,
Yihui
--
Yihui Xie 
Web: http://yihui.name


On Tue, Dec 9, 2014 at 11:18 AM, Duncan Murdoch
 wrote:
> On 09/12/2014 11:13 AM, Yihui Xie wrote:
>>
>> 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.
>
>
> Over the last while I've been writing an HTML vignette, and I really want to
> compliment Yihui and the other rmarkdown folks for doing a fantastic job
> with them.  I haven't had to deal with encoding issues, but overall markdown
> + R + HTML is a very pleasant way to work.   I just wish someone would
> implement reverse search ... :-).
>
> Duncan Murdoch

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Re: [Rd] UTF8 markdown vignette

[Duncan Murdoch]

On 09/12/2014 11:13 AM, Yihui Xie wrote:

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).


 Yes, "utf8" works; it will be sent to the vignette engine as "UTF-8".

I was surprised about the missing docs.  The documented way to do this 
is to use


%\SweaveUTF8

but the source says the recommended way is to use

%\VignetteEncoding{}

and it's certainly a little more engine-agnostic.  I'll add something to the 
docs if Kurt doesn't get there first.



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.


Over the last while I've been writing an HTML vignette, and I really 
want to compliment Yihui and the other rmarkdown folks for doing a 
fantastic job with them.  I haven't had to deal with encoding issues, 
but overall markdown + R + HTML is a very pleasant way to work.   I just 
wish someone would implement reverse search ... :-).


Duncan Murdoch


Regards,
Yihui
--
Yihui Xie 
Web: http://yihui.name


On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch  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.
>> $£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
äëïöüÿ áéà óúý à èìòù ãñçµ
>
> 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.dun...@gmail.com]
>> Verzonden: dinsdag 9 december 2014 11:04
>> Aan: ONKELINX, Thierry; r-devel@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,

Re: [Rd] R on the Cydia Store

[Henrik Bengtsson]

On Dec 9, 2014 6:38 AM, "Apps Embedded"  wrote:
>
> Hi,
>
> We have published an Android app called R Console on the Play Store since
> Décember 2013.
> https://play.google.com/store/apps/details?id=com.appsopensource.R
> https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium
>
> In the mean time, we have developped its equivalent app for the App Store.
> We released it on march 2014. We have been approved from this date by Apple
> to publish it world wide.
> Recently, we learnt that GPL app are not compatible with the App Store
> distribution licence.

What I would like to write here, would fall under "this is certainly
not a topic for R devel", so I refrain.

However, I can say that it's likely your problems wouldn't have stopped there;

[R] R on the iPhone/iPad? Not so mucha GPL violation
https://stat.ethz.ch/pipermail/r-help/2010-June/240901.html

/Henrik

>
> Thus we decided to remove the iOS app from the App Store several days ago.
>
> We are thinking of publishing the same app published under Cydia with a
> freemium model.
> Its licence would be GPL v3.
>
> What we would like to do under Cydia with R Console is to have the
> following behavior :
> - free version will be able to run recommended packages and graphics are
> not enabled. A small ad banner is present on top of the app.
> - premium version will be the same as the free version except the ad banner
> will not be present anymore and 3 compilers will be integrated into the app
> in order to be able to compile and run most of the Cran packages from
> source.
> - graphics may be added in a second step.
>
> The app will be considered as a bundle of open-source tools. This bundle
> will be under the Gnu General Public Licence version 3. Each open-source
> tool which contributes to the overall bundle will stay in its original
> licence (R is GPL v2 for instance) but the bundle will be GPL v3.
>
>
> >From your point of view, do you see any legal issue with this project under
> Cydia for jailbroken iOS devices?
> >From a trademark point of view, is the name of the apps "R Console Free"
> and "R Console Premium" ok ?
>
> Thanks for your help.
>
> Apps Embedded Team.
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] UTF8 markdown vignette

[Yihui Xie]

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 
Web: http://yihui.name


On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch  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.
>> $£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
>> äëïöüÿ áéà óúý à èìòù ãñçµ
>
> 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.dun...@gmail.com]
>> Verzonden: dinsdag 9 december 2014 11:04
>> Aan: ONKELINX, Thierry; r-devel@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 --vanill

[Rd] R on the Cydia Store

[Apps Embedded]

Hi,

We have published an Android app called R Console on the Play Store since
Décember 2013.
https://play.google.com/store/apps/details?id=com.appsopensource.R
https://play.google.com/store/apps/details?id=com.appsopensource.Rpremium

In the mean time, we have developped its equivalent app for the App Store.
We released it on march 2014. We have been approved from this date by Apple
to publish it world wide.
Recently, we learnt that GPL app are not compatible with the App Store
distribution licence.

Thus we decided to remove the iOS app from the App Store several days ago.

We are thinking of publishing the same app published under Cydia with a
freemium model.
Its licence would be GPL v3.

What we would like to do under Cydia with R Console is to have the
following behavior :
- free version will be able to run recommended packages and graphics are
not enabled. A small ad banner is present on top of the app.
- premium version will be the same as the free version except the ad banner
will not be present anymore and 3 compilers will be integrated into the app
in order to be able to compile and run most of the Cran packages from
source.
- graphics may be added in a second step.

The app will be considered as a bundle of open-source tools. This bundle
will be under the Gnu General Public Licence version 3. Each open-source
tool which contributes to the overall bundle will stay in its original
licence (R is GPL v2 for instance) but the bundle will be GPL v3.


>From your point of view, do you see any legal issue with this project under
Cydia for jailbroken iOS devices?
>From a trademark point of view, is the name of the apps "R Console Free"
and "R Console Premium" ok ?

Thanks for your help.

Apps Embedded Team.

[[alternative HTML version deleted]]

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Re: [Rd] UTF8 markdown vignette

[Duncan Murdoch]

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.
> $£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
> äëïöüÿ áéà óúý à èìòù ãñçµ

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
> 
> 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.onkel...@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.dun...@gmail.com]
> Verzonden: dinsdag 9 december 2014 11:04
> Aan: ONKELINX, Thierry; r-devel@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.onkel...@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 t

Re: [Rd] UTF8 markdown vignette

[ONKELINX, Thierry]

Dear Duncan,

The UTF-8 characters aren't properly rendered in the pdf version of the 
vignette.
$£€ âêîûô äëïöüÿ áéíóúý àèìòù ãñ çµ is rendered as $£€ âêîûô 
äëïöüÿ áéà óúý à èìòù ãñçµ

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.onkel...@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.dun...@gmail.com]
Verzonden: dinsdag 9 december 2014 11:04
Aan: ONKELINX, Thierry; r-devel@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.onkel...@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 o>
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Disclaimer Bezoek onze website / Visit our 
website
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] UTF8 markdown vignette

[Duncan Murdoch]

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.onkel...@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
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] UTF8 markdown vignette

[ONKELINX, Thierry]

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.

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.onkel...@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

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel