Re: [Rd] UTF8 markdown vignette

[ONKELINX, Thierry]

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_0.6.4fortunes_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.onkel...@inbo.be
www.inbo.be

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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: xieyi...@gmail.com [mailto:xieyi...@gmail.com] Namens Yihui Xie
Verzonden: woensdag 10 december 2014 4:37
Aan: Duncan Murdoch
CC: ONKELINX, Thierry; r-devel@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 
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

[Brian G. Peterson]

In the event that a lawyer is consulted, I would suggest finding one 
with real experience in open source law.  In my experience, even most 
intellectual property or software attorneys have little to no experience 
with open source law, and I've heard the most dreadful and incorrect 
utterances from them on the topic of open source licenses.


Duncan is correct that parts of R may be incompatible with GPL-3, and 
that is a matter for an attorney.


I installed the premium version of the Android application this morning.

It appears to contain the required license statement (though whether 
that license is valid I cannot say, as discussed in this thread).  It 
also contains a link to:


https://code.google.com/p/rconsoleapp/

The development team is not listed here either, just 'Apps Embedded' and 
more similar redirection.  If these are legal entities, and proper 
copyright assignments have been done for the 'app collection', this may 
be fine, but it is rather outside the spirit of most open source projects.


The code is also not actually available at the link above.  What is 
available is an external link to Google Drive, where a 34 MB tarball of 
different tarballs exists, in a single archive.  Again, consistent with 
most open source projects, perhaps one of the several source code 
management tools provided by code.google.com could be used to create a 
source code repository which could be accessed by other open source 
developers, and examined more easily than the tarball.


It's not clear that anything obvious has been done outside the letter of 
the GPL.  It is also not clear than any improper use has been made of R 
Foundation trademarks (such as the R logo).


If a lawyer is consulted, one way to find  such a lawyer would be to 
start with someone at the Software Freedom Conservancy:


https://sfconservancy.org/

They have contacts with attorneys with experience in GPL licensing and 
commercialization, in multiple countries.


Regards,

Brian

On 12/09/2014 06:31 PM, Marc Schwartz wrote:

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 mailto:marc_schwa...@me.com>>:


On Dec 9, 2014, at 3:34 PM, Duncan Murdoch mailto:murdoch.dun...@gmail.com>> wrote:

On 09/12/2014, 4:26 PM, Marc Schwartz wrote:



On Dec 9, 2014, at 10:44 AM, Henrik Bengtsson mailto:h...@biostat.ucsf.edu>> wrote:

On Dec 9, 2014 6:38 AM, "Apps Embedded" mailto:apps.embed...@gmail.com>> 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 cont

Re: [Rd] R on the Cydia Store

[Apps Embedded]

Hi,

Thanks for your remarks.
We have sent an e-mail to the r-foundat...@r-project.org this morning to
introduce ourself and our work to the R foundation.

>From your advices, we are going to :
- create an open source git repository for this whole project instead of
giving a source tarball
- contact the Software Freedom Conservancy for :
- the licencing validation
- the trademark point of view
- the copyright remark
- limit our work to the Android Play Store.

Best regards.

Apps Embedded Team.



2014-12-10 11:34 GMT+01:00 Brian G. Peterson :

> In the event that a lawyer is consulted, I would suggest finding one with
> real experience in open source law.  In my experience, even most
> intellectual property or software attorneys have little to no experience
> with open source law, and I've heard the most dreadful and incorrect
> utterances from them on the topic of open source licenses.
>
> Duncan is correct that parts of R may be incompatible with GPL-3, and that
> is a matter for an attorney.
>
> I installed the premium version of the Android application this morning.
>
> It appears to contain the required license statement (though whether that
> license is valid I cannot say, as discussed in this thread).  It also
> contains a link to:
>
> https://code.google.com/p/rconsoleapp/
>
> The development team is not listed here either, just 'Apps Embedded' and
> more similar redirection.  If these are legal entities, and proper
> copyright assignments have been done for the 'app collection', this may be
> fine, but it is rather outside the spirit of most open source projects.
>
> The code is also not actually available at the link above.  What is
> available is an external link to Google Drive, where a 34 MB tarball of
> different tarballs exists, in a single archive.  Again, consistent with
> most open source projects, perhaps one of the several source code
> management tools provided by code.google.com could be used to create a
> source code repository which could be accessed by other open source
> developers, and examined more easily than the tarball.
>
> It's not clear that anything obvious has been done outside the letter of
> the GPL.  It is also not clear than any improper use has been made of R
> Foundation trademarks (such as the R logo).
>
> If a lawyer is consulted, one way to find  such a lawyer would be to start
> with someone at the Software Freedom Conservancy:
>
> https://sfconservancy.org/
>
> They have contacts with attorneys with experience in GPL licensing and
> commercialization, in multiple countries.
>
> Regards,
>
> Brian
>
> On 12/09/2014 06:31 PM, Marc Schwartz wrote:
>
>> 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 >> marc_schwa...@me.com>>:
>>>
>>>  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.R>
>>> https://play.google.com/store/apps/details?id=com.
>>> appsopensource.Rpremium >> 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 

Re: [Rd] UTF8 markdown vignette

[Duncan Murdoch]

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 
> 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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