From baptiste.auguie at gmail.com  Tue Sep  9 16:29:37 2014
From: baptiste.auguie at gmail.com (Baptiste Auguie)
Date: Tue, 9 Sep 2014 11:29:37 -0300
Subject: [Rd] r wiki
In-Reply-To: <21519.1306.551292.683057@stat.math.ethz.ch>
References: <6604241409959069@web8j.yandex.ru>
	<540B2825.40403@statistik.tu-dortmund.de>
	<618E9DC0-7ADA-4E6F-95CD-3551B55386B3@umons.ac.be>
	<CANROs4fk_Ve6tV0qRrqn+BeiCkpRBe8z6Q4vCXB-T79ArzNO-g@mail.gmail.com>
	<CABtg=Km5oaFJCGDKpC_5qVhCm+a_MhjnNhntnAGKQjgeBvx1Yw@mail.gmail.com>
	<846A1514-C508-46EF-978F-685C0DE3B730@sciviews.org>
	<21519.1306.551292.683057@stat.math.ethz.ch>
Message-ID: <CANLFJPpg0tGZyas0SfYT5CPgCbfH7TWhdvi4TzD0=fDG9=mUSg@mail.gmail.com>

One small technical issue currently limiting the deployment of true
reproducible wikis based on knitr + github-markdown is the lack of reverse
synchronisation between the rendered output (markdown), edited online, and
the original Rmd source. It think the combination of wiki features +
reproducible source code has great potential for community-driven
documentation (even for individual packages), but this relatively new
use-case for reproducible documents may highlight a limitation in knitr's
current framework [1].

On a more general note, and considering the positive sentiment toward
github in the R community, it might be a good time to register a
semi-official R-project organisation to regroup such initiatives,

https://help.github.com/articles/creating-a-new-organization-account

In the long-run, it would be nice to centralise some valuable resources
that have appeared independently over the years, such as the R wiki, the R
graph gallery [?], the unofficial CRAN mirror [2], the unofficial r-source
mirror [3], and probably many others I forget or don't know about.

Regards,

baptiste

[1] related discussion here: https://github.com/yihui/knitr/issues/536
[?] http://addictedtor.free.fr/graphiques/
[2] https://github.com/cran, https://github.com/metacran/
[3] https://github.com/wch/r-source

On 9 September 2014 10:48, Martin Maechler <maechler at stat.math.ethz.ch>
wrote:

> >>>>> Philippe Grosjean <phgrosjean at sciviews.org>
> >>>>>     on Tue, 9 Sep 2014 08:45:14 +0200 writes:
>
>     > Yihui and G?bor, I agree with you, and I also think that
>     > using Travis CI would be very nice. However, there are
>     > hundreds of page on the R wiki to migrate? and syntax is a
>     > little bit different than Markdown.
>
>     > Of course, a solution would be to start again from
>     > scratch, but I think that those who have contributed to
>     > the R Wiki deserve more respect. Any suggestion, or idea
>     > about this?
>
> (and we have seen more on this thread ..)
>
> As one contributor to the former wiki and maintainer of the
> good olde mailing lists, I completely agree (with
> Yihui and G?bor and you) that it's best to move it over to an
> infrastructure which takes care of authentication of legitimate
> users and protection from thieves burglers, spammers, and the like.
>
> Markdown is definitely much better for R users (given knittr and
> Rmd ..), and github is currently the place to host -- and once
> it ceases to be that, markdown will be easier to migrate from.
>
> Martin
>
>     > Best,
>
>     > Philippe On 08 Sep 2014, at 23:12, G?bor Cs?rdi
>     > <csardi.gabor at gmail.com> wrote:
>
>     >> I second this suggestion.
>     >>
>     >> One possible complication I see is that if you would like
>     >> to run the R code (to display its output for example),
>     >> then AFAIK you cannot simply use Jekyll on Github's side,
>     >> but would need some additional infrastructure.
>     >>
>     >> It might be possible to use Travis (or some other) CI for
>     >> it, and avoid installing additional software and/or
>     >> servers, but anyway, this requires some care and effort.
>     >>
>     >> If you don't want to run the code, then it is very easy,
>     >> apart from the (one-time) migration cost.
>     >>
>     >> Best, Gabor
>     >>
>     >> On Mon, Sep 8, 2014 at 4:15 PM, Yihui Xie
>     >> <xie at yihui.name> wrote:
>     >>> I want to make a humble suggestion: migrate the wiki to
>     >>> Github, and build the pages using Jekyll+Markdown. That
>     >>> way, I think it will attract more volunteers. Simply
>     >>> look how many pull requests that Hadley has got for his
>     >>> up-coming book hosted on Github
>     >>> (http://adv-r.had.co.nz):
>     >>> https://github.com/hadley/adv-r/pulls I have had the
>     >>> experience of maintaining web servers and different
>     >>> wiki/CMS systems (including Dokuwiki -- I have even
>     >>> written a PHP plugin for it), and eventually I found I
>     >>> could not afford the time on the job of a system
>     >>> admin. Now I never do that again, and I just focus on
>     >>> maintaining the content. Let the professionals do the
>     >>> hosting and compilation service, and my life has become
>     >>> so much better (no more worries about security holes and
>     >>> attacks).
>     >>>
>     >>> Regards, Yihui
>     >>> --
>     >>> Yihui Xie <xieyihui at gmail.com> Web: http://yihui.name
>     >>>
>     >>>
>     >>> On Mon, Sep 8, 2014 at 12:10 PM, Philippe GROSJEAN
>     >>> <Philippe.GROSJEAN at umons.ac.be> wrote:
>     >>>> Uwe and all,
>     >>>>
>     >>>> I have problems with the R wiki engine. It seems that
>     >>>> there is a systematic attack of the R wiki site that
>     >>>> produces an overconsumption of the server's CPU, and
>     >>>> consequently, my provider did shutdown the whole
>     >>>> SciViews.org web site.
>     >>>>
>     >>>> Now, it is a bad time for me to work on this (very busy
>     >>>> with exams + Master and PhD theses). I am currently
>     >>>> looking for an expert in CMS to look at the problem. I
>     >>>> don't know when I will be able to solve this and reopen
>     >>>> the R Wiki.
>     >>>>
>     >>>> Best,
>     >>>>
>     >>>> Philippe
>     >>>> ..............................................<?}))><........
>     >>>> ) ) ) ) ) ( ( ( ( ( Prof. Philippe Grosjean ) ) ) ) ) (
>     >>>> ( ( ( ( Numerical Ecology of Aquatic Systems ) ) ) ) )
>     >>>> Mons University, Belgium ( ( ( ( (
>     >>>> ..............................................................
>     >>>>
>     >>>> On 06 Sep 2014, at 17:28, Uwe Ligges
>     >>>> <ligges at statistik.tu-dortmund.de> wrote:
>     >>>>
>     >>>>> Rather than asking here, I'd ask Philippe Grosjean
>     >>>>> directly, hence CCIng.
>     >>>>>
>     >>>>> Best, Uwe Ligges
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>> On 06.09.2014 01:17, Andr? Z. D. A. wrote:
> >>>>> This does not answer you, but if you are looking for
>     >>>>> something that existed on that wiki, it may help:
> >>>>>
> >>>>>
> https://web.archive.org/web/20140112055032/http://rwiki.sciviews.org/
> >>>>> doku.php
> >>>>>
> >>>>> And that wiki doesn't look like it had a lot of activity:
> >>>>>
> https://web.archive.org/web/20140301000000*/http://rwiki.sciviews.org/
>     >>>
>     >>> ______________________________________________
>     >>> R-devel at r-project.org mailing list
>     >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>     >>
>     >> ______________________________________________
>     >> R-devel at r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

	[[alternative HTML version deleted]]



[Rd] r wiki
Baptiste Auguie