[Rd] r wiki
Baptiste Auguie
baptiste.auguie at gmail.com
Tue Sep 9 16:29:37 CEST 2014
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 Gábor, 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 Gábor 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, Gábor Csárdi
> > <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, André 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/
> >>>
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> >>
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