From: Sebastien Vauban <sva-news-D0wtAvR13HarG/iDocfnWg@public.gmane.org>
To: emacs-orgmode-mXXj517/zsQ@public.gmane.org
Subject: Re: Babel-R TBLFM example
Date: Mon, 25 Aug 2014 09:51:10 +0200 [thread overview]
Message-ID: <861ts5knwx.fsf@somewhere.org> (raw)
In-Reply-To: CAOm4EMsm5a80w3rvEZazVLXqrO5=AdW_jNfEwTJpkWgP6N5ggA@mail.gmail.com
Shiyuan wrote:
> I am looking at a simpler example, the pie-chart example as in this link:
> http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming
>
> This example(src code attached in the end) first generates a table by a
> shell command and then run a R one-liner which uses the table. However,
> when the R code is evaluated, I got an error about the object dirs not
> found. This is what I got in the buffer running R:
> -------------------------------
> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient',
> show.error.locations=TRUE)
>>
> Error in pie(dirs[, 1], labels = dirs[, 2]) (from
> test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found
> -----------------------------------------------
>
> It looks like that the conversion is wrong. When I run
> `org-babel-expand-src-block`
> on the R source code, I don't see the R object dirs is expanded to
> anything. I don't understand how the conversion works, and how Babel passes
> the table to R. Any explanation is appreciated. Which function/file should
> I look at? Are there working examples for passing a table to R? Thanks.
>
> #+name: directories
> #+begin_src shell :results replace
> cd ~ && du -sc * |grep -v total
> #+end_src
>
> #+RESULTS: directories
> | 8 | #*message*-20140319-231047# |
> | 1168376 | Documents |
> | 9952288 | Downloads |
> | 8 | xmodmap2~ |
>
> #+name: directory-pie-chart(dirs = directories)
> #+begin_src R :session R-pie-example :file ~/tmp/dirs.png
> pie(dirs[,1], labels = dirs[,2])
> #+end_src
AFAICT, the arguments to code blocks may not be defined and set in the
`name' line anymore: this must be done on the `begin_src' line.
So, the following should work:
#+name: directory-pie-chart
#+begin_src R :var dirs=directories :session R-pie-example :file ~/tmp/dirs.png
pie(dirs[,1], labels = dirs[,2])
#+end_src
Best regards,
Seb
--
Sebastien Vauban
next prev parent reply other threads:[~2014-08-25 7:51 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-06-25 6:55 Babel-R TBLFM example Shiyuan
2014-07-28 13:21 ` Bastien
2014-07-29 6:15 ` Shiyuan
2014-07-29 13:20 ` Bastien
2014-08-24 23:02 ` Shiyuan
2014-08-25 7:51 ` Sebastien Vauban [this message]
2014-08-26 6:18 ` Shiyuan
2014-08-26 6:57 ` Thomas S. Dye
2014-08-26 7:23 ` Sebastien Vauban
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