emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
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

  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 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

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://www.orgmode.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=861ts5knwx.fsf@somewhere.org \
    --to=sva-news-d0wtavr13harg/idocfnwg@public.gmane.org \
    --cc=emacs-orgmode-mXXj517/zsQ@public.gmane.org \
    --subject='Re: Babel-R TBLFM example' \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link

Code repositories for project(s) associated with this inbox:

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).