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From: Shiyuan <gshy2014@gmail.com>
To: Bastien <bzg@gnu.org>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: Babel-R TBLFM example
Date: Sun, 24 Aug 2014 16:02:33 -0700	[thread overview]
Message-ID: <CAOm4EMsm5a80w3rvEZazVLXqrO5=AdW_jNfEwTJpkWgP6N5ggA@mail.gmail.com> (raw)
In-Reply-To: <8761igfgio.fsf@bzg.ath.cx>

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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.

Shiyuan


------------------------------
#+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


On Tue, Jul 29, 2014 at 6:20 AM, Bastien <bzg@gnu.org> wrote:

> Hi Shiyuan,
>
> Shiyuan <gshy2014@gmail.com> writes:
>
> > Thanks Bastien. I see ob-R.el from org-mode repos has been updated.
> > So is the org-R from git-repos ready to use? Could you suggest  a
> > good place to start learning the new org-R? The source file ob-R.el?
>
> The recent committers to ob-R.el we be more in a position to help here
> but yes, reading the source is certainly a good start.
>
> I hope we will have a clear picture of what changed in ob-R.el in 8.3,
> together with updated tutorials.
>
> Best,
>
> --
>  Bastien
>

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  reply	other threads:[~2014-08-24 23:02 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 [this message]
2014-08-25  7:51         ` Sebastien Vauban
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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