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[Orgmode] Re: [babel] R: New handling of file output
From: |
Dan Davison |
Subject: |
[Orgmode] Re: [babel] R: New handling of file output |
Date: |
Tue, 21 Dec 2010 16:57:46 +0000 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/23.2 (darwin) |
Dan Davison <address@hidden> writes:
> Please note the following changes to the way that org-babel handles
> file output. These may break existing org-babel files which use
> the :file header argument.
>
> :file <filename> should be understood as saying "write the result
> to <filename> and return a link to <filename>".
>
> This works for all languages. For graphics languages (e.g. ditaa, dot,
> gnuplot) there is no change in behavior: "result" in the above is the
> graphics, and a link to the image is placed in the org buffer. For
> general-purpose languages (e.g. emacs-lisp, python, R, ruby, shell),
> the "result" written to file is the normal org-babel result (string,
> number, table).
>
> This is a backwards-incompatible change for R, which was previously
> interpreting :file to mean "send graphics to file". I will send a
> separate email concerning R.
Previously R understood :file <filename> to mean "save graphics to
<filename>"[1]; now R behaves like other languages and sends the normal
org-babel result to file (string, number, table). To tell R to save
graphics[1] to file, use :results graphics.
Some examples:
Wrong!
#+begin_src R :file img.png
hist(rnorm(100))
"img.png is going to contain this string."
#+end_src
Use :results graphics save graphics:
#+begin_src R :file img.png :results graphics
hist(rnorm(100))
"But now img.png is going to contain graphics."
#+end_src
You may want to use `org-babel-default-header-args:R' to make this
more convenient:
#+begin_src emacs-lisp
(setq org-babel-default-header-args:R
'((:results . "graphics")))
#+end_src
Alternatively the :results graphics header can be set in a property
drawer for the subtree, or a #+babel: line, as usual.
Now this will do what was intended
#+begin_src R :file img.png
hist(rnorm(100))
#+end_src
Here is an example of saving something other than base graphics to file,
and returning a link to the file. Note that :file is not used, and the
filename must be returned. This could be used to save images created by
non-base graphics libraries:
#+begin_src R :results file :var file="savefile"
write.something.to.file <- function(f) cat("hello", file=f)
write.something.to.file(f=file)
file
#+end_src
Dan
* Footnotes
[1] This only works for "base" graphics.
>
> In order to return a file link from a src block without telling babel
> to save any results to that file, use :results <filename> and do not
> use :file. The code block can of course write arbitrary content to
> <filename>.
>
> Some examples:
>
> Save the output of ls -l as a .csv file (recall that :results value is
> the default):
>
> #+begin_src sh :file dirlisting.csv :sep ,
> ls -l
> #+end_src
>
> Send the text output of ls -l directly to file:
>
> #+begin_src sh :results output :file dirlisting.txt
> ls -l
> #+end_src
>
> Dan
>
>
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