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Re: [Orgmode] Re: [babel] R: New handling of file output


From: Thomas S. Dye
Subject: Re: [Orgmode] Re: [babel] R: New handling of file output
Date: Sat, 1 Jan 2011 11:49:05 -1000

Aloha all,

Should :results graphic be documented in the :results header argument section of the Org-mode manual, or in the R-specific documentation?

All the best,
Tom

On Dec 21, 2010, at 6:57 AM, Dan Davison wrote:

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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