Re: [org-babel-R] Help: In converting an .org file to pdf, do I need to re-run the R code even if I ran them previously?

From: "Thomas S. Dye" <tsd@tsdye.com>
To: Sunny Srivastava <research.baba@gmail.com>
Cc: emacs-orgmode mailing list <emacs-orgmode@gnu.org>
Subject: Re: [org-babel-R] Help: In converting an .org file to pdf, do I need to re-run the R code even if I ran them previously?
Date: Thu, 2 Dec 2010 05:33:53 -1000	[thread overview]
Message-ID: <D9062237-CA4D-45EA-B068-76481B0A61A5@tsdye.com> (raw)
In-Reply-To: <AANLkTik6zc6xfFnaqN3p4c=BwEBLhr7Ld0-m4N_vR_E7@mail.gmail.com>

Aloha Sunny,

On Dec 1, 2010, at 11:05 PM, Sunny Srivastava wrote:

> Hello Org-moders:
>
> I am trying to use org-mode, instead of Sweave, to write a report  
> for a statistical analysis. During the process of writing, I prefer  
> to export the org file to pdf to see the output (for sanity check).  
> However, every time I do this, I get a question in minibuffer to  
> choose if I want to "run the R code". I have three questions related  
> to this:
>
> 1. Can I turn this feature off and let "org-babel-R" (sorry if this  
> is something else) automatically choose YES if the code has not been  
> run already and NO if the code has been already run.
>

This is the :cache header argument.  The setting you want is :cache yes.

> 2. Currently, if the code was run already, I choose NO. I am  
> assuming this won't affect the results. Am I correct? (If I change  
> something in the code I run it using C-c in org-mode before  
> exporting it to pdf)
>
> 3. Is there a way to know which R code chunk is "org-babel-R" asking  
> to run, when it asks the question about running the R code.
>

This behavior has changed relatively recently. I believe that with a  
recent version, answering NO won't abandon the evaluation of  
subsequent code blocks, and that the code block name is visible when  
the question is asked.  This is something I don't use, so you'd have  
to pull and see for yourself.

For me, it is preferable to disable the query.  To disable the query,  
I set this:

#+begin_src emacs-lisp :tangle yes
    (setq org-confirm-babel-evaluate nil)
#+end_src

hth,
Tom
> I looked in the uses of org-babel-R webpage on worg, but could not  
> see anything related to this. Sorry if I missed something or the  
> query is too basic.
>
> Thank you.
>
> Regards,
> S.
>
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