Re: [babel][PATCHES] ob-R patches for review

["Charles C. Berry" <ccberry@ucsd.edu>]

On Mon, 12 May 2014, Rainer M Krug wrote:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>>>> If not would you mind submitting a version of the patches split into
>>>> multiple commits with as much of the hard-coded R code as feasible
>>>> placed into customizable variables along the lines of the
>>>> `org-babel-R-assign-elisp-function' variable suggested by Charles.
>>>
>>> I am thinking of actually not providing the R code in org-variables, but
>>> to put them into R files and to source them. By doing this, the
>>> customization could be done in R, which will be much easier for R users
>>> then to customize emacs variables.
>>>
>>
>> I think this is a bad idea, such external R source files may be hard to
>> manage and load reliably across systems
>
> I see your points, but I am looking at ESS (which is loading .R files as
> well into the ESSR environment) and whose loading mechanism I want
> to piggy back the loading of .R for org. If I understand the variable
> transfer from org to R correctly, it anyway only works on local R
> sessions, which makes it even easier to do then ESS which also caters
> for remote R sessions.
> My idea is to have all R code in one directory and to let ESS load it
> upon initialization of ESS (which is a dependency of running R from org
> anyway, if I am not mistaken).

Not quite. You can run R src blocks without (require 'ess) if they require 
no session. (I do not claim that anyone actually runs R src blocks who 
lacks a working ESS installation, just saying...)


> I have a prototype working, and will keep
> you posted. The complication would be that a newer version of ESS would
> be needed.
>

Maybe load the ESS and R files if

   (and (fboundp 'ess-version)
        (not (string<
              (ess-version)
              "ess-version: <least-version>")))

and fallback to the existing version of ob-R.el (or something like it) 
otherwise.

> The other option would be to just copy the code ESS uses into org, which
> would make the process independent of changes in ESS. But I don't like
> the duplication of code.
>
>> and it is not clear where they should live in the Org-mode repository.
>
> I would suggest in a etc/R.
>

IIUC, someone on ESS core will support your effort. So maybe you can have 
an etc/ESSR/R/org-mode.R file.

Since you will have a mix of elisp and R, it might make sense to have 
minimal callouts on the org-mode side to an elisp wrapper on the ESS side. 
Then you can maintain the trickier elisp on the ESS side, so changes in 
elisp that require changes in R or vice versa can be made in unison.

>> Additionally, if the variables simply hold R code text, then users can
>> easily initialize them from R files locally with something like the
>> following.
>>
>>     (setq org-babel-R-assign-elisp-function
>>           (with-temp-buffer
>>             (insert-file-contents-literally "personal.R")
>>             (buffer-string)))
>>
>> I think this approach is much simpler.
>
> True - but I like the simplicity of being able to customize the
> behavior of org-babel-R by writing an R function without having to thin
> about elisp. But maybe there is a way of doing both...
>

noweb will do it. Quote the chunk like this:

#+BEGIN_SRC emacs-lisp :noweb yes :tangle elisp-R.el
   (setq rlines "
<<r-code>>")
#+END_SRC


HTH,

Chuck


Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at ucsd edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, CA 92093-0901