From: "Charles C. Berry" <ccberry@ucsd.edu>
To: Rainer M Krug <Rainer@krugs.de>
Cc: Bastien <bzg@gnu.org>,
"emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>,
Eric Schulte <schulte.eric@gmail.com>
Subject: Re: [babel][PATCHES] ob-R patches for review
Date: Mon, 12 May 2014 15:05:11 -0700 [thread overview]
Message-ID: <alpine.OSX.2.00.1405121405050.6955@charles-berrys-macbook.local> (raw)
In-Reply-To: <m2a9amu86j.fsf@krugs.de>
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
next prev parent reply other threads:[~2014-05-12 22:11 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-04-29 12:43 [babel][PATCHES] ob-R patches for review Rainer M Krug
2014-04-29 18:15 ` Charles Berry
2014-04-30 12:28 ` Rainer M Krug
2014-04-30 22:49 ` Charles C. Berry
2014-05-01 9:10 ` Rainer M Krug
2014-05-07 10:27 ` Eric Schulte
2014-05-08 2:26 ` Charles Berry
2014-05-08 10:02 ` Rainer M Krug
2014-05-09 9:11 ` Rainer M Krug
2014-05-09 12:02 ` Rainer M Krug
2014-05-08 9:57 ` Rainer M Krug
2014-05-09 13:03 ` Bastien
2014-05-09 13:45 ` Rainer M Krug
2014-05-09 14:34 ` Eric Schulte
2014-05-12 8:33 ` Rainer M Krug
2014-05-12 12:23 ` Suvayu Ali
2014-05-12 12:41 ` Rainer M Krug
2014-05-12 14:01 ` Queestion concerning lists - was: " Rainer M Krug
2014-05-12 15:23 ` Eric Schulte
2014-05-12 15:21 ` Eric Schulte
2014-05-12 19:08 ` Rainer M Krug
2014-05-12 22:05 ` Charles C. Berry [this message]
[not found] ` <m2y4y2f499.fsf@krugs.de>
2014-05-16 18:22 ` Charles C. Berry
2014-06-06 16:11 ` Eric Schulte
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