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* org-babel with R, scrolling an inferior ESS process
@ 2010-02-16 16:00 Erik Iverson
  2010-02-17  2:24 ` Dan Davison
  0 siblings, 1 reply; 4+ messages in thread
From: Erik Iverson @ 2010-02-16 16:00 UTC (permalink / raw)
  To: emacs-orgmode

Hello,

I have been a happy user of ESS with R for years.  Recently, I've begun 
to use org-mode for a lot of things, so of course I am interested in 
org-babel. I checked out a version of org-mode yesterday (2-15-2010) 
from git.

Using just ESS,  I would write a source file, test.R, and define a 
function in it, say

#identity function
test <- function(x) {
	x
}
test(3)

I could then type C-c C-c (coincidentally, and happily, this is the ESS 
keybinding used to send a block of code to the inferior *R* process) to 
send the above lines to the running *R* process, and the output would 
show up in the *R* buffer, and scroll to the bottom of the *R* buffer 
since I have set

(setq comint-scroll-to-bottom-on-output t)

in my .emacs.

However, now I hope to write a file, test.org, and write something like:

* Identity function
#+begin_src R :session :results output silent
   test <- function(x) {
     x
   }
   test(3)
#+end_src

If I use C-c ' to open an R code buffer and C-c C-c, I see the same 
behavior as in ESS. However, when I do C-c C-c on the code block *in the 
test.org buffer*, the code is sent to the *R* buffer, but it does not 
scroll.  In the *R* buffer, once I do scroll to the bottom, I see the 
following:

 >
test <- function(x) {
   x
}
test(3)
'org_babel_R_eoe'

 > test <- function(x) {
+   x
+ }
 > test(3)
[1] 3
 > 'org_babel_R_eoe'
[1] "org_babel_R_eoe"

Can anyone
1) replicate that you don't see the scrolling, even with the 
comint-scroll-to-bottom-on-output variable set to 't'?
2) suggest a way to get the *R* buffer to scroll to the bottom when I 
execute a source block from an org-mode file to a running *R* session?

I am surprised by this behavior since I just assumed comint-mode should 
do the right thing, so I'm not sure where the issue is! Even if this 
can't be changed, I think org-babel is going to be a great use to me, 
thank you!

Best Regards,
Erik Iverson

^ permalink raw reply	[flat|nested] 4+ messages in thread

* Re: org-babel with R, scrolling an inferior ESS process
  2010-02-16 16:00 org-babel with R, scrolling an inferior ESS process Erik Iverson
@ 2010-02-17  2:24 ` Dan Davison
  2010-02-18 15:37   ` Erik Iverson
  0 siblings, 1 reply; 4+ messages in thread
From: Dan Davison @ 2010-02-17  2:24 UTC (permalink / raw)
  To: Erik Iverson; +Cc: emacs-orgmode

Hi Erik,

[...]
> * Identity function
> #+begin_src R :session :results output silent
>   test <- function(x) {
>     x
>   }
>   test(3)
> #+end_src
>
> If I use C-c ' to open an R code buffer and C-c C-c, I see the same
> behavior as in ESS. However, when I do C-c C-c on the code block *in
> the test.org buffer*, the code is sent to the *R* buffer, but it does
> not scroll.  In the *R* buffer, once I do scroll to the bottom, I see
> the following:
>
>>
> test <- function(x) {
>   x
> }
> test(3)
> 'org_babel_R_eoe'
>
>> test <- function(x) {
> +   x
> + }
>> test(3)
> [1] 3
>> 'org_babel_R_eoe'
> [1] "org_babel_R_eoe"
>
> Can anyone
> 1) replicate that you don't see the scrolling, even with the
> comint-scroll-to-bottom-on-output variable set to 't'?

Yes, this has been on my todo list for a while! Definitely time to fix it.

> 2) suggest a way to get the *R* buffer to scroll to the bottom when I
> execute a source block from an org-mode file to a running *R* session?

It seems to be fixable by changing a couple of save-window-excursions
into save-excursions (patch below). I haven't thought of anything that
this will break, but in any case I suspect that Eric S. will apply the
correct fix to the main git repo soon.

As for the 'org_babel_R_eoe' stuff, that is org-babel internals that
ideally would not be exposed to the user. I suspect that it is possible
to remove it from the comint buffer -- Eric S. is definitely best placed
to comment on the best way of doing that.

I'm sure this is obvious to you, but while we're on the topic: the
reason that the org-babel R comint evaluation behaviour differs from ESS
is because org-babel required a common mechanism that would work for all
the supported languages; we were aware all along that ESS had already
done an excellent job of doing that for R (plus some other languages).

Please do let us know of any other improvements we can make to using
org-babel with ESS. Good integration with ESS has been one of our aims
from the beginning.

Dan


--8<---------------cut here---------------start------------->8---
commit d84c426027653a41ad02992d06d7c151d26d1f4b
Author: Dan Davison <davison@stats.ox.ac.uk>
Date:   Tue Feb 16 21:08:09 2010 -0500

    babel: allow point to move to end of comint buffer

diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index 1fe2826..c3f9e19 100644
--- a/contrib/babel/lisp/langs/org-babel-R.el
+++ b/contrib/babel/lisp/langs/org-babel-R.el
@@ -39,7 +39,7 @@
   "Execute a block of R code with org-babel.  This function is
 called by `org-babel-execute-src-block'."
   (message "executing R source code block...")
-  (save-window-excursion
+  (save-excursion
     (let* ((processed-params (org-babel-process-params params))
            (result-type (fourth processed-params))
            (session (org-babel-R-initiate-session (first processed-params)))
diff --git a/contrib/babel/lisp/org-babel-comint.el b/contrib/babel/lisp/org-babel-comint.el
index d65f054..e693a40 100644
--- a/contrib/babel/lisp/org-babel-comint.el
+++ b/contrib/babel/lisp/org-babel-comint.el
@@ -45,7 +45,7 @@
 body inside the protection of `save-window-excursion' and
 `save-match-data'."
   (declare (indent 1))
-  `(save-window-excursion
+  `(save-excursion
      (save-match-data
        (unless (org-babel-comint-buffer-livep ,buffer)
          (error (format "buffer %s doesn't exist or has no process" ,buffer)))
--8<---------------cut here---------------end--------------->8---


>
> I am surprised by this behavior since I just assumed comint-mode
> should do the right thing, so I'm not sure where the issue is! Even if
> this can't be changed, I think org-babel is going to be a great use to
> me, thank you!
>
> Best Regards,
> Erik Iverson
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

^ permalink raw reply related	[flat|nested] 4+ messages in thread

* Re: org-babel with R, scrolling an inferior ESS process
  2010-02-17  2:24 ` Dan Davison
@ 2010-02-18 15:37   ` Erik Iverson
  2010-02-18 17:39     ` Eric Schulte
  0 siblings, 1 reply; 4+ messages in thread
From: Erik Iverson @ 2010-02-18 15:37 UTC (permalink / raw)
  To: Dan Davison; +Cc: emacs-orgmode

Hello,

<snip>

>> Can anyone
>> 1) replicate that you don't see the scrolling, even with the
>> comint-scroll-to-bottom-on-output variable set to 't'?
> 
> Yes, this has been on my todo list for a while! Definitely time to fix it.

Great, I'd be happy to test out the code when it's ready!

> 
>> 2) suggest a way to get the *R* buffer to scroll to the bottom when I
>> execute a source block from an org-mode file to a running *R* session?
> 
> It seems to be fixable by changing a couple of save-window-excursions
> into save-excursions (patch below). I haven't thought of anything that
> this will break, but in any case I suspect that Eric S. will apply the
> correct fix to the main git repo soon.
> 
> As for the 'org_babel_R_eoe' stuff, that is org-babel internals that
> ideally would not be exposed to the user. I suspect that it is possible
> to remove it from the comint buffer -- Eric S. is definitely best placed
> to comment on the best way of doing that.
> 

That would be great, too!


> Please do let us know of any other improvements we can make to using
> org-babel with ESS. Good integration with ESS has been one of our aims
> from the beginning.

I will let you know as I continue using it.  The ultimate improvement 
IMO would be some sort of good multi-mode support, so that things 
between #+begin_src/#+end_src would be fontified according to their 
mode. And when I, for example, move into an R source section in my 
org-mode buffer, all ESS key bindings would work.

I have read a couple recent threads about getting functionality like 
this via two-mode-mode for instance, but they have some quirks that make 
it unusable for me.  Are you and Eric working on anything like this?  I 
have been investigating different options and will let you know if I 
find anything promising!

Thanks!
Erik

^ permalink raw reply	[flat|nested] 4+ messages in thread

* Re: org-babel with R, scrolling an inferior ESS process
  2010-02-18 15:37   ` Erik Iverson
@ 2010-02-18 17:39     ` Eric Schulte
  0 siblings, 0 replies; 4+ messages in thread
From: Eric Schulte @ 2010-02-18 17:39 UTC (permalink / raw)
  To: Erik Iverson; +Cc: Dan Davison, emacs-orgmode

Erik Iverson <eriki@ccbr.umn.edu> writes:

[...]

>> Please do let us know of any other improvements we can make to using
>> org-babel with ESS. Good integration with ESS has been one of our aims
>> from the beginning.
>
> I will let you know as I continue using it.  The ultimate improvement
> IMO would be some sort of good multi-mode support, so that things
> between #+begin_src/#+end_src would be fontified according to their
> mode. And when I, for example, move into an R source section in my
> org-mode buffer, all ESS key bindings would work.
>
> I have read a couple recent threads about getting functionality like
> this via two-mode-mode for instance, but they have some quirks that
> make it unusable for me.  Are you and Eric working on anything like
> this?  I have been investigating different options and will let you
> know if I find anything promising!
>

Hi Erik,

This is a very popular feature request, but as far as I know it is not
possible due to limitations ingrained fairly deep into the core of
Emacs.  To my knowledge the best such mode for embedding multiple major
modes in a single buffer is MuMaMo-mode [1] which has been applied to
source-code blocks in Org-mode buffers [2], but as mentioned in that
thread, it's far from stable.

Best -- Eric

>
> Thanks!
> Erik

Footnotes: 
[1]  http://www.emacswiki.org/cgi-bin/wiki/MuMaMo

[2]  http://article.gmane.org/gmane.emacs.orgmode/8112/match=mumamo

^ permalink raw reply	[flat|nested] 4+ messages in thread

end of thread, other threads:[~2010-02-18 17:39 UTC | newest]

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2010-02-16 16:00 org-babel with R, scrolling an inferior ESS process Erik Iverson
2010-02-17  2:24 ` Dan Davison
2010-02-18 15:37   ` Erik Iverson
2010-02-18 17:39     ` Eric Schulte

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