Re: Help debugging R source code block output problem with :session

[Dylan Schwilk <dylan@schwilk.org>]

Yes, the modified comint-prompt-regexp works for my use cases and 
I'm back to expected output and what I had last time I taught the 
course. This was my instinct for a simple solution as well, but 
I've not tested against remote sessions and graphical outputs as 
Charles Berry warns.

I'll take a look at your ob-session-async, thanks!

-Dylan


On Sat 29 Aug 2020 at 02:24, Jack Kamm <jackkamm@gmail.com> wrote:

> Hi Dylan,
>
>> The patch does fix that issue -- but it introduces a different 
>> bug 
>> for code blocks with ~:session~: the R block now only produces 
>> output from the last statement evaluated.
>
> Of course, you're right. Good catch.
>
> Here's another attempt. It fixes the issue by modifying the R 
> comint
> regular expression, requiring it to match at the beginning of 
> the line.
>
> I think this should fix most cases, including the examples you
> sent. Still, it's not totally robust -- for example, it will 
> still
> mangle multiline strings, if one of the lines starts with a 
> substring
> that looks like a prompt.
>
> I'd be interested to hear if the attached patch works for the 
> common
> cases you encounter, such as with tibbles.
>
> As an aside, I personally use an alternative implementation of 
> ob-R
> sessions that doesn't suffer from this issue, and also provides 
> some
> other benefits like async evaluation [1]. I'm planning to submit 
> these
> changes to org-mode someday, but am not ready yet. But you may 
> want to
> check it out, it was able to solve the issue in the other thread 
> I
> linked as well.
>
> [1] https://github.com/jackkamm/ob-session-async
>
> From 9eaf81d708f88d06f14f9b6b9cf4182dd0fbb997 Mon Sep 17 
> 00:00:00 2001
> From: Jack Kamm <jackkamm@gmail.com>
> Date: Sat, 29 Aug 2020 00:07:58 -0700
> Subject: [PATCH] ob-R: Fix prompt mangling in session output
>
> * lisp/ob-R.el (org-babel-R-evaluate-session): Force comint 
> prompt
> regexp to start at beginning of line, to prevent
> org-babel-comint-with-output from splitting mid-line.
>
> Fixes https://orgmode.org/list/875zgjh8wn.fsf@gmail.com/ and
> https://orgmode.org/list/87r1rqled0.fsf@havana/
> ---
>  lisp/ob-R.el | 12 +++++++-----
>  1 file changed, 7 insertions(+), 5 deletions(-)
>
> diff --git a/lisp/ob-R.el b/lisp/ob-R.el
> index 5e9d35f58..10b3b6fe3 100644
> --- a/lisp/ob-R.el
> +++ b/lisp/ob-R.el
> @@ -450,11 +450,13 @@ (defun org-babel-R-evaluate-session
>  		      (car (split-string line "\n")))
>  		     (substring line (match-end 1))
>  		   line))
> -	       (org-babel-comint-with-output (session 
> org-babel-R-eoe-output)
> -		 (insert (mapconcat 'org-babel-chomp
> -				    (list body 
> org-babel-R-eoe-indicator)
> -				    "\n"))
> -		 (inferior-ess-send-input)))))) "\n"))))
> +	       (with-current-buffer session
> +		 (let ((comint-prompt-regexp (concat "^" 
> comint-prompt-regexp)))
> +		   (org-babel-comint-with-output (session 
> org-babel-R-eoe-output)
> +		     (insert (mapconcat 'org-babel-chomp
> +					(list body 
> org-babel-R-eoe-indicator)
> +					"\n"))
> +		     (inferior-ess-send-input)))))))) "\n"))))
>  
>  (defun org-babel-R-process-value-result (result column-names-p)
>    "R-specific processing of return value.


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