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From: "Berry, Charles" via "General discussions about Org-mode." <emacs-orgmode@gnu.org>
To: Jack Kamm <jackkamm@gmail.com>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>,
	Dylan Schwilk <dylan@schwilk.org>
Subject: Re: Help debugging R source code block output problem with :session
Date: Mon, 7 Sep 2020 17:37:51 +0000
Message-ID: <48AD2294-E831-44D7-B564-0F7B4019C61B@health.ucsd.edu> (raw)
In-Reply-To: <87pn6y9dqy.fsf@gmail.com>

Jack,

This does not work for my remote session.

I run from macOS locally and on a Linux host remotely.  I use 

	M-x shell RET
	R RET
	M-x ess-remote RET R RET

to start the R session.

The problem is that tempfiles on the remote host are like "/tmp/RtmpeFHudh/file23a66d2fc1f9", but emacs tries to use '/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/babel-OSXKNd/R-oNOVVB'

`org-babel-temp-file' doesn't honor remote connections AFAICS.

Maybe there is some comint or tramp idiom that would solve this, but I do not know what it is.

Chuck

> On Sep 7, 2020, at 1:45 AM, Jack Kamm <jackkamm@gmail.com> wrote:
> 
> I just realized my patch had an issue where it freezes if there is an
> error in the source block.
> 
> I'm attaching a second patch, to be applied on top of the first one, that fixes the issue.
> 
> diff --git a/lisp/ob-R.el b/lisp/ob-R.el
> index b37e3965a..5ddf0ebd1 100644
> --- a/lisp/ob-R.el
> +++ b/lisp/ob-R.el
> @@ -441,7 +441,7 @@ (defun org-babel-R-evaluate-session
>     (output
>      (let* ((tmp-file (org-babel-temp-file "R-")))
>        (with-temp-file tmp-file
> -	 (insert (concat body "\n" org-babel-R-eoe-indicator)))
> +	 (insert body))
>        (with-current-buffer session
> 	 (let* ((process (get-buffer-process (current-buffer)))
> 		(string-buffer "")
> @@ -450,8 +450,9 @@ (defun org-babel-R-evaluate-session
> 					    (concat string-buffer text)))
> 		       comint-output-filter-functions)))
> 	   (ess-send-string
> -	    process (format "source('%s', print.eval=TRUE)"
> -			    (org-babel-process-file-name tmp-file 'noquote)))
> +	    process (format "tryCatch(source('%s', print.eval=TRUE), finally=print(%s))"
> +			    (org-babel-process-file-name tmp-file 'noquote)
> +			    org-babel-R-eoe-indicator))
> 	   (while (not (string-match (regexp-quote org-babel-R-eoe-output)
> 				     string-buffer))
> 	     (accept-process-output process))




  reply	other threads:[~2020-09-07 17:38 UTC|newest]

Thread overview: 22+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2020-08-28 20:11 Dylan Schwilk
2020-08-29  2:36 ` Jack Kamm
2020-08-29  4:07   ` Dylan Schwilk
2020-08-29  7:24     ` Jack Kamm
2020-08-29 20:35       ` Berry, Charles via General discussions about Org-mode.
2020-08-30  4:37         ` Dylan Schwilk
2020-08-30 15:08         ` Jack Kamm
2020-09-07  8:18         ` Jack Kamm
2020-09-07  8:45           ` Jack Kamm
2020-09-07 17:37             ` Berry, Charles via General discussions about Org-mode. [this message]
2020-09-07 20:07               ` Jack Kamm
2020-09-07 22:12                 ` Berry, Charles via General discussions about Org-mode.
2020-09-08  1:06                   ` Jack Kamm
2020-09-08  2:08                     ` Berry, Charles via General discussions about Org-mode.
2020-09-08 14:51                       ` Jack Kamm
2020-09-08 16:45                         ` Berry, Charles via General discussions about Org-mode.
2020-09-08 17:41                           ` Jack Kamm
2020-09-18 16:39                             ` Dylan Schwilk
2020-10-28 13:13                 ` Jack Kamm
2020-10-28 13:46                   ` Jeremie Juste
2020-08-30  4:18       ` Dylan Schwilk
2021-05-03  8:53       ` Jeremie Juste

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