emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
From: "Berry, Charles" via "General discussions about Org-mode." <emacs-orgmode@gnu.org>
To: James Powell <powellj@pdx.edu>
Cc: emacs-org list <emacs-orgmode@gnu.org>
Subject: Re: Bug: :session results in unfriendly error reporting
Date: Mon, 16 Aug 2021 18:25:37 +0000	[thread overview]
Message-ID: <FC24C431-9095-4E05-ACD3-FB72BB73852D@health.ucsd.edu> (raw)
In-Reply-To: <5406173c-742f-1e4c-a8da-2d73b4e668ca@pdx.edu>


> On Aug 15, 2021, at 4:41 PM, James Powell <powellj@pdx.edu> wrote:
> I write a deliberate syntax error into a code block:
> : #+begin_src R :session
> :   x <- 1
> :   y xx z
> : #+end_src
> I put my cursor in there and C-c C-c.
> What I expect: a gentle useful report about the error.

Right. But there is no error as far as babel is concerned. R has handled the condition. So there is nothing for babel to see/do.

> Maybe even org would move the cursor to the point of the
> error in the org buffer.  If not, at least the buffer
> "*Org-Babel Error Output*" will open and show me the error,
> something like this (see also [1]),
> : Error: unexpected symbol in:
> : "x <- 1
> : y xx"
> : -UUU:@**--F2  *Org-Babel Error Output*   All L17    (Compilation etu) 4:13PM 0.53 Mail --------------------------------------------------$

`:results output' might help you here, since it will send the terminal output back to babel.

If that doesn't suffice, you might use handlers provided by R to find your way out. But I think that will get sticky as what you create in your example is a parse error.  

If the source blocks are eval'ed as part of an export, you have the option of exporting via ox-ravel[*] and using the knitr chunk options to handle errors in the way you want.

> What happens instead:
> - the *R* buffer is displayed.  It contains a long spammy traceback
>   that has run off of the top of the screen.  To learn more I have to
>   move the cursor into the *R* buffer and page back to the top of the
>   traceback.
> On the other hand, if I set ":session none", I get much friendlier
> behavior.  The Error Output buffer opens with the simple error message
> in it as I showed above when I use this source block:
> : #+begin_src R :session none
> :   x <- 1
> :   y xx z
> : #+end_src

Running R in this fashion starts a fresh process which signals an error that babel can handle.  I see no easy way to get sessions to sends signals that babel can process.

> I do not want to abandon :session because my code reads in a lot of
> data to get started and I want my scripts, not my environment to be
> "real" so I am not depending on R's ability to save and reload the
> workspace at all [2] or on "Org's (clever and useful but) somewhat clunky
> and inflexible method of passing data explicitly" [3].

One of the motivating factors for creating ox-ravel[*] was to have flexible caching of R objects. This is provided in knitr, Sweave, and similar report generators. For interactive use, knit-ing a document that has caching enabled at the start of a session is a fast and painless way to get all the objects needed to modify a document.



[*] https://github.com/chasberry/orgmode-accessories

> Is there a way to get back to the "Error Output" buffer opening with a
> simple message /while/ having :session being enabled?
> thank you,
>   James P.
> References
> [1] "Currently the only action Babel takes with STDERR is to display it in a
>     pop-up buffer when code block evaluation fails" (Eric Schulte in 2012, at
> https://lists.gnu.org/archive/html/emacs-orgmode/2012-03/msg00057.html).
> [2] « what will you save as your lasting record of what happened?
>   [...[ As a beginning R user, it's OK to consider your environment
>   [...]  "real."  However, in the long run, you'll be much better off
>   if you consider your R scripts as "real." » (p. 111, Wickham, H. "R
>   for data science : import, tidy, transform, visualize, and model
>   data" O'Reilly Media, 2016).  To facilitate this, I have disabled
>   'save workspace' permanently:
>   : q <- function (save = "no", status = 0, runLast = TRUE)
>   : .Internal(quit(save, status, runLast))
> [3] «When I look at Org and think of "session-based" blocks, I see a
>     potential big benefit in having multiple source-blocks throughout
>     my document share the same session»
> (https://lists.gnu.org/archive/html/emacs-orgmode/2011-06/msg00654.html,
>     the only good hit for a search for "session Org-Babel Error Output" at
>     https://lists.gnu.org/archive/html/emacs-orgmode/ as of
>     [2021-08-15 Sun]).
> -- 
> James E. Powell, MS
> Pronouns: he/him/his
> Applied Physics PhD Candidate
> Department of Physics
> Portland State University
> Home page: http://web.pdx.edu/~powellj
> Office: SRTC 409B Phone: +1-503-725-8515

  reply	other threads:[~2021-08-16 18:26 UTC|newest]

Thread overview: 7+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-08-15 23:41 Bug: :session results in unfriendly error reporting James Powell
2021-08-16 18:25 ` Berry, Charles via General discussions about Org-mode. [this message]
2021-08-17  5:02   ` Greg Minshall
2021-08-17  6:23     ` Tim Cross
2021-08-17  7:44       ` Greg Minshall
2021-09-27  8:42         ` Bastien
2021-09-27  9:52       ` Greg Minshall

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:

  List information: https://www.orgmode.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=FC24C431-9095-4E05-ACD3-FB72BB73852D@health.ucsd.edu \
    --to=emacs-orgmode@gnu.org \
    --cc=ccberry@health.ucsd.edu \
    --cc=powellj@pdx.edu \


* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
Code repositories for project(s) associated with this public inbox


This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).