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>
James,
> 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.
HRH,
Chuck
[*] 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
>
>
>
next prev parent 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
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