From: Rainer M Krug <Rainer@krugs.de>
To: "Charles C. Berry" <ccberry@ucsd.edu>
Cc: Aaron Ecay <aaronecay@gmail.com>,
emacs-orgmode@gnu.org, Eric Schulte <schulte.eric@gmail.com>
Subject: Re: R code block produces only partial output
Date: Sat, 09 Aug 2014 10:54:29 +0200 [thread overview]
Message-ID: <m2bnrucabe.fsf@krugs.de> (raw)
In-Reply-To: <alpine.OSX.2.00.1408071111430.348@charles-berrys-macbook.local> (Charles C. Berry's message of "Thu, 7 Aug 2014 11:42:29 -0700")
[-- Attachment #1: Type: text/plain, Size: 3227 bytes --]
"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Thu, 7 Aug 2014, Aaron Ecay wrote:
>
>> Hi Chuck,
>>
>> Thanks for your feedback.
>>
>> 2014ko abuztuak 7an, "Charles C. Berry"-ek idatzi zuen:
>>> Hi Aaron,
>>>
>>> I like what you are trying to do, but ...
>>>
>>> 1) The change has at least one bug: Remote sessions are broken by this
>>> change.
>>>
>>> 2) The behavior of :results output is modified in ways that might not be
>>> desired. i.e. warnings and errors will not show up in the output.
>>>
>
> [snip issue 1 discussion]
>
>>>
>>> Issue 2) ===========
>>>
>>> ECM:
>>>
>>> #+NAME: aa
>>> #+BEGIN_SRC R :session R2 :results output
>>> warning("this is a warning")
>>> 1+1
>>> #+END_SRC
>>>
>>> #+RESULTS: aa
>>> : [1] 2
>>>
>>> For some purposes having the warnings in the #+RESULTS: block is helpful.
>>>
>>> And when revising code, having the errors in the #+RESULTS helps -
>>> especially if I have to put aside work in progress.
>>
>> Hmm. Certainly, the previous behavior should be retained for now. In
>> the longer term, I’d like to see a system whereby R errors trigger elisp
>> errors. This is so that the execution of a whole document (subtree,
>> etc.) will be halted by the first error, rather than continuing what may
>> be a long series of commands that will not give valid output. What do
>> you think?
>>
>
> I need a while to sort through this. stop(), warning(), and message()
> will print to the session but not show up in what capture.output
> retains.
>
> sink() has the ability to capture those things, but there is added
> baggage.
>
> I fear some study of ?conditions is needed. My knowledge of condition
> handling in R is scant.
>
> As for stopping on error, I think that anything that changes current
> behavior at this late date ought to be configurable.
>
> FWIW, when I export documents, I sometimes get innocuous errors that I
> am happy did not stop the run in its tracks - like formatting one
> table fails with an error but all else went through. And sometimes I
> wish it had stopped.
I agree here with Charles. An example where R errors do *not* trigger do
not abort export are graphs: the graph generation, when using R, is
wrapped in a tryCatch() block and shows the error in the exported
document as well as in the R session but does not abort.
A case where it is very useful to continue export is when creating
lecture notes or slides to demonstrate errors.
If there is the wish for R errors to trigger elisp errors, a header
argument would be needed to specify if errors and warnings in R should
trigger errors in elisp or if they should be ignored and the error
message displayed and the export should be continued.
Cheers,
Rainer
>
> Best,
>
> Chuck
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]
next prev parent reply other threads:[~2014-08-09 8:54 UTC|newest]
Thread overview: 41+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-08-04 11:18 R code block produces only partial output Andreas Kiermeier
2014-08-04 11:53 ` Eric Schulte
2014-08-04 12:23 ` Andreas Kiermeier
2014-08-04 13:10 ` Eric Schulte
2014-08-05 0:46 ` Andreas Kiermeier
2014-08-05 4:00 ` John Hendy
2014-08-05 4:31 ` Andreas Kiermeier
2014-08-05 18:05 ` Charles Berry
2014-08-05 19:02 ` Eric Schulte
2014-08-05 19:11 ` John Hendy
2014-08-05 19:57 ` Nick Dokos
2014-08-05 20:10 ` Nick Dokos
2014-08-05 22:21 ` Charles C. Berry
2014-08-06 3:32 ` Aaron Ecay
2014-08-06 11:30 ` Eric Schulte
2014-08-07 6:00 ` Aaron Ecay
2014-08-07 17:42 ` Charles C. Berry
2014-08-07 18:06 ` Aaron Ecay
2014-08-07 18:42 ` Charles C. Berry
2014-08-07 19:06 ` Thomas S. Dye
2014-08-09 8:54 ` Rainer M Krug [this message]
2014-08-16 5:05 ` Aaron Ecay
2014-08-16 18:50 ` Charles C. Berry
2014-08-16 20:58 ` Aaron Ecay
2014-08-17 6:03 ` Achim Gratz
2014-08-19 0:13 ` Aaron Ecay
2014-08-19 5:36 ` Achim Gratz
2014-08-23 8:32 ` Aaron Ecay
2014-08-23 9:24 ` Andreas Kiermeier
2014-08-23 17:10 ` Aaron Ecay
2014-08-23 18:35 ` Thomas S. Dye
2014-08-23 19:37 ` Ista Zahn
2014-08-24 0:10 ` Charles C. Berry
2014-08-28 5:24 ` Aaron Ecay
2014-09-01 5:00 ` Aaron Ecay
2014-09-01 16:08 ` Charles C. Berry
2014-08-09 8:48 ` Rainer M Krug
2014-08-06 1:11 ` Andreas Kiermeier
2014-08-06 2:21 ` Charles C. Berry
2014-08-06 3:24 ` Aaron Ecay
2014-08-06 15:59 ` Charles C. Berry
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:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
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=m2bnrucabe.fsf@krugs.de \
--to=rainer@krugs.de \
--cc=aaronecay@gmail.com \
--cc=ccberry@ucsd.edu \
--cc=emacs-orgmode@gnu.org \
--cc=schulte.eric@gmail.com \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* 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
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
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).