From: John Hendy <jw.hendy@gmail.com>
To: nicholas.dokos@hp.com, John Hendy <jw.hendy@gmail.com>,
emacs-orgmode@gnu.org, cberry@tajo.ucsd.edu
Subject: Re: Bug? R: Org babel block execution *drastically* slower than in ESS session directly
Date: Tue, 13 Nov 2012 22:52:14 -0600 [thread overview]
Message-ID: <CA+M2ft8W2euDc+cMZsjRwHEMCHWP7Waa1QQvjDz+YuqoQqKyuw@mail.gmail.com> (raw)
In-Reply-To: <87d2zgrhhr.fsf@gmail.com>
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On Tue, Nov 13, 2012 at 9:27 PM, Aaron Ecay <aaronecay@gmail.com> wrote:
> I just ran into this problem. It is caused by the calls to
> ‘org-babel-import-elisp-from-file’ on lines 310 and 343 of ‘ob-R.el’
> (for non-session and session code blocks respectively). I determined
> this by setting ‘debug-on-quit’ to t in Emacs, then hitting C-g when cpu
> usage spiked, and examining the backtrace.
>
>
Yes! I'm not crazy! I'm not very familiar with the debug options in emacs
and had a heck of a time setting it up right the last time. Thanks so much
for checking this out.
> It seems like Emacs tries to read in the last value of the R command, to
> print it in the minibuffer. It gets bogged down doing so. As a
> stopgap, putting NULL as the last line of the source block fixes the
> problem (the value “returned” by the block is just NULL). I believe
> setting “:results output” (as opposed to “value”) would also make the
> bug disappear, since the output will be very small. This is likely what
> made cberry’s test differ from John’s.
>
>
Crazy. I really wondered if it had something to do with trying to spit out
the results into the minibuffer. Why is that behavior included?
> I’m not sure what the right strategy would be for a fix. Two ideas
> would be:
> 1) adding a sanity check to o-b-import-elisp-from-file, which asks the
> user whether to really import very large files (or just ignores such
> files)
>
Are you sure it's only on file import? I was generating some large output
when I first experienced this. It was only to avoid running that code that
I wrote it to file once and decided to just read it once per session
afterward (thinking reading would be faster than generating the input on
demand). I was generating a grid of interactions with something akin to:
#+begin_src R
dat <- expand.grid(var1 = seq(0, 40000, by = 200), var2 = seq(0, 40000, by
= 200))
#+end_src
I can check this tomorrow if you'd like, but I remember it lagging as it
tried to print all of that into the minibuffer.
> 2) adding a new :results handling header arg “really-silent” (probably
> with a better name...) that discards the result entirely, not even
> printing it to the minibuffer.
>
>
I like this, in addition to changing the minibuffer output as it is. It
would be fantastic to have the minibuffer say more than it does already
(something akin to "Block execution complete"). I have to change to the R
buffer to see if there were any errors. I like how the LaTeX exporter tells
you if PDF export failed. It'd be nice to see something like (in addition
to no results in the minibuffer), "Block execution complete but with
errors."
Thanks again, and I'm glad you were able to track this down.
John
> --
> Aaron Ecay
>
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next prev parent reply other threads:[~2012-11-14 4:52 UTC|newest]
Thread overview: 217+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-10-31 6:12 Bug? R: Org babel block execution *drastically* slower than in ESS session directly John Hendy
2012-10-31 16:41 ` cberry
2012-10-31 17:18 ` John Hendy
2012-10-31 20:12 ` cberry
2012-10-31 20:23 ` John Hendy
2012-10-31 20:56 ` Thomas S. Dye
2012-10-31 23:00 ` Nick Dokos
2012-10-31 22:53 ` Nick Dokos
2012-11-01 14:53 ` John Hendy
2012-11-01 15:38 ` Nick Dokos
2012-11-01 18:17 ` John Hendy
2012-11-01 18:18 ` John Hendy
2012-11-01 18:48 ` Nick Dokos
2012-11-14 3:27 ` Aaron Ecay
2012-11-14 4:52 ` John Hendy [this message]
2012-11-14 6:32 ` Aaron Ecay
2012-11-14 8:28 ` Thomas S. Dye
2012-11-14 8:35 ` Andreas Leha
2012-11-16 15:45 ` Eric Schulte
2012-11-16 17:47 ` Andreas Leha
2012-11-16 19:00 ` John Hendy
2012-11-16 20:25 ` Achim Gratz
2012-11-17 17:12 ` Eric Schulte
2012-11-18 0:41 ` Aaron Ecay
2012-11-18 0:57 ` Eric Schulte
2012-11-18 1:41 ` Aaron Ecay
2012-11-19 1:18 ` Eric Schulte
2012-11-19 5:11 ` Eric Schulte
-- strict thread matches above, loose matches on Subject: below --
2013-03-19 21:40 python sessions Gary Oberbrunner
2013-03-20 0:04 ` John Hendy
2013-03-20 3:07 ` Nick Dokos
2013-03-20 6:44 ` Andreas Röhler
2013-03-20 12:54 ` Ista Zahn
2013-03-20 14:08 ` Nick Dokos
2013-03-20 14:28 ` Gary Oberbrunner
2013-03-20 17:21 ` Andreas Röhler
2013-03-20 7:08 ` Andreas Röhler
2013-03-20 15:38 ` John Hendy
2013-03-20 15:42 ` John Hendy
2013-03-20 16:06 ` Nick Dokos
[not found] ` <CAFChFygsUeBejEY6m2bSU0C5cjLYz0nUADH=s+BYxajfZ2sKKQ@mail.gmail.com>
2013-03-20 16:12 ` Fwd: " Gary Oberbrunner
2013-03-20 17:08 ` Andreas Röhler
2013-03-20 17:25 ` Nick Dokos
2013-03-20 17:54 ` John Hendy
2013-03-20 18:15 ` Nick Dokos
2013-03-20 18:32 ` Ista Zahn
2013-03-20 18:39 ` Nick Dokos
2013-03-20 18:43 ` Andreas Röhler
2013-03-20 19:42 ` Ista Zahn
2013-03-20 19:53 ` Andreas Röhler
2013-03-20 20:12 ` Ista Zahn
2013-03-20 20:25 ` Gary Oberbrunner
2013-03-20 22:06 ` Ista Zahn
2013-03-20 18:42 ` Andreas Röhler
2013-03-20 19:01 ` Andreas Röhler
[not found] ` <CAFChFygPrhuHHyMo2Vk2_OdksWVB=oACA7jnOXN+itUNqh-nqw@mail.gmail.com>
[not found] ` <CA+M2ft9bO7DU61vVeYrhduVvkg1V6PMuiyvsOy5tNWuXcSUEpw@mail.gmail.com>
[not found] ` <CAFChFyhbeXE4HNLKA6Ubii+MtQwD7=4khAypa+--coZrQiJekA@mail.gmail.com>
2013-03-21 1:22 ` Gary Oberbrunner
2013-03-21 1:54 ` John Hendy
2013-03-21 1:56 ` Gary Oberbrunner
2013-03-21 7:42 ` Andreas Röhler
2013-03-21 7:43 ` Bastien
2013-03-21 8:13 ` Andreas Röhler
2013-03-23 22:07 ` Eric Schulte
2013-03-24 1:29 ` John Hendy
2013-03-24 22:59 ` Eric Schulte
2013-03-25 2:38 ` Nick Dokos
2013-03-25 2:59 ` John Hendy
2013-03-25 6:34 ` Andreas Röhler
2013-03-25 15:40 ` Eric Schulte
2013-03-25 15:55 ` John Hendy
2013-03-25 16:07 ` Eric Schulte
2013-03-25 16:41 ` Nick Dokos
2013-03-25 16:01 ` Ista Zahn
2013-03-25 16:23 ` John Hendy
2013-03-25 16:43 ` Eric Schulte
2013-03-25 17:27 ` Andreas Röhler
2013-03-25 17:41 ` John Hendy
2013-03-25 18:16 ` Ista Zahn
2013-03-25 19:30 ` Ivan Andrus
2013-03-24 7:47 ` Andreas Röhler
2013-03-24 14:47 ` John Hendy
2013-03-24 15:30 ` Andreas Röhler
2013-03-24 16:58 ` Nick Dokos
2013-03-24 16:59 ` John Hendy
2013-03-24 18:41 ` Nick Dokos
2013-03-25 20:46 ` Andreas Röhler
2013-03-25 21:37 ` Eric Schulte
2013-03-26 6:29 ` Andreas Röhler
2013-03-26 12:32 ` Eric Schulte
2013-03-26 21:41 ` Gary Oberbrunner
2013-03-26 21:47 ` John Hendy
2013-03-27 6:19 ` Andreas Röhler
2013-03-30 7:19 ` Andreas Röhler
2012-08-26 20:11 Alternate format for datetree c b
2012-08-27 1:16 ` John Hendy
2012-08-27 4:04 ` Nick Dokos
2012-08-27 6:08 ` John Hendy
2012-08-28 8:49 ` Ian Barton
2012-08-28 12:49 ` Nick Dokos
2012-08-28 12:50 ` Nick Dokos
2012-08-29 7:49 ` Ian Barton
[not found] ` <lists@manor-farm.org>
2012-08-29 14:17 ` Nick Dokos
2012-08-29 14:25 ` John Hendy
2012-08-29 20:01 ` Ian Barton
2012-09-06 7:46 ` Ian Barton
2012-09-06 5:42 ` c b
2012-09-06 6:26 ` Nick Dokos
2012-09-06 7:00 ` Jambunathan K
2012-09-06 15:33 ` John Hendy
2012-09-06 16:08 ` Jonathan Leech-Pepin
2011-11-02 2:22 Pass LaTeX exporter option prior to \documentclass John Hendy
2011-11-02 2:43 ` suvayu ali
2011-11-02 10:30 ` suvayu ali
2011-11-03 17:48 ` John Hendy
2011-11-03 17:55 ` suvayu ali
2011-11-03 18:07 ` John Hendy
2011-11-04 17:29 ` Nick Dokos
2011-11-04 19:29 ` suvayu ali
2011-10-19 14:54 Prompt for time when clocking in? Nathan Neff
2011-10-19 15:12 ` John Hendy
2011-10-19 15:35 ` Nick Dokos
2011-10-20 16:15 ` Nathan Neff
2011-10-20 17:09 ` Nick Dokos
2011-10-20 17:44 ` Nathan Neff
2011-10-19 16:37 ` Bernt Hansen
2011-08-05 22:15 Handling errors in command line exporting of agenda? John Hendy
2011-08-05 23:34 ` suvayu ali
2011-08-05 23:35 ` suvayu ali
2011-08-08 18:12 ` John Hendy
2011-08-08 18:28 ` suvayu ali
2011-08-08 18:53 ` John Hendy
2011-08-08 18:59 ` suvayu ali
2011-08-08 19:48 ` John Hendy
2011-08-08 20:22 ` suvayu ali
2011-08-08 20:31 ` John Hendy
2011-08-08 20:33 ` Nick Dokos
2011-08-08 20:37 ` Nick Dokos
2011-08-08 20:54 ` John Hendy
2011-08-08 21:09 ` Nick Dokos
2011-08-08 21:27 ` John Hendy
2011-08-08 21:30 ` suvayu ali
2011-08-08 22:17 ` Nick Dokos
2011-08-08 21:46 ` suvayu ali
2011-06-15 10:29 BUG: Newest org-mode interferes with desktop save Rainer M Krug
2011-06-15 16:49 ` Eric Schulte
2011-06-15 17:35 ` Nick Dokos
2011-06-15 18:23 ` Rainer M Krug
2011-06-15 18:21 ` Rainer M Krug
2011-06-15 18:31 ` Eric Schulte
2011-06-15 18:59 ` Rainer M Krug
2011-06-15 22:40 ` Nick Dokos
2011-06-16 7:15 ` Rainer M Krug
2011-06-16 7:29 ` Jambunathan K
2011-06-16 8:22 ` Rainer M Krug
2011-05-24 15:54 Passing font size to exported LaTeX table John Hendy
2011-05-24 16:44 ` Sebastien Vauban
2011-05-24 18:57 ` John Hendy
2011-05-24 19:25 ` Nick Dokos
2011-05-24 19:31 ` John Hendy
2011-05-24 19:58 ` Thomas S. Dye
2011-05-24 20:42 ` Nick Dokos
2011-05-24 21:12 ` Nick Dokos
2011-05-24 21:19 ` Nick Dokos
2011-05-25 7:22 ` Thomas S. Dye
2011-05-27 0:58 ` suvayu ali
2011-05-27 6:46 ` Thomas S. Dye
2011-05-27 7:07 ` suvayu ali
2011-05-27 16:17 ` Thomas S. Dye
2011-05-27 16:50 ` Suvayu Ali
2011-05-27 17:37 ` Thomas S. Dye
2011-05-27 18:30 ` Suvayu Ali
2011-05-27 21:25 ` Thomas S. Dye
2011-05-28 7:17 ` Sebastien Vauban
2011-05-28 10:14 ` Suvayu Ali
2011-05-28 15:21 ` Nick Dokos
2011-05-28 18:10 ` Suvayu Ali
2011-06-01 18:50 ` Nick Dokos
2011-06-01 19:08 ` Suvayu Ali
2011-06-10 22:31 ` Suvayu Ali
2011-06-13 1:38 ` suvayu ali
2011-06-13 1:52 ` Nick Dokos
2011-06-13 2:40 ` Suvayu Ali
2011-06-13 3:29 ` Nick Dokos
2011-06-13 3:45 ` Thomas S. Dye
2011-06-13 4:27 ` Nick Dokos
2011-06-13 4:56 ` Suvayu Ali
2011-06-13 5:29 ` Nick Dokos
2011-06-13 6:42 ` Suvayu Ali
2011-05-24 20:06 ` Nick Dokos
2011-05-24 19:42 ` Sebastien Vauban
2010-08-21 19:30 Gnuplot unevenly spaced non-numeric data plot? John Hendy
2010-08-21 20:35 ` Eric S Fraga
2010-08-21 20:41 ` Nick Dokos
2010-08-21 21:11 ` John Hendy
2010-08-21 22:41 ` John Hendy
2010-08-21 23:17 ` Nick Dokos
2010-08-23 14:22 ` John Hendy
2010-08-23 15:16 ` Nick Dokos
[not found] ` <AANLkTi=WTLBL1Giq0GTrjCo-A1s=iP4u1Qxn57cH-xnB@mail.gmail.com>
[not found] ` <AANLkTimSVm=-2o39CQ9wSMT276Dee4Tuj9jLKJH-c+cd@mail.gmail.com>
2010-08-24 2:44 ` [For Worg?] " John Hendy
2010-08-24 5:25 ` suvayu ali
2010-08-24 5:56 ` Nick Dokos
2010-08-25 0:32 ` Eric Schulte
2010-08-25 1:06 ` John Hendy
2010-08-25 1:35 ` Eric Schulte
2010-08-25 18:38 ` John Hendy
2010-08-25 18:52 ` Eric Schulte
[not found] ` <jw.hendy@gmail.com>
2012-03-12 21:13 ` Beamer specific setupfile? John Hendy
2012-03-12 21:48 ` Nick Dokos
2012-03-12 22:09 ` John Hendy
2012-03-12 22:30 ` Nick Dokos
2012-03-12 22:44 ` Nick Dokos
2012-03-13 5:02 ` John Hendy
2012-03-13 5:46 ` Nick Dokos
2012-04-25 8:16 ` Eric Fraga
2012-04-25 8:59 ` Eric Fraga
2012-03-12 23:01 ` Nick Dokos
2012-03-12 21:51 ` Nick Dokos
2012-03-12 22:05 ` Nick Dokos
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