Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-18 Thread Eric Schulte
Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 17an, Eric Schulte-ek idatzi zuen: Oh!, thanks for catching this, I just pushed up a fix. This is no longer a (complete) fix for the original problem, though. (A large part of) the slowdown comes from reading the results from a temp

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-18 Thread Eric Schulte
Eric Schulte schulte.e...@gmail.com writes: Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 17an, Eric Schulte-ek idatzi zuen: Oh!, thanks for catching this, I just pushed up a fix. This is no longer a (complete) fix for the original problem, though. (A large part of) the slowdown

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-17 Thread Eric Schulte
Achim Gratz strom...@nexgo.de writes: Andreas Leha writes: I would suggest simply none for the new really-silent. Yes please, especially since I tried :results none two days ago to achieve that effect and wondered why it wouldn't work. :-) Great, since none seems like the obvious choice I

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-17 Thread Aaron Ecay
2012ko azaroak 16an, Eric Schulte-ek idatzi zuen: The attached patch adds a really-silent results header argument. To see the impact compare the running time of the following two code blocks. Unfortunately, the attached patch doesn’t work correctly. This can be seen by replacing the “seq”

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-17 Thread Eric Schulte
Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 16an, Eric Schulte-ek idatzi zuen: The attached patch adds a really-silent results header argument. To see the impact compare the running time of the following two code blocks. Unfortunately, the attached patch doesn’t work

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-17 Thread Aaron Ecay
2012ko azaroak 17an, Eric Schulte-ek idatzi zuen: Oh!, thanks for catching this, I just pushed up a fix. This is no longer a (complete) fix for the original problem, though. (A large part of) the slowdown comes from reading the results from a temp file and transforming them into an elispy

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-16 Thread Eric Schulte
Andreas Leha andreas.l...@med.uni-goettingen.de writes: t...@tsdye.com (Thomas S. Dye) writes: Aloha Aaron, Welcome to Org-mode. Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 13an, John Hendy-ek idatzi zuen: [...] Crazy. I really wondered if it had something to do with trying

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-16 Thread Andreas Leha
Hi Eric, Eric Schulte schulte.e...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: t...@tsdye.com (Thomas S. Dye) writes: Aloha Aaron, Welcome to Org-mode. Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 13an, John Hendy-ek idatzi zuen: [...] Crazy.

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-16 Thread John Hendy
On Fri, Nov 16, 2012 at 11:47 AM, Andreas Leha andreas.l...@med.uni-goettingen.de wrote: Hi Eric, Eric Schulte schulte.e...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: t...@tsdye.com (Thomas S. Dye) writes: Aloha Aaron, Welcome to Org-mode.

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-16 Thread Achim Gratz
Andreas Leha writes: I would suggest simply none for the new really-silent. Yes please, especially since I tried :results none two days ago to achieve that effect and wondered why it wouldn't work. :-) Regards, Achim. -- +[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+ SD

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-14 Thread Thomas S. Dye
Aloha Aaron, Welcome to Org-mode. Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 13an, John Hendy-ek idatzi zuen: [...] 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? “:results silent” just

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-14 Thread Andreas Leha
t...@tsdye.com (Thomas S. Dye) writes: Aloha Aaron, Welcome to Org-mode. Aaron Ecay aarone...@gmail.com writes: 2012ko azaroak 13an, John Hendy-ek idatzi zuen: [...] Crazy. I really wondered if it had something to do with trying to spit out the results into the minibuffer. Why is that

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-13 Thread Aaron Ecay
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

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-13 Thread John Hendy
On Tue, Nov 13, 2012 at 9:27 PM, Aaron Ecay aarone...@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

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-13 Thread Aaron Ecay
2012ko azaroak 13an, John Hendy-ek idatzi zuen: [...] 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? “:results silent” just means “silent except for the minibuffer”; IDK why. Are you sure it's only on

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-01 Thread John Hendy
On Wed, Oct 31, 2012 at 5:53 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Wed, Oct 31, 2012 at 3:12 PM, cbe...@tajo.ucsd.edu wrote: John Hendy jw.he...@gmail.com writes: On Wed, Oct 31, 2012 at 11:41 AM, span dir=ltrmailto:

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-01 Thread Nick Dokos
John Hendy jw.he...@gmail.com wrote: o run top (or whatever equivalent is available on your OS) and see   whether the CPU (or one of the CPUs) gets pegged at 100% utilization   and stays there. If yes, that's an indication of an infinite loop   somewhere. - quit any other

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-01 Thread John Hendy
On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: o run top (or whatever equivalent is available on your OS) and see whether the CPU (or one of the CPUs) gets pegged at 100% utilization and stays there. If yes,

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-01 Thread John Hendy
On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: o run top (or whatever equivalent is available on your OS) and see whether the CPU (or one of the CPUs) gets pegged at 100% utilization and stays there. If yes,

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-11-01 Thread Nick Dokos
John Hendy jw.he...@gmail.com wrote: On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote:     o run top (or whatever equivalent is available on your OS) and see       whether the CPU (or one of the CPUs) gets pegged

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread cberry
John Hendy jw.he...@gmail.com writes: I edited the subject to be more concise/clear.I let orgmode chug away on reading in some ~10-30mb csv files for nearly 30min. [rest deleted] You need an ECM. I cannot reproduce your issue. This runs in the same amount of time, whether I execute the

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread John Hendy
On Wed, Oct 31, 2012 at 11:41 AM, cbe...@tajo.ucsd.edu wrote: John Hendy jw.he...@gmail.com writes: I edited the subject to be more concise/clear.I let orgmode chug away on reading in some ~10-30mb csv files for nearly 30min. [rest deleted] You need an ECM. I did my best to provide

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread cberry
John Hendy jw.he...@gmail.com writes: On Wed, Oct 31, 2012 at 11:41 AM, span dir=ltrmailto:cbe...@tajo.ucsd.edu/span wrote: John Hendy mailto:jw.he...@gmail.com writes: I edited the subject to be more concise/clear.I let orgmode chug away on reading in some ~10-30mb csv files for nearly

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread John Hendy
On Wed, Oct 31, 2012 at 3:12 PM, cbe...@tajo.ucsd.edu wrote: John Hendy jw.he...@gmail.com writes: On Wed, Oct 31, 2012 at 11:41 AM, span dir=ltrmailto: cbe...@tajo.ucsd.edu/span wrote: John Hendy mailto:jw.he...@gmail.com writes: I edited the subject to be more concise/clear.I let

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread Thomas S. Dye
Hi John, Have you tried wrapping your R read in system.time()? If you are right about :results silent eating up lots of time, then this should fix the problem. system.time yields just a bit of output, so shouldn't slow things down if writing out the data is indeed the problem as you suspect.

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread Nick Dokos
John Hendy jw.he...@gmail.com wrote: On Wed, Oct 31, 2012 at 3:12 PM, cbe...@tajo.ucsd.edu wrote: John Hendy jw.he...@gmail.com writes: On Wed, Oct 31, 2012 at 11:41 AM,  span dir=ltrmailto:cbe...@tajo.ucsd.edu/span wrote: John Hendy mailto:jw.he...@gmail.com writes:

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread Nick Dokos
Thomas S. Dye t...@tsdye.com wrote: Hi John, Have you tried wrapping your R read in system.time()? If you are right about :results silent eating up lots of time, then this should fix the problem. system.time yields just a bit of output, so shouldn't slow things down if writing out the