From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Hendy Subject: Re: Bug? R: Org babel block execution *drastically* slower than in ESS session directly Date: Wed, 31 Oct 2012 15:23:53 -0500 Message-ID: References: <874nlappb1.fsf@tajo.ucsd.edu> <878vam1jvh.fsf@tajo.ucsd.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=f46d04451a156659ad04cd60aeb0 Return-path: Received: from eggs.gnu.org ([208.118.235.92]:44694) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1TTepP-000631-T9 for emacs-orgmode@gnu.org; Wed, 31 Oct 2012 16:23:57 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1TTepO-0002dm-Ev for emacs-orgmode@gnu.org; Wed, 31 Oct 2012 16:23:55 -0400 Received: from mail-we0-f169.google.com ([74.125.82.169]:45562) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1TTepO-0002dW-4i for emacs-orgmode@gnu.org; Wed, 31 Oct 2012 16:23:54 -0400 Received: by mail-we0-f169.google.com with SMTP id u3so989406wey.0 for ; Wed, 31 Oct 2012 13:23:53 -0700 (PDT) In-Reply-To: <878vam1jvh.fsf@tajo.ucsd.edu> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: cberry@tajo.ucsd.edu Cc: emacs-orgmode@gnu.org --f46d04451a156659ad04cd60aeb0 Content-Type: text/plain; charset=UTF-8 On Wed, Oct 31, 2012 at 3:12 PM, wrote: > John Hendy writes: > > > On Wed, Oct 31, 2012 at 11:41 AM, cberry@tajo.ucsd.edu> wrote: > > John Hendy 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 one, other than the file, which > I offered to provide if others requested that I upload it somewhere. Since > you have done so, so have I: > > - https://docs.google.com/open?id=0BzQupOSnvw08WHdabHh5VVczRGM > > > Let me know if that doesn't work. I put it on Google docs and > sometimes have issues with the sharing settings... > > Not an ECM in my book, but ... > > What else would you like? I provided: - the config - the data - how to [attempt to] reproduce - the org-mode text > On my 4 year old MacBook: > > ,---- > | > | #+PROPERTY: session *R* > | > | #+name: bigcsv > | #+begin_src R > | bigcsv <- Sys.glob("~/Downloads/*.csv") > | #+end_src > | > | #+RESULTS: bigcsv > | : /Users/cberry/Downloads/test-file.csv > | > | #+name: readbig > | #+begin_src R :results output > | system.time( > | tmp <- read.csv(bigcsv) > | ) > | > | #+end_src > | > | #+RESULTS: readbig > | : user system elapsed > | : 5.679 0.306 6.002 > | > `---- > > About the same as running from ESS. > > Not sure what to say. Looking for ways to troubleshoot or confirm. Since you can't confirm, any suggestions on where I should look for my issue? I can't explain it! All I know is that org chugs and chugs and the direct execution in ESS session is lightning fast. FYI, > > > dim(tmp) > [1] 964805 9 > > > Was that just to show the size, or is something wrong with my file? > Chuck > > Thanks for attempting to replicate! John > [ rest deleted ] > > > > --f46d04451a156659ad04cd60aeb0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On Wed, Oct 31, 2012 at 3:12 PM, <cberry@tajo.ucsd.edu> = wrote:
John Hendy <jw.hendy@gmail.com= > writes:

> On Wed, Oct 31, 2012 at 11:41 AM, =C2=A0<span dir=3D"ltr"= ><mailto:cberry@tajo.ucsd.edu= ></span> wrote:
> John Hendy <mailto:jw.hendy@g= mail.com> writes:
>
>> I edited the subject to be more concise/clear.I let orgmode chug a= way
>> on reading in some ~10-30mb csv files for nearly 30min.
>
> [rest deleted]
>
> You need an ECM.I did my best to provide one, other than the file, whi= ch I offered to provide if others requested that I upload it somewhere. Sin= ce you have done so, so have I:
> -=C2=A0https://docs.google.com/open?id=3D0BzQupOSnvw= 08WHdabHh5VVczRGM

> Let me know if that doesn&#39;t work. I put it on Google docs and = sometimes have issues with the sharing settings...

Not an ECM in my book, but ...


What else would you like? I provided:<= /div>
- the config
- the data
- how to [attempt to]= reproduce
- the org-mode text

=C2=A0
On my 4 year old MacBook:

,----
|
| #+PROPERTY: session *R*
|
| #+name: bigcsv
| #+begin_src R
| bigcsv <- Sys.glob("~/Downloads/*.csv")
| #+end_src
|
| #+RESULTS: bigcsv
| : /Users/cberry/Downloads/test-file.csv
|
| #+name: readbig
| #+begin_src R :results output
| =C2=A0 system.time(
| =C2=A0 =C2=A0 tmp <- read.csv(bigcsv)
| =C2=A0 =C2=A0 )
|
| #+end_src
|
| #+RESULTS: readbig
| : =C2=A0 =C2=A0user =C2=A0system elapsed
| : =C2=A0 5.679 =C2=A0 0.306 =C2=A0 6.002
|
`----

About the same as running from ESS.


Not sure what to say. Looking for ways= to troubleshoot or confirm. Since you can't confirm, any suggestions o= n where I should look for my issue? I can't explain it! All I know is t= hat org chugs and chugs and the direct execution in ESS session is lightnin= g fast.



FYI,

> dim(tmp)
[1] 964805 =C2=A0 =C2=A0 =C2=A09



Was that just to show the size, or is = something wrong with my file?
=C2=A0
Chuck



Thanks for attempting t= o replicate!
John
=C2=A0
[ rest deleted ]




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