From: Manish <mailtomanish.sharma@gmail.com>
To: Dan Davison <davison@stats.ox.ac.uk>
Cc: emacs-orgmode@gnu.org, "d.tchin" <d.tchin@voila.fr>
Subject: Re: org-babel-R and windows ?
Date: Wed, 13 Jan 2010 09:46:45 +0530 [thread overview]
Message-ID: <e7cdbe31001122016t30e2358ct4c6786413b0d4efe@mail.gmail.com> (raw)
In-Reply-To: <878wc3kyli.fsf@stats.ox.ac.uk>
On Tue, Jan 12, 2010 at 11:13 PM, Dan Davison wrote:
[snip: snipped (43 lines)]
>
> The org-babel default is to invoke R as an external shell command, and I
> think this is what is causing the problem. It requires that the emacs
> function shell-command can use the string "R" to invoke an R process,
> i.e. the R installation and the shell path must be such that this is the
> case.
>
> Seeing as you have ESS installed, how about using session-based
> evaluation? This means that org-babel uses an interactive R session
> running under the control of ESS. In general it is a better way to work
> with R in org-babel. It is described in the section "Session-based
> Evaluation" in
>
> http://orgmode.org/worg/org-contrib/babel/intro.php
>
> and also in the reference manual:
>
> http://orgmode.org/worg/org-contrib/babel/reference.php#header-argument-session
>
> basically you just set the :session header argument, e.g.
>
> #+srcname:trial
> #+begin_src R :session org-babel-R-session
> c(4,5,6,7,8,9)
> #+end_src
>
Thanks for the advice regarding using sessions. It works now. But I
have something interesting to report.
With following test org file, evaluation of R block fails to produce
desired results. If the lines with "require" are removed, the
evaluation works fine. R session buffer contents are pasted below as
well just in case they are of any help.
--8<---------------cut here---------------start------------->8---
* Test
Here's how to set it up.
(require 'org_babel_init)
(require 'org_babel_R)
(org_babel_load_library_of_babel)
#+srcname: strings
#+begin_src R :colnames t :session org-babel-R-strings
t(sort(table(tolower(scan("~/personal/test-org-babel.org", what="",
na.strings="|"))), decreasing=TRUE)[1:10])
#+end_src
#+results: strings
--8<---------------cut here---------------end--------------->8---
--8<---------------cut here---------------start------------->8---
R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(chmhelp = FALSE)
> options(STERM='iESS', editor='gnuclient.exe')
>
t(sort(table(tolower(scan("~/personal/test-org-babel.org", what="",
na.strings="|"))), decreasing=TRUE)[1:10])
write.table(.Last.value, file="d:/home/zms/tmp/org-babel-R1752nPK",
sep="\t", na="nil",row.names=FALSE, col.names=TRUE, quote=FALSE)
'org_babel_R_eoe'
> t(sort(table(tolower(scan("~/personal/test-org-babel.org", what="", na.strings="|"))), decreasing=TRUE)[1:10])
Read 27 items
strings #+begin_src #+end_src #+results: #+srcname:
[1,] 2 1 1 1 1
(org_babel_load_library_of_babel) (require * :colnames :session
[1,] 1 1 1 1 1
> write.table(.Last.value, file="d:/home/zms/tmp/org-babel-R1752nPK", sep="\t", na="nil",row.names=FALSE, col.names=TRUE, quote=FALSE)
> 'org_babel_R_eoe'
[1] "org_babel_R_eoe"
>
--8<---------------cut here---------------end--------------->8---
Thank you
--
Manish
next prev parent reply other threads:[~2010-01-13 4:17 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2010-01-12 13:24 org-babel-R and windows ? d.tchin
2010-01-12 14:56 ` [babel] " Giovanni Ridolfi
2010-01-12 17:05 ` Manish
2010-01-12 17:43 ` Dan Davison
2010-01-12 18:05 ` Eric Schulte
2010-01-13 4:16 ` Manish [this message]
2010-01-13 9:20 ` d.tchin
2010-01-13 19:39 ` Dan Davison
2010-01-14 8:37 ` Sébastien Vauban
2010-01-14 17:39 ` [babel] " Dan Davison
2010-01-14 19:39 ` Sébastien Vauban
2010-01-15 9:32 ` Stefan Vollmar
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