[babel] Problems sourcing R code

[babel] Problems sourcing R code

[Weiss, Bernd]

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Dear all,

I am having trouble sourcing R code from within an org-file via
org-babel, i.e. I cant' replicate the most simple examples

#+begin_src R :results value
matrix(rnorm(6), nrow=2)
#+end_src

That's the error message I get whenever I type in C-c C-c:

"executing R source code block...
Die Syntax für den Dateinamen, Verzeichnisnamen oder die
Datenträgerbezeichnung ist falsch.
No result returned by source block"


However, I am not having any problems with the shell-example

#+begin_src sh
  echo "This file takes up `du -h org-babel.org |sed 's/\([0-9k]*\)[
]*org-babel.org/\1/'`"
#+end_src

Org-R works as expected, i.e. I can source the following example without
any problems

#+RR: x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
#+R: title:"continuous-data" output-to-buffer:t


My setup:
- - MS-Win Vista
- - GNU Emacs 23.1.1 (i386-mingw-nt6.0.6002) of 2009-07-30 on SOFT-MJASON
- - Org-mode: Org-mode version 6.32trans (release_6.32b.127.g471c2);
- - ESS: v5.5
- - my .emacs/_emacs-File: <http://metaanalyse.de/tmp/_emacs>


Thanks in advance for your help

Bernd
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Re: [babel] Problems sourcing R code

[Dan Davison]

"Weiss, Bernd " <bernd.weiss@uni-koeln.de> writes:

> Dear all,
>
> I am having trouble sourcing R code from within an org-file via
> org-babel, i.e. I cant' replicate the most simple examples
>
> #+begin_src R :results value
> matrix(rnorm(6), nrow=2)
> #+end_src
>
> That's the error message I get whenever I type in C-c C-c:
>
> "executing R source code block...
> Die Syntax für den Dateinamen, Verzeichnisnamen oder die
> Datenträgerbezeichnung ist falsch.
> No result returned by source block"

Dear Bernd,

This is a problem relating to running R as an external shell process
under Windows. For the time-being, please use the :session header
argument to specify that evaluation is to take place in a persistent
emacs R session. Alternatively, you could use the following
configuration code to force R blocks to always use the specified session
(you can change the session name of course):

(setq org-babel-default-header-args:R '((:session . "*my-R-session*")))

Session-based evaluation is described briefly at

http://orgmode.org/worg/org-contrib/babel/org-babel.php#basic-functionality

Thanks for the report. We will investigate the issues with running R as
an external process under Windows.

Best wishes,

Dan

>
>
> However, I am not having any problems with the shell-example
>
> #+begin_src sh
>   echo "This file takes up `du -h org-babel.org |sed 's/\([0-9k]*\)[
> ]*org-babel.org/\1/'`"
> #+end_src
>
> Org-R works as expected, i.e. I can source the following example without
> any problems
>
> #+RR: x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
> #+R: title:"continuous-data" output-to-buffer:t
>
>
> My setup:
> - MS-Win Vista
> - GNU Emacs 23.1.1 (i386-mingw-nt6.0.6002) of 2009-07-30 on SOFT-MJASON
> - Org-mode: Org-mode version 6.32trans (release_6.32b.127.g471c2);
> - ESS: v5.5
> - my .emacs/_emacs-File: <http://metaanalyse.de/tmp/_emacs>
>
>
> Thanks in advance for your help
>
> Bernd
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Remember: use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: [babel] Problems sourcing R code

[Weiss, Bernd]

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Hash: SHA1

Dan Davison schrieb:
> "Weiss, Bernd " <bernd.weiss@uni-koeln.de> writes:
> 
>> Dear all,
>>
>> I am having trouble sourcing R code from within an org-file via
>> org-babel, i.e. I cant' replicate the most simple examples
>>
>> #+begin_src R :results value
>> matrix(rnorm(6), nrow=2)
>> #+end_src
>>
>> That's the error message I get whenever I type in C-c C-c:
>>
>> "executing R source code block...
>> Die Syntax für den Dateinamen, Verzeichnisnamen oder die
>> Datenträgerbezeichnung ist falsch.
>> No result returned by source block"
> 
> Dear Bernd,
> 
> This is a problem relating to running R as an external shell process
> under Windows. For the time-being, please use the :session header
> argument to specify that evaluation is to take place in a persistent
> emacs R session. Alternatively, you could use the following
> configuration code to force R blocks to always use the specified session
> (you can change the session name of course):
> 
> (setq org-babel-default-header-args:R '((:session . "*my-R-session*")))
> 
> Session-based evaluation is described briefly at
> 
> http://orgmode.org/worg/org-contrib/babel/org-babel.php#basic-functionality
> 
> Thanks for the report. We will investigate the issues with running R as
> an external process under Windows.


Dear Dan,

that works, thanks a lot!

Bernd
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