Babel problem (was how do scientists use org mode?)

Babel problem (was how do scientists use org mode?)

[John Hendy]

Hi Chris; this digressed enough into a babel problem that I started a
new subject for the list.

On Thu, Feb 2, 2012 at 11:19 AM, Christopher W. Ryan
<cryan@binghamton.edu> wrote:
> Just tried a similar thing on my computer at work: WinXP, emacs-22.3.1,
> org-mode 7.7.  I tried both R and python.  With this in my .emacs file:
>
> ;; active Babel languages
> (org-babel-do-load-languages
>  'org-babel-load-languages
>  '((R . t)
>   (python . t)
>   ))
>
> Here are the contents of the org file I am playing with:
>
> #+begin_src R
> rnorm(10)
> #+end_src
>
> #+begin_src python
> print "Hello, World!"
> #+end_src
>
>
> C-c C-c the first block results in a message like this:
>
> Evaluate this R code block on your system? (yes or no)
>
> Answering yes yields:
>
> No org-babel-execute function for R!
>
> Trying the same in the python block yields the same results, except with
> "python" substituted for "R" in all the messages.
>
> Any suggestions where I am going wrong?

Silly question... do you have both R and python installed on your
computer? Perhaps provide the paths of your R and python executable
files. Win settings can be tricky sometimes. Another question would
be, how do you typically use R and python directly?

John

>
> Thanks.
>
> --Chris Ryan
>

Re: Babel problem (was how do scientists use org mode?)

[Christopher W. Ryan]

John and Nick--

The question about whether I have python on my machine is not silly--I
am. Got so carried away I forgot I was on my work computer, which indeed
does not have python. But I do have R and perl, and similar code blocks
in either language yield the same problem, so I'll just focus on them as
examples (he said, sheepishly.)

I usually interface with R via emacs ESS. Currently ESS is using R
version 2.11.1.

R executable is in C:\Program Files\R\R-2.11.1\bin

I usually interface with perl via another text editor, Programmer's
Notepad, set up with drop-down menu item to execute the file in perl.

Perl executable is in C:\strawberry\perl\bin

C:\Org\org-7.7\lisp contains, among others, files called ob-R.el and
ob-perl.el

Currently my path variable looks like this:

Files\QuickTime\QTSystem\;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Xpdf;C:\strawberry\perl\bin;C:\strawberry\c\bin;C:\strawberry\perl\site\bin


My .emacs now contains:

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (python . t)
   (perl . t)
   ))


As to Nick's questions,

M-x locate-library RET ob-R RET

tells me ob-R is located in C:\Org\org-7.7\lisp\ob-R.el

M-: to evaluate (require 'ob-R.el)

yields ob-R in the minibuffer

Then C-c C-c in the R code block yields

Code block produced not output.

in the minibuffer,

and a new buffer that says,

'R' is not recognized as an internal or external command,
operable program or batch file.


I tried evaluating (require 'ob-perl) and this yielded

ob-perl

in the minibuffer, and thereafter the perl code block executed properly.

I wonder if I need to put the path to R in my PATH variable? (come to
think of it, don't know why it's not already there); its absence has so
far not prevented me from using R via ESS.

Thanks.

--Chris


Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu


John Hendy wrote:
> Hi Chris; this digressed enough into a babel problem that I started a
> new subject for the list.
> 
> On Thu, Feb 2, 2012 at 11:19 AM, Christopher W. Ryan
> <cryan@binghamton.edu> wrote:
>> Just tried a similar thing on my computer at work: WinXP, emacs-22.3.1,
>> org-mode 7.7.  I tried both R and python.  With this in my .emacs file:
>>
>> ;; active Babel languages
>> (org-babel-do-load-languages
>>  'org-babel-load-languages
>>  '((R . t)
>>   (python . t)
>>   ))
>>
>> Here are the contents of the org file I am playing with:
>>
>> #+begin_src R
>> rnorm(10)
>> #+end_src
>>
>> #+begin_src python
>> print "Hello, World!"
>> #+end_src
>>
>>
>> C-c C-c the first block results in a message like this:
>>
>> Evaluate this R code block on your system? (yes or no)
>>
>> Answering yes yields:
>>
>> No org-babel-execute function for R!
>>
>> Trying the same in the python block yields the same results, except with
>> "python" substituted for "R" in all the messages.
>>
>> Any suggestions where I am going wrong?
> 
> Silly question... do you have both R and python installed on your
> computer? Perhaps provide the paths of your R and python executable
> files. Win settings can be tricky sometimes. Another question would
> be, how do you typically use R and python directly?
> 
> John
> 
>>
>> Thanks.
>>
>> --Chris Ryan
>>

Re: Babel problem (was how do scientists use org mode?)

[Nick Dokos]

Christopher W. Ryan <cryan@binghamton.edu> wrote:

> John and Nick--
> 
> The question about whether I have python on my machine is not silly--I
> am. Got so carried away I forgot I was on my work computer, which indeed
> does not have python. But I do have R and perl, and similar code blocks
> in either language yield the same problem, so I'll just focus on them as
> examples (he said, sheepishly.)
> 
> I usually interface with R via emacs ESS. Currently ESS is using R
> version 2.11.1.
> 
> R executable is in C:\Program Files\R\R-2.11.1\bin
> 
> I usually interface with perl via another text editor, Programmer's
> Notepad, set up with drop-down menu item to execute the file in perl.
> 
> Perl executable is in C:\strawberry\perl\bin
> 
> C:\Org\org-7.7\lisp contains, among others, files called ob-R.el and
> ob-perl.el
> 
> Currently my path variable looks like this:
> 
> Files\QuickTime\QTSystem\;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Xpdf;C:\strawberry\perl\bin;C:\strawberry\c\bin;C:\strawberry\perl\site\bin
> 
> 
> My .emacs now contains:
> 
> ;; active Babel languages
> (org-babel-do-load-languages
>  'org-babel-load-languages
>  '((R . t)
>    (python . t)
>    (perl . t)
>    ))
> 
> 
> As to Nick's questions,
> 
> M-x locate-library RET ob-R RET
> 
> tells me ob-R is located in C:\Org\org-7.7\lisp\ob-R.el
> 
> M-: to evaluate (require 'ob-R.el)
> 
> yields ob-R in the minibuffer
> 
> Then C-c C-c in the R code block yields
> 
> Code block produced not output.
> 
> in the minibuffer,
> 
> and a new buffer that says,
> 
> 'R' is not recognized as an internal or external command,
> operable program or batch file.
> 

It's probably a path issue as you surmise below.

ob-R.el includes the following:

(defvar org-babel-R-command "R --slave --no-save"
  "Name of command to use for executing R code.")

Try setting something like

(setq org-bable-R-command "/full/path/to/R --slave --no-save")

in your .emacs, although the exact format for Windows is going to 
be different. This is meant as a test, not as a fix: if that works,
then you can figure out how to change your path and get rid of the
hack.

> 
> I tried evaluating (require 'ob-perl) and this yielded
> 
> ob-perl
> 
> in the minibuffer, and thereafter the perl code block executed properly.
> 

Ok, that's promising.

> I wonder if I need to put the path to R in my PATH variable? (come to
> think of it, don't know why it's not already there); its absence has so
> far not prevented me from using R via ESS.
> 

Probably.

Nick