From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Christopher W. Ryan" Subject: Re: Babel problem (was how do scientists use org mode?) Date: Thu, 02 Feb 2012 13:59:03 -0500 Message-ID: <4F2ADCF7.9070402@binghamton.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:49705) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rt1sD-0005LO-Gq for emacs-orgmode@gnu.org; Thu, 02 Feb 2012 13:59:13 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rt1s9-0004d8-6w for emacs-orgmode@gnu.org; Thu, 02 Feb 2012 13:59:09 -0500 Received: from hrndva-omtalb.mail.rr.com ([71.74.56.123]:42126) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rt1s9-0004c5-1B for emacs-orgmode@gnu.org; Thu, 02 Feb 2012 13:59:05 -0500 In-Reply-To: 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: emacs-orgmode@gnu.org 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 > 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 >>