* Babel problem (was how do scientists use org mode?) @ 2012-02-02 17:27 John Hendy 2012-02-02 18:59 ` Christopher W. Ryan 0 siblings, 1 reply; 3+ messages in thread From: John Hendy @ 2012-02-02 17:27 UTC (permalink / raw) To: Christopher W. Ryan; +Cc: emacs-orgmode 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 > ^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Babel problem (was how do scientists use org mode?) 2012-02-02 17:27 Babel problem (was how do scientists use org mode?) John Hendy @ 2012-02-02 18:59 ` Christopher W. Ryan 2012-02-02 20:12 ` Nick Dokos 0 siblings, 1 reply; 3+ messages in thread From: Christopher W. Ryan @ 2012-02-02 18:59 UTC (permalink / raw) To: emacs-orgmode 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 >> ^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Babel problem (was how do scientists use org mode?) 2012-02-02 18:59 ` Christopher W. Ryan @ 2012-02-02 20:12 ` Nick Dokos 0 siblings, 0 replies; 3+ messages in thread From: Nick Dokos @ 2012-02-02 20:12 UTC (permalink / raw) To: Christopher W. Ryan; +Cc: nicholas.dokos, emacs-orgmode 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 ^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2012-02-02 20:12 UTC | newest] Thread overview: 3+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2012-02-02 17:27 Babel problem (was how do scientists use org mode?) John Hendy 2012-02-02 18:59 ` Christopher W. Ryan 2012-02-02 20:12 ` Nick Dokos
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