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* Problem whit with code evaluation
@ 2010-08-19  0:12 Blanchette, Marco
  2010-08-19  2:37 ` Dan Davison
  0 siblings, 1 reply; 6+ messages in thread
From: Blanchette, Marco @ 2010-08-19  0:12 UTC (permalink / raw)
  To: emacs-orgmode@gnu.org

Sorry again if this is common knowledge, but the road to orgmode power user
is seeded with challenges!

I am trying to write an R function that would take 3 arguments, hopefully
set up in an org table and have a function run every rows, taking every
column as arguments to produce a set of report files... But I am going a bit
ahead of myself as I am stuck quite early in the development...

My problem is quite basic. For some reason, I can¹t seems to be able to
execute the following lines in the org buffer using org-babel-execute-buffer
or to export an html of the files. The code block just don't execute and
return errors.

* Examples take from
[[http://orgmode.org/worg/org-contrib/babel/intro.php#sec-7]]

* The python example
#+source: square(x)
#+begin_src python
x*x
#+end_src

#+call: square(x=6)

* The elisp example of the fibonacci series using a table as argument

#+tblname: fibonacci-inputs
| 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
| 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |

#+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
#+begin_src emacs-lisp
  (defun fibonacci (n)
    (if (or (= n 0) (= n 1))
        n
      (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
  
  (mapcar (lambda (row)
            (mapcar #'fibonacci row)) fib-inputs)
#+end_src

* Then my own trial in R
#+srcname: test(x y)
#+begin_src R
   p <- x*y
#+end_src

#+call test(x=4 y=9)
#+function test(x=3 y=8)

Is there something I am missing?

My current setup is:
GNU Emacs 23.1.50.1
org-mode (v7.01g)
R v2.11.1
XServer running Snow Leopard Server 10.6.4

Thanks for the help
-- 
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.

Kansas City, MO 64110

Tel: 816-926-4071 
Cell: 816-726-8419 
Fax: 816-926-2018 

^ permalink raw reply	[flat|nested] 6+ messages in thread

• * Re: Problem whit with code evaluation
    2010-08-19  0:12 Problem whit with code evaluation Blanchette, Marco
  @ 2010-08-19  2:37 ` Dan Davison
    2010-08-19  3:01   ` Blanchette, Marco
    0 siblings, 1 reply; 6+ messages in thread
  From: Dan Davison @ 2010-08-19  2:37 UTC (permalink / raw)
    To: Blanchette, Marco; +Cc: emacs-orgmode@gnu.org
  
  Hi Marco,
  
  "Blanchette, Marco" <MAB@stowers.org> writes:
  
  > Sorry again if this is common knowledge, but the road to orgmode power user
  > is seeded with challenges!
  >
  > I am trying to write an R function that would take 3 arguments, hopefully
  > set up in an org table and have a function run every rows, taking every
  > column as arguments to produce a set of report files... But I am going a bit
  > ahead of myself as I am stuck quite early in the development...
  >
  > My problem is quite basic. For some reason, I can¹t seems to be able to
  > execute the following lines in the org buffer using org-babel-execute-buffer
  > or to export an html of the files. The code block just don't execute and
  > return errors.
  >
  > * Examples take from
  > [[http://orgmode.org/worg/org-contrib/babel/intro.php#sec-7]]
  >
  > * The python example
  > #+source: square(x)
  > #+begin_src python
  > x*x
  > #+end_src
  
  This one's our fault. That should be
  #+begin_src python
  return x*x
  #+end_src
  
  I've changed it on Worg.
  
  > #+call: square(x=6)
  >
  > * The elisp example of the fibonacci series using a table as argument
  >
  > #+tblname: fibonacci-inputs
  > | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
  > | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
  >
  > #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
  > #+begin_src emacs-lisp
  >   (defun fibonacci (n)
  >     (if (or (= n 0) (= n 1))
  >         n
  >       (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
  >   
  >   (mapcar (lambda (row)
  >             (mapcar #'fibonacci row)) fib-inputs)
  > #+end_src
  
  OK, that works for me.
  
  >
  > * Then my own trial in R
  > #+srcname: test(x y)
                     ^
  missing comma
  
  > #+begin_src R
  >    p <- x*y
  > #+end_src
  >
  > #+call test(x=4 y=9)
          ^        ^
  
  missing colon, and missing comma
  
  > #+function test(x=3 y=8)
  
  That's not correct usage of #+function; you wanted #+lob: / #+call:
  there.
  
  There are two sets of synonymous terms. *Within* each of these sets, the
  terms are synonymous:
  
  {#+function,#+source,#+srcname}
  {#+lob,#+call}
  
  My edited version of your input is below.
  
  Hope that helps, do get back to the list if you have further questions.
  
  Dan
  
  
  --8<---------------cut here---------------start------------->8---
  * Examples take from
  [[http://orgmode.org/worg/org-contrib/babel/intro.php#sec-7]]
  
  * The python example
  #+source: square(x)
  #+begin_src python
  return x*x
  #+end_src
  
  #+call: square(x=6)
  
  #+results: square(x=6)
  : 36
  
  * The elisp example of the fibonacci series using a table as argument
  
  #+tblname: fibonacci-inputs
  | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
  | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
  
  #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
  #+begin_src emacs-lisp
    (defun fibonacci (n)
      (if (or (= n 0) (= n 1))
          n
        (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
    
    (mapcar (lambda (row)
              (mapcar #'fibonacci row)) fib-inputs)
  #+end_src
  
  #+results: fibonacci-seq
  | 1 | 1 | 2 |  3 |  5 |   8 |  13 |  21 |   34 |   55 |
  | 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
  
  * Then my own trial in R
  #+srcname: test(x, y)
  #+begin_src R
     p <- x*y
  #+end_src
  
  #+call: test(x=4, y=9)
  
  #+results: test(x=4, y=9)
  : 36
  
  #+lob: test(x=3, y=8)
  
  #+results: test(x=3, y=8)
  : 24
  --8<---------------cut here---------------end--------------->8---
  
  >
  > Is there something I am missing?
  >
  > My current setup is:
  > GNU Emacs 23.1.50.1
  > org-mode (v7.01g)
  > R v2.11.1
  > XServer running Snow Leopard Server 10.6.4
  >
  > Thanks for the help
  
  ^ permalink raw reply	[flat|nested] 6+ messages in thread

• • * Re: Problem whit with code evaluation
      2010-08-19  2:37 ` Dan Davison
    @ 2010-08-19  3:01   ` Blanchette, Marco
      2010-08-19  4:23     ` Dan Davison
      2010-08-19  5:05     ` Nick Dokos
      0 siblings, 2 replies; 6+ messages in thread
    From: Blanchette, Marco @ 2010-08-19  3:01 UTC (permalink / raw)
      To: Dan Davison; +Cc: emacs-orgmode@gnu.org
    
    Hmm... Thanks Dan.
    
    Do we have a different version of org-mode? I just pasted your code in emacs
    and try to execute it with M-x org-babel-execute-buffer RET without success.
    
    The emacs-lisp code works but the python and the R crashes with the
    following errors taken from the *Org-Babel Error* Output buffer
    
    Traceback (most recent call last):
      File "<stdin>", line 5, in <module>
      File "<stdin>", line 3, in main
    NameError: global name 'x' is not defined
    Error in main() : object 'x' not found
    Calls: write.table -> is.data.frame -> inherits -> main
    Execution halted
    
    The first 4 lines comes from the python script while the last 3 come from
    the R script
    
    Here is my .emacs org-mode configs in case you are wondering...
    
    ;;Load org-mode and set global keys
    (require 'org-install)
    (add-to-list 'auto-mode-alist '("\\.org$" . org-mode))
    (add-hook 'org-mode-hook 'turn-on-font-lock) ; not needed when
    global-font-lock-mode is on
    (define-key global-map "\C-cl" 'org-store-link)
    (define-key global-map "\C-ca" 'org-agenda)
    (setq org-log-done t)
    (setq org-startup-indented t)
    
    
    ;; active Babel languages
    (org-babel-do-load-languages
     'org-babel-load-languages
     '(
       (R . t)
       (sh .t)
       (python . t)
       (emacs-lisp . t)
       )
     )
    
    Thanks again
    
    
    On 8/18/10 9:37 PM, "Dan Davison" <davison@stats.ox.ac.uk> wrote:
    
    > * The python example
    > #+source: square(x)
    > #+begin_src python
    > return x*x
    > #+end_src
    > 
    > #+call: square(x=6)
    > 
    > #+results: square(x=6)
    > : 36
    > 
    > * The elisp example of the fibonacci series using a table as argument
    > 
    > #+tblname: fibonacci-inputs
    > | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
    > | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
    > 
    > #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
    > #+begin_src emacs-lisp
    >   (defun fibonacci (n)
    >     (if (or (= n 0) (= n 1))
    >         n
    >       (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
    >  
    >   (mapcar (lambda (row)
    >             (mapcar #'fibonacci row)) fib-inputs)
    > #+end_src
    > 
    > #+results: fibonacci-seq
    > | 1 | 1 | 2 |  3 |  5 |   8 |  13 |  21 |   34 |   55 |
    > | 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
    > 
    > * Then my own trial in R
    > #+srcname: test(x, y)
    > #+begin_src R
    >    p <- x*y
    > #+end_src
    > 
    > #+call: test(x=4, y=9)
    > 
    > #+results: test(x=4, y=9)
    > : 36
    > 
    > #+lob: test(x=3, y=8)
    > 
    > #+results: test(x=3, y=8)
    > : 24
    
    --
    Marco Blanchette, Ph.D.
    Assistant Investigator
    Stowers Institute for Medical Research
    1000 East 50th St.
    
    Kansas City, MO 64110
    
    Tel: 816-926-4071
    Cell: 816-726-8419
    Fax: 816-926-2018
    
    ^ permalink raw reply	[flat|nested] 6+ messages in thread

  • • * Re: Problem whit with code evaluation
        2010-08-19  3:01   ` Blanchette, Marco
      @ 2010-08-19  4:23     ` Dan Davison
        2010-08-19  5:05     ` Nick Dokos
        1 sibling, 0 replies; 6+ messages in thread
      From: Dan Davison @ 2010-08-19  4:23 UTC (permalink / raw)
        To: Blanchette, Marco; +Cc: emacs-orgmode@gnu.org
      
      "Blanchette, Marco" <MAB@stowers.org> writes:
      
      > Hmm... Thanks Dan.
      >
      > Do we have a different version of org-mode? I just pasted your code in emacs
      > and try to execute it with M-x org-babel-execute-buffer RET without success.
      
      Hi Marco,
      
      Sorry, I was rushing and missed that you were using
      org-babel-execute-buffer. I'll look into it.
      
      Dan
      
      >
      > The emacs-lisp code works but the python and the R crashes with the
      > following errors taken from the *Org-Babel Error* Output buffer
      >
      > Traceback (most recent call last):
      >   File "<stdin>", line 5, in <module>
      >   File "<stdin>", line 3, in main
      > NameError: global name 'x' is not defined
      > Error in main() : object 'x' not found
      > Calls: write.table -> is.data.frame -> inherits -> main
      > Execution halted
      >
      > The first 4 lines comes from the python script while the last 3 come from
      > the R script
      >
      > Here is my .emacs org-mode configs in case you are wondering...
      >
      > ;;Load org-mode and set global keys
      > (require 'org-install)
      > (add-to-list 'auto-mode-alist '("\\.org$" . org-mode))
      > (add-hook 'org-mode-hook 'turn-on-font-lock) ; not needed when
      > global-font-lock-mode is on
      > (define-key global-map "\C-cl" 'org-store-link)
      > (define-key global-map "\C-ca" 'org-agenda)
      > (setq org-log-done t)
      > (setq org-startup-indented t)
      >
      >
      > ;; active Babel languages
      > (org-babel-do-load-languages
      >  'org-babel-load-languages
      >  '(
      >    (R . t)
      >    (sh .t)
      >    (python . t)
      >    (emacs-lisp . t)
      >    )
      >  )
      >
      > Thanks again
      >
      >
      > On 8/18/10 9:37 PM, "Dan Davison" <davison@stats.ox.ac.uk> wrote:
      >
      >> * The python example
      >> #+source: square(x)
      >> #+begin_src python
      >> return x*x
      >> #+end_src
      >> 
      >> #+call: square(x=6)
      >> 
      >> #+results: square(x=6)
      >> : 36
      >> 
      >> * The elisp example of the fibonacci series using a table as argument
      >> 
      >> #+tblname: fibonacci-inputs
      >> | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
      >> | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
      >> 
      >> #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
      >> #+begin_src emacs-lisp
      >>   (defun fibonacci (n)
      >>     (if (or (= n 0) (= n 1))
      >>         n
      >>       (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
      >>  
      >>   (mapcar (lambda (row)
      >>             (mapcar #'fibonacci row)) fib-inputs)
      >> #+end_src
      >> 
      >> #+results: fibonacci-seq
      >> | 1 | 1 | 2 |  3 |  5 |   8 |  13 |  21 |   34 |   55 |
      >> | 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
      >> 
      >> * Then my own trial in R
      >> #+srcname: test(x, y)
      >> #+begin_src R
      >>    p <- x*y
      >> #+end_src
      >> 
      >> #+call: test(x=4, y=9)
      >> 
      >> #+results: test(x=4, y=9)
      >> : 36
      >> 
      >> #+lob: test(x=3, y=8)
      >> 
      >> #+results: test(x=3, y=8)
      >> : 24
      >
      > --
      > Marco Blanchette, Ph.D.
      > Assistant Investigator
      > Stowers Institute for Medical Research
      > 1000 East 50th St.
      >
      > Kansas City, MO 64110
      >
      > Tel: 816-926-4071
      > Cell: 816-726-8419
      > Fax: 816-926-2018
      >
      >
      > _______________________________________________
      > Emacs-orgmode mailing list
      > Please use `Reply All' to send replies to the list.
      > Emacs-orgmode@gnu.org
      > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
      
      ^ permalink raw reply	[flat|nested] 6+ messages in thread

    • * Re: Re: Problem whit with code evaluation
        2010-08-19  3:01   ` Blanchette, Marco
        2010-08-19  4:23     ` Dan Davison
      @ 2010-08-19  5:05     ` Nick Dokos
        2010-08-19 13:38       ` Dan Davison
        1 sibling, 1 reply; 6+ messages in thread
      From: Nick Dokos @ 2010-08-19  5:05 UTC (permalink / raw)
        To: Blanchette, Marco; +Cc: Dan Davison, nicholas.dokos, emacs-orgmode@gnu.org
      
      Blanchette, Marco <MAB@stowers.org> wrote:
      
      > Hmm... Thanks Dan.
      > 
      > Do we have a different version of org-mode? I just pasted your code in emacs
      > and try to execute it with M-x org-babel-execute-buffer RET without success.
      > 
      > The emacs-lisp code works but the python and the R crashes with the
      > following errors taken from the *Org-Babel Error* Output buffer
      > 
      > Traceback (most recent call last):
      >   File "<stdin>", line 5, in <module>
      >   File "<stdin>", line 3, in main
      > NameError: global name 'x' is not defined
      > Error in main() : object 'x' not found
      > 
      > On 8/18/10 9:37 PM, "Dan Davison" <davison@stats.ox.ac.uk> wrote:
      > 
      > > * The python example
      > > #+source: square(x)
      > > #+begin_src python
      > > return x*x
      > > #+end_src
      > > 
      > > #+call: square(x=6)
      > > 
      > > #+results: square(x=6)
      > > : 36
      > > 
      
      I think that's because the first source block cannot be evaluated: it
      only makes sense when it is #+called. If you place the cursor in that
      first source block and press C-c C-c, you get exactly the same error. If
      you do the same on the #+call, it works. Since org-babel-execute-buffer
      just steps through the buffer and executes every source block, it's not
      too surprising that you get those errors.
      
      So I guess the question is whether org-babel-execute-buffer should be
      smarter about which source blocks to execute.
      
      Nick
      
      ^ permalink raw reply	[flat|nested] 6+ messages in thread

    • • * Re: Problem whit with code evaluation
          2010-08-19  5:05     ` Nick Dokos
        @ 2010-08-19 13:38       ` Dan Davison
          0 siblings, 0 replies; 6+ messages in thread
        From: Dan Davison @ 2010-08-19 13:38 UTC (permalink / raw)
          To: nicholas.dokos; +Cc: Blanchette, Marco, emacs-orgmode@gnu.org
        
        Nick Dokos <nicholas.dokos@hp.com> writes:
        
        > Blanchette, Marco <MAB@stowers.org> wrote:
        >
        >> Hmm... Thanks Dan.
        >> 
        >> Do we have a different version of org-mode? I just pasted your code in emacs
        >> and try to execute it with M-x org-babel-execute-buffer RET without success.
        >> 
        >> The emacs-lisp code works but the python and the R crashes with the
        >> following errors taken from the *Org-Babel Error* Output buffer
        >> 
        >> Traceback (most recent call last):
        >>   File "<stdin>", line 5, in <module>
        >>   File "<stdin>", line 3, in main
        >> NameError: global name 'x' is not defined
        >> Error in main() : object 'x' not found
        >> 
        >> On 8/18/10 9:37 PM, "Dan Davison" <davison@stats.ox.ac.uk> wrote:
        >> 
        >> > * The python example
        >> > #+source: square(x)
        >> > #+begin_src python
        >> > return x*x
        >> > #+end_src
        >> > 
        >> > #+call: square(x=6)
        >> > 
        >> > #+results: square(x=6)
        >> > : 36
        >> > 
        >
        > I think that's because the first source block cannot be evaluated: it
        > only makes sense when it is #+called. If you place the cursor in that
        > first source block and press C-c C-c, you get exactly the same error. If
        > you do the same on the #+call, it works. Since org-babel-execute-buffer
        > just steps through the buffer and executes every source block, it's not
        > too surprising that you get those errors.
        >
        > So I guess the question is whether org-babel-execute-buffer should be
        > smarter about which source blocks to execute.
        
        [By the way, lob/call lines were not exporting results correctly in any
        case; I've just pushed a fix.]
        
        
        Nick is right. 
        
        So first a couple of workarounds:
        
        1. For export, you can use ':exports none' or ':exports code' on the
        function blocks which cannot be executed on their own.
        
        2. You can supply default arguments to function blocks, which permits
        them to be executed: #+source: square(x=0)
        
        But (1) doesn't solve the `org-babel-execute-buffer' issue, and (2)
        isn't a nice solution.
        
        I've pasted a version of your examples below which exports without error
        using workaround (1). It requires a fresh pull of Org from the git repo.
        
        So what is a good solution here? I may be missing an existing solution
        but two that come to mind are
        
        1. Extend the existing :eval header arg, introducing a new value, say
           ':eval called' or ':eval passive' that says that while the block may
           not be executed itself, it may be called as a function.
        
        2. Demand that such blocks use the keyword #+function: as opposed
           to #+source or #+srcname.
        
        I'm initially attracted to (2).
        
        Dan
        
        --8<---------------cut here---------------start------------->8---
        #+babel: :exports both
        
        Examples take from
        [[http://orgmode.org/worg/org-contrib/babel/intro.php#sec-7]]
        
        * The python example
        #+source: square(x)
        #+begin_src python :exports code
        return x*x
        #+end_src
        
        #+call: square(x=6)
        
        * The elisp example of the fibonacci series using a table as argument
        
        #+tblname: fibonacci-inputs
        | 1 | 2 | 3 | 4 |  5 |  6 |  7 |  8 |  9 | 10 |
        | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
        
        #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
        #+begin_src emacs-lisp :exports both
          (defun fibonacci (n)
            (if (or (= n 0) (= n 1))
                n
              (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
          
          (mapcar (lambda (row)
                    (mapcar #'fibonacci row)) fib-inputs)
        #+end_src
        
        * Then my own trial in R
        #+srcname: test(x, y)
        #+begin_src R :exports code
           p <- x*y
        #+end_src
        
        #+call: test(x=4, y=9)
        
        text inbetween to force line break.
        
        #+lob: test(x=3, y=8)
        --8<---------------cut here---------------end--------------->8---
        
        
        
        >
        > Nick
        >
        > _______________________________________________
        > Emacs-orgmode mailing list
        > Please use `Reply All' to send replies to the list.
        > Emacs-orgmode@gnu.org
        > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
        
        ^ permalink raw reply	[flat|nested] 6+ messages in thread

end of thread, other threads:[~2010-08-19 13:38 UTC | newest]

Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2010-08-19  0:12 Problem whit with code evaluation Blanchette, Marco
2010-08-19  2:37 ` Dan Davison
2010-08-19  3:01   ` Blanchette, Marco
2010-08-19  4:23     ` Dan Davison
2010-08-19  5:05     ` Nick Dokos
2010-08-19 13:38       ` Dan Davison

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