org-babel R, export, and :result value raw

org-babel R, export, and :result value raw

[Christophe Rhodes]

Hi,

Consider the following org-mode file, assuming that org-babel support
for emacs lisp and R is active:

--- begin ---
#+TITLE: Foo

#+begin_src emacs-lisp :exports results :results value raw
"[[file:foo.png]]"
#+end_src

#+results:
[[foo.png]]

#+begin_src R :exports results :results value raw
"[[file:bar.png]]"
#+end_src

#+results: 
[[file:bar\.png]]
---  end  ---

The problem is probably obvious from the above, but to be explicit: the
intent is to generate raw org-mode from the code blocks (this case is
hugely simplified from my actual application), producing links to images
which will then be part of the eventual exported document.  For emacs
lisp, this works fine; for R, the path through files and specifically
org-babel-import-elisp-from-file / org-babel-string-read causes the
return value to be misinterpreted, introducing an extra backslash, and
therefore generating bogus export files.

(This used to work for my use case in org-mode 7.4, and does not work in
org-mode 7.6; I looked at HEAD to see if I could identify a fix, but did
not find one -- I'm sorry if I missed it)

Thanks,

Christophe

Re: org-babel R, export, and :result value raw

[Nick Dokos]

Christophe Rhodes <csr21@cantab.net> wrote:

> Hi,
> 
> Consider the following org-mode file, assuming that org-babel support
> for emacs lisp and R is active:
> 
> --- begin ---
> #+TITLE: Foo
> 
> #+begin_src emacs-lisp :exports results :results value raw
> "[[file:foo.png]]"
> #+end_src
> 
> #+results:
> [[foo.png]]
> 
> #+begin_src R :exports results :results value raw
> "[[file:bar.png]]"
> #+end_src
> #+results: 
> [[file:bar\.png]]
> ---  end  ---
> 
> The problem is probably obvious from the above, but to be explicit: the
> intent is to generate raw org-mode from the code blocks (this case is
> hugely simplified from my actual application), producing links to images
> which will then be part of the eventual exported document.  For emacs
> lisp, this works fine; for R, the path through files and specifically
> org-babel-import-elisp-from-file / org-babel-string-read causes the
> return value to be misinterpreted, introducing an extra backslash, and
> therefore generating bogus export files.
> 
> (This used to work for my use case in org-mode 7.4, and does not work in
> org-mode 7.6; I looked at HEAD to see if I could identify a fix, but did
> not find one -- I'm sorry if I missed it)
> 

This bisects to the following commit:

--8<---------------cut here---------------start------------->8---
commit b6912331715c7da08927b3636b6721af5f5e0c41
Author: Eric Schulte <schulte.eric@gmail.com>
Date:   Tue Mar 1 10:31:00 2011 -0700

    ob: allow passing elisp vectors through to code blocks
    
    * lisp/ob.el (org-babel-read): Pass elisp vectors through to code
      blocks.

diff --git a/lisp/ob.el b/lisp/ob.el
index ea1c968..b0b5fb6 100644
--- a/lisp/ob.el
+++ b/lisp/ob.el
@@ -1913,16 +1913,15 @@ (defun org-babel-script-escape (str)
 
 (defun org-babel-read (cell &optional inhibit-lisp-eval)
   "Convert the string value of CELL to a number if appropriate.
-Otherwise if cell looks like lisp (meaning it starts with a \"(\"
-or a \"'\") then read it as lisp, otherwise return it unmodified
-as a string.  Optional argument NO-LISP-EVAL inhibits lisp
-evaluation for situations in which is it not appropriate."
+Otherwise if cell looks like lisp (meaning it starts with a
+\"(\", \"'\", \"`\" or a \"[\") then read it as lisp, otherwise
+return it unmodified as a string.  Optional argument NO-LISP-EVAL
+inhibits lisp evaluation for situations in which is it not
+appropriate."
   (if (and (stringp cell) (not (equal cell "")))
       (or (org-babel-number-p cell)
           (if (and (not inhibit-lisp-eval)
-		   (or (equal "(" (substring cell 0 1))
-		       (equal "'" (substring cell 0 1))
-		       (equal "`" (substring cell 0 1))))
+		   (member (substring cell 0 1) '("(" "'" "`" "[")))
               (eval (read cell))
             (progn (set-text-properties 0 (length cell) nil cell) cell)))
     cell))
--8<---------------cut here---------------end--------------->8---

If I revert it, I get the 7.4 behavior.

The problem is that  "[..." looks like a lisp vector to this function.

Nick

Re: org-babel R, export, and :result value raw

[Eric Schulte]

Hi Christophe,

This issue of result wrappers (e.g., raw org html) not playing well with
result types (e.g., vector, scalar) came up a couple of months ago on
this mailing list and was not resolved.

I've just pushed up a change which should fix this problem, along with
an R-specific fix so that R respects the "scalar" and "verbatim"
:results header arguments so that the following now works.

#+begin_src R :results raw scalar
"[[file:bar.png]]"
#+end_src

Best -- Eric

Christophe Rhodes <csr21@cantab.net> writes:

> Hi,
>
> Consider the following org-mode file, assuming that org-babel support
> for emacs lisp and R is active:
>
> --- begin ---
> #+TITLE: Foo
>
> #+begin_src emacs-lisp :exports results :results value raw
> "[[file:foo.png]]"
> #+end_src
>
> #+results:
> [[foo.png]]
>
> #+begin_src R :exports results :results value raw
> "[[file:bar.png]]"
> #+end_src
> #+results: 
> [[file:bar\.png]]
> ---  end  ---
>
> The problem is probably obvious from the above, but to be explicit: the
> intent is to generate raw org-mode from the code blocks (this case is
> hugely simplified from my actual application), producing links to images
> which will then be part of the eventual exported document.  For emacs
> lisp, this works fine; for R, the path through files and specifically
> org-babel-import-elisp-from-file / org-babel-string-read causes the
> return value to be misinterpreted, introducing an extra backslash, and
> therefore generating bogus export files.
>
> (This used to work for my use case in org-mode 7.4, and does not work in
> org-mode 7.6; I looked at HEAD to see if I could identify a fix, but did
> not find one -- I'm sorry if I missed it)
>
> Thanks,
>
> Christophe
>
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/