BUG? table output despite "#+begin_src sh :results verbatim"

BUG? table output despite "#+begin_src sh :results verbatim"

[Cook, Malcolm]

Hi,

In org 7.9.3d, under Gnu emacs 24.2.1 / linux:

I find that org-mode is tablizing shell output despite require 'verbatim' results.

#+begin_src sh :results  verbatim
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
| 1 |
| 2 |
| 3 |


The same happens if I used 'scalar' in place of verbatim.

I see that :results processing is somewhat happening, as evidenced by using ":results org" , as below.

#+begin_src sh :results   org
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
#+BEGIN_SRC org
| 1 |
| 2 |
| 3 |
#+END_SRC

Any tips/workarounds/upgrades needed?

Malcolm Cook
Computational Biology - Stowers Institute for Medical Research

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Thomas S. Dye]

Aloha Malcolm,

"Cook, Malcolm" <MEC@stowers.org> writes:

> Hi,
>
> In org 7.9.3d, under Gnu emacs 24.2.1 / linux:
>
> I find that org-mode is tablizing shell output despite require
> verbatim' results.
>
> #+begin_src sh :results  verbatim
>   echo 1
>   echo 2
>   echo 3
> #+end_src
>
> #+results:
> | 1 |
> | 2 |
> | 3 |

Hmm, I get this:

#+begin_src sh :results  verbatim
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
: 1
: 2
: 3

#+begin_src sh :results  scalar
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
: 1
: 2
: 3

#+begin_src sh :results  table
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
| 1 |
| 2 |
| 3 | 

#+begin_src sh :results  list
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
- (1)
- (2)
- (3)

#+begin_src sh :results org
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
#+BEGIN_SRC org
| 1 |
| 2 |
| 3 |
#+END_SRC

Not sure why our results differ, though.

Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Cook, Malcolm]

Thomas,

Thanks for checking.

What does 

meta-x org-version

tell you

??

~Malcolm


 .-----Original Message-----
 .From: Thomas S. Dye [mailto:tsd@tsdye.com]
 .Sent: Friday, January 25, 2013 1:44 PM
 .To: Cook, Malcolm
 .Cc: 'emacs-orgmode@gnu.org'
 .Subject: Re: BUG? table output despite "#+begin_src sh :results verbatim"
 .
 .Aloha Malcolm,
 .
 ."Cook, Malcolm" <MEC@stowers.org> writes:
 .
 .> Hi,
 .>
 .> In org 7.9.3d, under Gnu emacs 24.2.1 / linux:
 .>
 .> I find that org-mode is tablizing shell output despite require
 .> verbatim' results.
 .>
 .> #+begin_src sh :results  verbatim
 .>   echo 1
 .>   echo 2
 .>   echo 3
 .> #+end_src
 .>
 .> #+results:
 .> | 1 |
 .> | 2 |
 .> | 3 |
 .
 .Hmm, I get this:
 .
 .#+begin_src sh :results  verbatim
 .  echo 1
 .  echo 2
 .  echo 3
 .#+end_src
 .
 .#+results:
 .: 1
 .: 2
 .: 3
 .
 .#+begin_src sh :results  scalar
 .  echo 1
 .  echo 2
 .  echo 3
 .#+end_src
 .
 .#+results:
 .: 1
 .: 2
 .: 3
 .
 .#+begin_src sh :results  table
 .  echo 1
 .  echo 2
 .  echo 3
 .#+end_src
 .
 .#+results:
 .| 1 |
 .| 2 |
 .| 3 |
 .
 .#+begin_src sh :results  list
 .  echo 1
 .  echo 2
 .  echo 3
 .#+end_src
 .
 .#+results:
 .- (1)
 .- (2)
 .- (3)
 .
 .#+begin_src sh :results org
 .  echo 1
 .  echo 2
 .  echo 3
 .#+end_src
 .
 .#+results:
 .#+BEGIN_SRC org
 .| 1 |
 .| 2 |
 .| 3 |
 .#+END_SRC
 .
 .Not sure why our results differ, though.
 .
 .Tom
 .
 .--
 .Thomas S. Dye
 .http://www.tsdye.com

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Thomas S. Dye]

"Cook, Malcolm" <MEC@stowers.org> writes:

> Thomas,
>
> Thanks for checking.
>
> What does 
>
> meta-x org-version
>
> tell you
>
> ??

Org-mode version 7.9.3d (release_7.9.3d-830-g780b45 @ /Users/dk/.emacs.d/src/org-mode/lisp/)

-- 
T.S. Dye & Colleagues, Archaeologists
735 Bishop St, Suite 315, Honolulu, HI 96813
Tel: 808-529-0866, Fax: 808-529-0884
http://www.tsdye.com

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Cook, Malcolm]

THanks Thomas, I see we are running same version of org....

Has anyone else reading this got an idea what would cause org to table-ize shell output despite a `:results verbatim` in the source block header?

Thanks!

~Malcolm


 .-----Original Message-----
 .From: Thomas S. Dye [mailto:tsd@tsdye.com]
 .Sent: Friday, January 25, 2013 2:31 PM
 .To: Cook, Malcolm
 .Cc: 'emacs-orgmode@gnu.org'
 .Subject: Re: BUG? table output despite "#+begin_src sh :results verbatim"
 .
 ."Cook, Malcolm" <MEC@stowers.org> writes:
 .
 .> Thomas,
 .>
 .> Thanks for checking.
 .>
 .> What does
 .>
 .> meta-x org-version
 .>
 .> tell you
 .>
 .> ??
 .
 .Org-mode version 7.9.3d (release_7.9.3d-830-g780b45 @ /Users/dk/.emacs.d/src/org-mode/lisp/)
 .
 .--
 .T.S. Dye & Colleagues, Archaeologists
 .735 Bishop St, Suite 315, Honolulu, HI 96813
 .Tel: 808-529-0866, Fax: 808-529-0884
 .http://www.tsdye.com

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Sebastien Vauban]

Hi Thomas and Malcolm,

Thomas S. Dye wrote:
> Aloha Malcolm,
>
> "Cook, Malcolm" <MEC-5NBH63dZDaxAfugRpC6u6w@public.gmane.org> writes:
>
>> Hi,
>>
>> In org 7.9.3d, under Gnu emacs 24.2.1 / linux:
>>
>> I find that org-mode is tablizing shell output despite require
>> verbatim' results.
>>
>> #+begin_src sh :results  verbatim
>>   echo 1
>>   echo 2
>>   echo 3
>> #+end_src
>>
>> #+results:
>> | 1 |
>> | 2 |
>> | 3 |
>
> Hmm, I get this:
>
> #+begin_src sh :results  verbatim
>   echo 1
>   echo 2
>   echo 3
> #+end_src
>
> #+results:
> : 1
> : 2
> : 3
>
> #+begin_src sh :results  scalar
>   echo 1
>   echo 2
>   echo 3
> #+end_src
>
> #+results:
> : 1
> : 2
> : 3

In both cases (verbatim or scalar, which are synonyms), I do have:

#+begin_src sh :results  verbatim
  echo 1
  echo 2
  echo 3
#+end_src

#+results:
#+begin_example
1
2
3
#+end_example

(I configured Babel so that to get lines prefixed by ":" only if there
is *one* line of results)

For the rest, I got the same as you:

> #+begin_src sh :results  table
>   echo 1
>   echo 2
>   echo 3
> #+end_src
>
> #+results:
> | 1 |
> | 2 |
> | 3 | 
>
> #+begin_src sh :results  list
>   echo 1
>   echo 2
>   echo 3
> #+end_src
>
> #+results:
> - (1)
> - (2)
> - (3)

... and wonder why the figures here are enclosed between parentheses...

Best regards,
  Seb

-- 
Sebastien Vauban

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Eric Schulte]

"Cook, Malcolm" <MEC@stowers.org> writes:

> THanks Thomas, I see we are running same version of org....
>
> Has anyone else reading this got an idea what would cause org to
> table-ize shell output despite a `:results verbatim` in the source
> block header?
>
> Thanks!
>

Hi Malcolm,

Try starting emacs without any of your personalized configuration loaded
using the -Q option.  If the problem disappears, then it is due to
something in your personal config.

If you still experience the problem you may want to ensure that you
aren't using `org-babel-execute-src-block' from an old version of
Org-mode by executing the following from your scratch buffer

    ;; emacs-lisp
    (when (require 'find-func)
      (find-function 'org-babel-execute-src-block))

and then ensuring that the file is in the current Org-mode installation
directory.

Cheers,

>
> ~Malcolm
>
>
>  .-----Original Message-----
>  .From: Thomas S. Dye [mailto:tsd@tsdye.com]
>  .Sent: Friday, January 25, 2013 2:31 PM
>  .To: Cook, Malcolm
>  .Cc: 'emacs-orgmode@gnu.org'
>  .Subject: Re: BUG? table output despite "#+begin_src sh :results verbatim"
>  .
>  ."Cook, Malcolm" <MEC@stowers.org> writes:
>  .
>  .> Thomas,
>  .>
>  .> Thanks for checking.
>  .>
>  .> What does
>  .>
>  .> meta-x org-version
>  .>
>  .> tell you
>  .>
>  .> ??
>  .
>  .Org-mode version 7.9.3d (release_7.9.3d-830-g780b45 @ /Users/dk/.emacs.d/src/org-mode/lisp/)
>  .
>  .--
>  .T.S. Dye & Colleagues, Archaeologists
>  .735 Bishop St, Suite 315, Honolulu, HI 96813
>  .Tel: 808-529-0866, Fax: 808-529-0884
>  .http://www.tsdye.com
>

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

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Achim Gratz]

Eric Schulte writes:
> If you still experience the problem you may want to ensure that you
> aren't using `org-babel-execute-src-block' from an old version of
> Org-mode by executing the following from your scratch buffer
>
>     ;; emacs-lisp
>     (when (require 'find-func)
>       (find-function 'org-babel-execute-src-block))

Unless you really want to open the source file of course, I'd rather use

  (symbol-file 'org-babel-execute-src-block)

for this check.  If the result is nil, then the function wasn't defined
at all.  If the function is currently defined as an autoload (but the
defining library has not been loaded), then you'll get a relative
filename that will resolve via load-path at the point of first use.  If
the library that defines the function has been loaded already, then
you'll get the absolute path to the file it has been loaded from.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

Waldorf MIDI Implementation & additional documentation:
http://Synth.Stromeko.net/Downloads.html#WaldorfDocs

Re: BUG? table output despite "#+begin_src sh :results verbatim"

[Cook, Malcolm]

Eric,

Mucho Kudos.... indeed.... I had an old patch to org-babel-execute:sh tucked away masking your released version.

'nuff said, except

Thanks, again, very much,

Mea culpa,

~Malcolm


 .-----Original Message-----
 .From: Eric Schulte [mailto:schulte.eric@gmail.com]
 .Sent: Saturday, January 26, 2013 1:37 PM
 .To: Cook, Malcolm
 .Cc: 'Thomas S. Dye'; Blanchette, Marco; 'emacs-orgmode@gnu.org'
 .Subject: Re: [O] BUG? table output despite "#+begin_src sh :results verbatim"
 .
 ."Cook, Malcolm" <MEC@stowers.org> writes:
 .
 .> THanks Thomas, I see we are running same version of org....
 .>
 .> Has anyone else reading this got an idea what would cause org to
 .> table-ize shell output despite a `:results verbatim` in the source
 .> block header?
 .>
 .> Thanks!
 .>
 .
 .Hi Malcolm,
 .
 .Try starting emacs without any of your personalized configuration loaded
 .using the -Q option.  If the problem disappears, then it is due to
 .something in your personal config.
 .
 .If you still experience the problem you may want to ensure that you
 .aren't using `org-babel-execute-src-block' from an old version of
 .Org-mode by executing the following from your scratch buffer
 .
 .    ;; emacs-lisp
 .    (when (require 'find-func)
 .      (find-function 'org-babel-execute-src-block))
 .
 .and then ensuring that the file is in the current Org-mode installation
 .directory.
 .
 .Cheers,
 .
 .>
 .> ~Malcolm
 .>
 .>
 .>  .-----Original Message-----
 .>  .From: Thomas S. Dye [mailto:tsd@tsdye.com]
 .>  .Sent: Friday, January 25, 2013 2:31 PM
 .>  .To: Cook, Malcolm
 .>  .Cc: 'emacs-orgmode@gnu.org'
 .>  .Subject: Re: BUG? table output despite "#+begin_src sh :results verbatim"
 .>  .
 .>  ."Cook, Malcolm" <MEC@stowers.org> writes:
 .>  .
 .>  .> Thomas,
 .>  .>
 .>  .> Thanks for checking.
 .>  .>
 .>  .> What does
 .>  .>
 .>  .> meta-x org-version
 .>  .>
 .>  .> tell you
 .>  .>
 .>  .> ??
 .>  .
 .>  .Org-mode version 7.9.3d (release_7.9.3d-830-g780b45 @ /Users/dk/.emacs.d/src/org-mode/lisp/)
 .>  .
 .>  .--
 .>  .T.S. Dye & Colleagues, Archaeologists
 .>  .735 Bishop St, Suite 315, Honolulu, HI 96813
 .>  .Tel: 808-529-0866, Fax: 808-529-0884
 .>  .http://www.tsdye.com
 .>
 .
 .--
 .Eric Schulte
 .http://cs.unm.edu/~eschulte