org-babel src block generated graphics included twice if CAPTION is added

org-babel src block generated graphics included twice if CAPTION is added

[Li Bowen]

Hi, 

If #+CAPTION is added, the figure will be included in the exported pdf
file twice. 

#+begin_src R :exports both :results graphics :file img.pdf
hist(rnorm(100))
#+end_src

#+CAPTION: Some description
#+RESULTS:
[[file:img.pdf]

Many thanks.

-- 
Sincerely,
Li Bowen.

Re: org-babel src block generated graphics included twice if CAPTION is added

[Jay Kerns]

Greetings Li,

On Sun, Mar 17, 2013 at 9:10 AM, Li Bowen <a0050726@nus.edu.sg> wrote:
> Hi,
>
> If #+CAPTION is added, the figure will be included in the exported pdf
> file twice.
>
> #+begin_src R :exports both :results graphics :file img.pdf
> hist(rnorm(100))
> #+end_src
>
> #+CAPTION: Some description
> #+RESULTS:
> [[file:img.pdf]
>


For that particular example maybe the quickest way to get rid of the
extra figure (that is caption-less) would be to use ":exports code"
instead of ":exports both".

I hope this helps,

-- 
Jay

Re: org-babel src block generated graphics included twice if CAPTION is added

[Nick Dokos]

Li Bowen <a0050726@nus.edu.sg> wrote:

> Hi, 
> 
> If #+CAPTION is added, the figure will be included in the exported pdf
> file twice. 
> 
> #+begin_src R :exports both :results graphics :file img.pdf
> hist(rnorm(100))
> #+end_src
> 
> #+CAPTION: Some description
> #+RESULTS:
> [[file:img.pdf]
> 
> Many thanks.
> 

I think the problem is that the code block does not "see" the previously
produced #RESULTS: (because of the intervening #CAPTION:), so when run
again it adds another #RESULTS: section.

I think the best way to deal with problems like this is to name your code blocks
(and results blocks).

Try the following:

--8<---------------cut here---------------start------------->8---
#+name: foo
#+begin_src R :exports both :results graphics :file img.pdf
hist(rnorm(100))
#+end_src

#+CAPTION: Some description
#+RESULTS: foo
[[file:img.pdf]]
--8<---------------cut here---------------end--------------->8---

Does it solve the problem?

Nick

Re: org-babel src block generated graphics included twice if CAPTION is added

[Jay Kerns]

On Sun, Mar 17, 2013 at 6:21 PM, Nick Dokos <nicholas.dokos@hp.com> wrote:

[snip]

> I think the best way to deal with problems like this is to name your code blocks (and results blocks).
>

[snip]

I can't speak for Li, but it works on my system and I like Nick's
solution better than mine.

Cheers,

-- 
Jay

Re: org-babel src block generated graphics included twice if CAPTION is added

[John Hendy]

On Sun, Mar 17, 2013 at 6:20 PM, Jay Kerns <gjkernsysu@gmail.com> wrote:
> On Sun, Mar 17, 2013 at 6:21 PM, Nick Dokos <nicholas.dokos@hp.com> wrote:
>
> [snip]
>
>> I think the best way to deal with problems like this is to name your code blocks (and results blocks).
>>
>
> [snip]
>
> I can't speak for Li, but it works on my system and I like Nick's
> solution better than mine.

This is my preferred syntax as well. This has come up before on the
list; essentially any #+options syntax before an un-named #+results
block will cause the results to be re-inserted. #+begin_center or any
#+attr_backend options result in the same duplicate insertion of
results.


Also, just in case it's not known, you don't have to manually name the
#+results block. Just create your babel block with a #+name: attribute
and when you run it with C-c C-c, a named #+result will automatically
be created.

John

>
> Cheers,
>
> --
> Jay
>

Re: org-babel src block generated graphics included twice if CAPTION is added

[Eric Schulte]

I just pushed up a patch which should allow code blocks to find un-named
results even when there are comment lines (such as #+options or
#+attr_backend) between the code block and the results.

Hope this helps,

John Hendy <jw.hendy@gmail.com> writes:

> On Sun, Mar 17, 2013 at 6:20 PM, Jay Kerns <gjkernsysu@gmail.com> wrote:
>> On Sun, Mar 17, 2013 at 6:21 PM, Nick Dokos <nicholas.dokos@hp.com> wrote:
>>
>> [snip]
>>
>>> I think the best way to deal with problems like this is to name your code blocks (and results blocks).
>>>
>>
>> [snip]
>>
>> I can't speak for Li, but it works on my system and I like Nick's
>> solution better than mine.
>
> This is my preferred syntax as well. This has come up before on the
> list; essentially any #+options syntax before an un-named #+results
> block will cause the results to be re-inserted. #+begin_center or any
> #+attr_backend options result in the same duplicate insertion of
> results.
>
>
> Also, just in case it's not known, you don't have to manually name the
> #+results block. Just create your babel block with a #+name: attribute
> and when you run it with C-c C-c, a named #+result will automatically
> be created.
>
> John
>
>>
>> Cheers,
>>
>> --
>> Jay
>>
>

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

Re: org-babel src block generated graphics included twice if CAPTION is added

[Achim Gratz]

Eric Schulte writes:
> I just pushed up a patch which should allow code blocks to find
> un-named results even when there are comment lines (such as #+options
> or #+attr_backend) between the code block and the results.

Shouldn't babel use org-element for things like this?


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

DIY Stuff:
http://Synth.Stromeko.net/DIY.html

Re: org-babel src block generated graphics included twice if CAPTION is added

[Eric Schulte]

Achim Gratz <Stromeko@nexgo.de> writes:

> Eric Schulte writes:
>> I just pushed up a patch which should allow code blocks to find
>> un-named results even when there are comment lines (such as #+options
>> or #+attr_backend) between the code block and the results.
>
> Shouldn't babel use org-element for things like this?
>

Yes, and many many many other things.

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

Re: org-babel src block generated graphics included twice if CAPTION is added

[John Hendy]

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On Sun, Mar 17, 2013 at 8:15 PM, Li Bowen <a0050726@nus.edu.sg> wrote:
> Thanks, John.
>
> I also noticed that #+options can lead to re-insertion.
>
> Your piece of instruction should go to the online documentation. It will
> save people hours of time from trouble-shooting. I suppose any one who
writes a report with figures using org-babel will face the same problem.

I've got some other changes to make to Worg... I'll look for a place to put
this as well, though Eric's patch probably makes this obsolete now! At
least your post, the nth inquiry about it to the mailing list, has gotten
us a patch! That counts for something!

By the way, I've run into this very thing before as well :)
- http://osdir.com/ml/emacs-orgmode-gnu/2012-07/msg00230.html

John

>
> John Hendy <jw.hendy@gmail.com> writes:
>
>> On Sun, Mar 17, 2013 at 6:20 PM, Jay Kerns <gjkernsysu@gmail.com> wrote:
>>> On Sun, Mar 17, 2013 at 6:21 PM, Nick Dokos <nicholas.dokos@hp.com>
wrote:
>>>
>>> [snip]
>>>
>>>> I think the best way to deal with problems like this is to name your
code blocks (and results blocks).
>>>>
>>>
>>> [snip]
>>>
>>> I can't speak for Li, but it works on my system and I like Nick's
>>> solution better than mine.
>>
>> This is my preferred syntax as well. This has come up before on the
>> list; essentially any #+options syntax before an un-named #+results
>> block will cause the results to be re-inserted. #+begin_center or any
>> #+attr_backend options result in the same duplicate insertion of
>> results.
>>
>>
>> Also, just in case it's not known, you don't have to manually name the
>> #+results block. Just create your babel block with a #+name: attribute
>> and when you run it with C-c C-c, a named #+result will automatically
>> be created.
>>
>> John
>>
>>>
>>> Cheers,
>>>
>>> --
>>> Jay
>>>
>
> --
> Sincerely,
> Li Bowen.

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