Using :results output org with new exporter exporting as verbatim with LaTeX

Using :results output org with new exporter exporting as verbatim with LaTeX

[John Hendy]

I have an org file with R src block that spits out some file names to
embed. I don't think I need to reproduce the block for testing
purposes, but the gist is that I use cat() to spit out some
=#+begin_center= and =[[filename]]= stuff.

R code block header:

#+name: src-block-name
#+begin_src R :session r :exports results :results output org


I'm getting a results block like so:

#+RESULTS: src-block-name
#+BEGIN_SRC org

[[./plots/filename1.pdf]]

[[./plots/filename2.pdf]]

[[./plots/filename3.pdf]]

#+END_SRC

I used this setup previously (and successfully) as described in this
mailing list thread. That particular post described my near successful
block, with the same sort of cat(paste()) commands I was using to
output the filenames in [[filename.pdf]] orgmode syntax. The final
success happened at the very end when Eric Schulte suggested I change
from :results output raw to :results output org.
- http://lists.gnu.org/archive/html/emacs-orgmode/2012-08/msg01222.html

Hence, I started with :results output org this time, but it didn't
work. It's being exported verbatim using =C-c C-e l p=. (Appears in
\begin{verbatim} ... \end{verbatim} in the output .tex file)

If I change to :results output raw, I simply get:

#+results

[[filename.pdf]]

This exports correctly.

If I change the :results output org #+results block to the following,
it also works correctly:

#+begin_org

[[filename.pdf]]

#+end_org

From the ob-doc-R, it appears that orgmode export might be expecting
#+begin_org, not #+begin_src org:
- http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html

#+begin_quote
The Org Mode source code block specifies :results org so the output is
wrapped in #+BEGIN_ORG … #+END_ORG. This way, arbitrary output can be
included and easily replaced on subsequent evaluations of the source
code block.
#+end_quote


Let me know the current proper way to accomplish what I'm trying to do.



Thanks,
John

Re: Using :results output org with new exporter exporting as verbatim with LaTeX

[Eric Schulte]

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

> I have an org file with R src block that spits out some file names to
> embed. I don't think I need to reproduce the block for testing
> purposes, but the gist is that I use cat() to spit out some
> =#+begin_center= and =[[filename]]= stuff.
>
> R code block header:
>
> #+name: src-block-name
> #+begin_src R :session r :exports results :results output org
>
>
> I'm getting a results block like so:
>
> #+RESULTS: src-block-name
> #+BEGIN_SRC org
>
> [[./plots/filename1.pdf]]
>
> [[./plots/filename2.pdf]]
>
> [[./plots/filename3.pdf]]
>
> #+END_SRC
>
> I used this setup previously (and successfully) as described in this
> mailing list thread. That particular post described my near successful
> block, with the same sort of cat(paste()) commands I was using to
> output the filenames in [[filename.pdf]] orgmode syntax. The final
> success happened at the very end when Eric Schulte suggested I change
> from :results output raw to :results output org.
> - http://lists.gnu.org/archive/html/emacs-orgmode/2012-08/msg01222.html
>
> Hence, I started with :results output org this time, but it didn't
> work. It's being exported verbatim using =C-c C-e l p=. (Appears in
> \begin{verbatim} ... \end{verbatim} in the output .tex file)
>
> If I change to :results output raw, I simply get:
>
> #+results
>
> [[filename.pdf]]
>
> This exports correctly.
>
> If I change the :results output org #+results block to the following,
> it also works correctly:
>
> #+begin_org
>
> [[filename.pdf]]
>
> #+end_org
>
> From the ob-doc-R, it appears that orgmode export might be expecting
> #+begin_org, not #+begin_src org:
> - http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html
>
> #+begin_quote
> The Org Mode source code block specifies :results org so the output is
> wrapped in #+BEGIN_ORG & #+END_ORG. This way, arbitrary output can be
> included and easily replaced on subsequent evaluations of the source
> code block.
> #+end_quote
>
>
> Let me know the current proper way to accomplish what I'm trying to do.
>
>
>
> Thanks,
> John
>

Hi John,

There has been some churn in results handling in the last year, in part
this is related to the new exporter.  I think the following is the
current best approach.

    #+begin_src sh :results output wrap
    cat <<EOF
    [[./plots/filename1.pdf]]

    [[./plots/filename2.pdf]]

    [[./plots/filename3.pdf]]
    EOF
    #+end_src

    #+RESULTS:
    :RESULTS:
    [[./plots/filename1.pdf]]

    [[./plots/filename2.pdf]]

    [[./plots/filename3.pdf]]
    :END:

I do feel bad that we had to add yet another results type (i.e. "wrap"),
but as I recall there were very good reasons for this decision and it
has made things cleaner on the implementation side.

Cheers,

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

Re: Using :results output org with new exporter exporting as verbatim with LaTeX

[John Hendy]

On Sat, Mar 23, 2013 at 5:12 PM, Eric Schulte <schulte.eric@gmail.com> wrote:
> John Hendy <jw.hendy@gmail.com> writes:
>
>> I have an org file with R src block that spits out some file names to
>> embed. I don't think I need to reproduce the block for testing
>> purposes, but the gist is that I use cat() to spit out some
>> =#+begin_center= and =[[filename]]= stuff.
>>
>> R code block header:
>>
>> #+name: src-block-name
>> #+begin_src R :session r :exports results :results output org
>>
>>
>> I'm getting a results block like so:
>>
>> #+RESULTS: src-block-name
>> #+BEGIN_SRC org
>>
>> [[./plots/filename1.pdf]]
>>
>> [[./plots/filename2.pdf]]
>>
>> [[./plots/filename3.pdf]]
>>
>> #+END_SRC
>>
>> I used this setup previously (and successfully) as described in this
>> mailing list thread. That particular post described my near successful
>> block, with the same sort of cat(paste()) commands I was using to
>> output the filenames in [[filename.pdf]] orgmode syntax. The final
>> success happened at the very end when Eric Schulte suggested I change
>> from :results output raw to :results output org.
>> - http://lists.gnu.org/archive/html/emacs-orgmode/2012-08/msg01222.html
>>
>> Hence, I started with :results output org this time, but it didn't
>> work. It's being exported verbatim using =C-c C-e l p=. (Appears in
>> \begin{verbatim} ... \end{verbatim} in the output .tex file)
>>
>> If I change to :results output raw, I simply get:
>>
>> #+results
>>
>> [[filename.pdf]]
>>
>> This exports correctly.
>>
>> If I change the :results output org #+results block to the following,
>> it also works correctly:
>>
>> #+begin_org
>>
>> [[filename.pdf]]
>>
>> #+end_org
>>
>> From the ob-doc-R, it appears that orgmode export might be expecting
>> #+begin_org, not #+begin_src org:
>> - http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html
>>
>> #+begin_quote
>> The Org Mode source code block specifies :results org so the output is
>> wrapped in #+BEGIN_ORG & #+END_ORG. This way, arbitrary output can be
>> included and easily replaced on subsequent evaluations of the source
>> code block.
>> #+end_quote
>>
>>
>> Let me know the current proper way to accomplish what I'm trying to do.
>>
>>
>>
>> Thanks,
>> John
>>
>
> Hi John,
>
> There has been some churn in results handling in the last year, in part
> this is related to the new exporter.  I think the following is the
> current best approach.
>
>     #+begin_src sh :results output wrap
>     cat <<EOF
>     [[./plots/filename1.pdf]]
>
>     [[./plots/filename2.pdf]]
>
>     [[./plots/filename3.pdf]]
>     EOF
>     #+end_src
>
>     #+RESULTS:
>     :RESULTS:
>     [[./plots/filename1.pdf]]
>
>     [[./plots/filename2.pdf]]
>
>     [[./plots/filename3.pdf]]
>     :END:
>
> I do feel bad that we had to add yet another results type (i.e. "wrap"),
> but as I recall there were very good reasons for this decision and it
> has made things cleaner on the implementation side.

I'm fine with whatever, though I think ob-R-doc is in need of a
refresher, since I don't particularly think raw vs. org (and now wrap,
which is non-existent in formal documentation from what I've seen) is
explained extremely well. I'd be happy to help, but I don't understand
the differences myself.

For example, in our previous discussion (from the thread linked in my
original post), it seems like raw was the /gist/ of what I wanted, but
raw didn't know how to replace org-specific syntax [[filename]]
properly, so I needed org.

I also can't find any references to =output wrap=. Tried googling
=output wrap R orgmode babel= and then ="output wrap" R orgmode babel=
to try to find some discussions on this.


Thanks for letting me know,
John

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

Re: Using :results output org with new exporter exporting as verbatim with LaTeX

[Charles Berry]

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

[deleted]

> wrap [...] is non-existent in formal documentation from what I've seen

It is in the manual:

  14.8.2.23 `:wrap'

See 

  http://orgmode.org/manual/wrap.html#wrap

or from emacs:

  C-h i m org RET C-s wrap RET RET

HTH,

Chuck

Re: Using :results output org with new exporter exporting as verbatim with LaTeX

[John Hendy]

On Sun, Mar 24, 2013 at 11:00 AM, Charles Berry <ccberry@ucsd.edu> wrote:
> John Hendy <jw.hendy <at> gmail.com> writes:
>
> [deleted]
>
>> wrap [...] is non-existent in formal documentation from what I've seen
>
> It is in the manual:
>
>   14.8.2.23 `:wrap'
>
> See
>
>   http://orgmode.org/manual/wrap.html#wrap
>
> or from emacs:
>
>   C-h i m org RET C-s wrap RET RET

Ah. Forgive my denseness! I guess I'm just perplexed by what "level"
these options fall in. The suggestion was to use =:results output
wrap=, not :wrap (hence searching for that instead of just ":wrap".
:wrap gets it's own high level documentation page while the other
options used similarly (if =:results output wrap= is the right syntax)
seem to be considred "sub options" of something else:
- http://orgmode.org/manual/results.html#results

(Also note that =wrap= doesn't appear on that list, even though it
does work with :results output). On that note, is there a discernible
difference in practice between:

:wrap syntax:

#+begin_results
blah
#+end_results

and :results output wrap syntax:

:results:
blah
:end:

John


>
> HTH,
>
> Chuck
>
>