Spurious source-code output?

Spurious source-code output?

[Ken.Williams]

Hi,

I've got the following source-code section in a sample org-mode document:

#+BEGIN_SRC R :exports output :results graphics :file t.png
plot(1:10, 1:10)
#+END_SRC

My intention is to show just the figure, not the source code, when I export to HTML.  But when I do 'C-c C-c' to evaluate the code (which produces a "#+results:" section as expected) and then 'C-c C-e b' to produce the HTML, I'm getting both the source code and the plot in the output.

I must be misunderstanding the BEGIN_SRC parameters?  Could anyone correct me?

I'm using Org-mode 7.5 with Aquamacs 2.2 (GNU Emacs 23.3.1).  Thanks.

--
Ken Williams
Senior Research Scientist

Thomson Reuters

http://labs.thomsonreuters.com

Re: Spurious source-code output?

[Nick Dokos]

<Ken.Williams@thomsonreuters.com> wrote:

> Hi,
> 
> I've got the following source-code section in a sample org-mode document:
> 
> #+BEGIN_SRC R :exports output :results graphics :file t.png
> plot(1:10, 1:10)
> #+END_SRC
> 
> My intention is to show just the figure, not the source code, when I export=
>  to HTML.  But when I do 'C-c C-c' to evaluate the code (which produces a "=
> #+results:" section as expected) and then 'C-c C-e b' to produce the HTML, =
> I'm getting both the source code and the plot in the output.
> 
> I must be misunderstanding the BEGIN_SRC parameters?  Could anyone correct =
> me?
> 
> I'm using Org-mode 7.5 with Aquamacs 2.2 (GNU Emacs 23.3.1).  Thanks.
> 

Try ``:exports results'' - the Org manual says:

,----
| 
| 14.8.2.5 `:exports'
| ...................
| 
| The `:exports' header argument specifies what should be included in HTML
| or LaTeX exports of the Org-mode file.
| 
|    * `code' The default.  The body of code is included into the
|      exported file.  E.g., `:exports code'.
| 
|    * `results' The result of evaluating the code is included in the
|      exported file. E.g., `:exports results'.
| 
|    * `both' Both the code and results are included in the exported
|      file. E.g., `:exports both'.
| 
|    * `none' Nothing is included in the exported file.  E.g., `:exports
|      none'.
`----

Nick

Re: Spurious source-code output?

[Ken.Williams]

On 5/5/11 10:37 AM, "Nick Dokos" <nicholas.dokos@hp.com> wrote:

><Ken.Williams@thomsonreuters.com> wrote:
>
>> Hi,
>> 
>> I've got the following source-code section in a sample org-mode
>>document:
>> 
>> #+BEGIN_SRC R :exports output :results graphics :file t.png
>> plot(1:10, 1:10)
>> #+END_SRC
>> 
>>
>Try ``:exports results'' - the Org manual says:
>[...]


Ack, I even looked at that very section of the manual just moments before
I posted.  Thanks for the help.


--
Ken Williams
Senior Research Scientist
Thomson Reuters
http://labs.thomsonreuters.com

Re: Spurious source-code output?

[Nick Dokos]

<Ken.Williams@thomsonreuters.com> wrote:

> 
> 
> On 5/5/11 10:37 AM, "Nick Dokos" <nicholas.dokos@hp.com> wrote:
> 
> ><Ken.Williams@thomsonreuters.com> wrote:
> >
> >> Hi,
> >> 
> >> I've got the following source-code section in a sample org-mode
> >>document:
> >> 
> >> #+BEGIN_SRC R :exports output :results graphics :file t.png
> >> plot(1:10, 1:10)
> >> #+END_SRC
> >> 
> >>
> >Try ``:exports results'' - the Org manual says:
> >[...]
> 
> 
> Ack, I even looked at that very section of the manual just moments before
> I posted.  Thanks for the help.
> 

I also note that ``:results graphics'' is not one of the options in
section 14.8.2.2, ":results", of the Org manual - but I guess it's not
causing a problem. I'll leave it to a babel expert to chime in here.

Nick

Re: Spurious source-code output?

[Thomas S. Dye]

Hi Nick,

Without claiming to be a babel expert, :results graphics is a language- 
specific option used for e.g. R code blocks.  You can find it  
documented in the appropriate language-specific sections.

All the best,
Tom

On May 5, 2011, at 5:55 AM, Nick Dokos wrote:

> <Ken.Williams@thomsonreuters.com> wrote:
>
>>
>>
>> On 5/5/11 10:37 AM, "Nick Dokos" <nicholas.dokos@hp.com> wrote:
>>
>>> <Ken.Williams@thomsonreuters.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I've got the following source-code section in a sample org-mode
>>>> document:
>>>>
>>>> #+BEGIN_SRC R :exports output :results graphics :file t.png
>>>> plot(1:10, 1:10)
>>>> #+END_SRC
>>>>
>>>>
>>> Try ``:exports results'' - the Org manual says:
>>> [...]
>>
>>
>> Ack, I even looked at that very section of the manual just moments  
>> before
>> I posted.  Thanks for the help.
>>
>
> I also note that ``:results graphics'' is not one of the options in
> section 14.8.2.2, ":results", of the Org manual - but I guess it's not
> causing a problem. I'll leave it to a babel expert to chime in here.
>
> Nick
>

Re: Spurious source-code output?

[Nick Dokos]

Thomas S. Dye <tsd@tsdye.com> wrote:

> Hi Nick,
> 
> Without claiming to be a babel expert, :results graphics is a language- 
> specific option used for e.g. R code blocks.  You can find it  
> documented in the appropriate language-specific sections.
> 

OK - thanks for the clarification! It might be a good idea to note
(perhaps in section 14.8.2, "Specific header arguments", or perhaps its
parent?) that individual languages might provide extensions to the
standard header args. Also, the link in the manual (section 14.7, "Languages")
to language-specific documentation should probably be changed to

   http://orgmode.org/worg/org-contrib/babel/languages.html

which provides some useful context. The current link just takes you to
the directory listing. Trivial patch for the latter problem is appended.

Thanks,
Nick

diff --git a/doc/org.texi b/doc/org.texi
index a0f6638..8cf5535 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11639,7 +11639,7 @@ Code blocks in the following languages are supported.
 
 Language-specific documentation is available for some languages.  If
 available, it can be found at
-@uref{http://orgmode.org/worg/org-contrib/babel/languages}.
+@uref{http://orgmode.org/worg/org-contrib/babel/languages.html}.
 
 The @code{org-babel-load-languages} controls which languages are enabled for
 evaluation (by default only @code{emacs-lisp} is enabled).  This variable can

[Patch] Documentation, was Re: Spurious source-code output?

[Thomas S. Dye]

[-- Attachment #1: Type: text/plain, Size: 152 bytes --]

Hi Nick,

Thanks for fixing the documentation link.

Here is a patch that adds a reference to language-specific header  
arguments.

All the best,
Tom


[-- Attachment #2: 0001-Refer-to-language-specific-Babel-header-arguments.patch --]
[-- Type: application/octet-stream, Size: 860 bytes --]

From 825fe69d493dd2e7eef414b85340e8e27400f78d Mon Sep 17 00:00:00 2001
From: Tom Dye <tsd@tsdye.com>
Date: Thu, 5 May 2011 08:24:24 -1000
Subject: [PATCH] Refer to language specific Babel header arguments

---
 doc/org.texi |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

diff --git a/doc/org.texi b/doc/org.texi
index 7142ce0..98842ba 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11885,6 +11885,9 @@ The following header arguments are defined:
 * eval::                        Limit evaluation of specific code blocks
 @end menu
 
+Additional header arguments are defined on a language-specific basis, see
+@ref{Languages}. 
+
 @node var, results, Specific header arguments, Specific header arguments
 @subsubsection @code{:var}
 The @code{:var} header argument is used to pass arguments to code blocks.
-- 
1.7.1


[-- Attachment #3: Type: text/plain, Size: 1530 bytes --]




On May 5, 2011, at 7:45 AM, Nick Dokos wrote:

> Thomas S. Dye <tsd@tsdye.com> wrote:
>
>> Hi Nick,
>>
>> Without claiming to be a babel expert, :results graphics is a  
>> language-
>> specific option used for e.g. R code blocks.  You can find it
>> documented in the appropriate language-specific sections.
>>
>
> OK - thanks for the clarification! It might be a good idea to note
> (perhaps in section 14.8.2, "Specific header arguments", or perhaps  
> its
> parent?) that individual languages might provide extensions to the
> standard header args. Also, the link in the manual (section 14.7,  
> "Languages")
> to language-specific documentation should probably be changed to
>
>   http://orgmode.org/worg/org-contrib/babel/languages.html
>
> which provides some useful context. The current link just takes you to
> the directory listing. Trivial patch for the latter problem is  
> appended.
>
> Thanks,
> Nick
>
> diff --git a/doc/org.texi b/doc/org.texi
> index a0f6638..8cf5535 100644
> --- a/doc/org.texi
> +++ b/doc/org.texi
> @@ -11639,7 +11639,7 @@ Code blocks in the following languages are  
> supported.
>
> Language-specific documentation is available for some languages.  If
> available, it can be found at
> -@uref{http://orgmode.org/worg/org-contrib/babel/languages}.
> +@uref{http://orgmode.org/worg/org-contrib/babel/languages.html}.
>
> The @code{org-babel-load-languages} controls which languages are  
> enabled for
> evaluation (by default only @code{emacs-lisp} is enabled).  This  
> variable can

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Nick Dokos]

Thomas S. Dye <tsd@tsdye.com> wrote:

> Hi Nick,
> 
> Thanks for fixing the documentation link.
> 
> Here is a patch that adds a reference to language-specific header
> arguments.
> 

I think it's still the case that attachments of MIME type
application/octet-stream will not be recorded in patchwork.  Please use
one of the types that patchwork will recognize (text/plain is the best -
remember the Orgmode motto!) or just insert it inline.

See http://thread.gmane.org/gmane.emacs.orgmode/25727.

I'll add a note to that effect to org-contribute.html on Worg
unless somebody tells me otherwise.

Nick

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Thomas S. Dye]

Ack.  There were problems earlier with my Mac Mail client and line  
breaks, IIRC, but here is the patch in-line.  I'm not sure how to make  
attachments follow specific MIME requirements.

All the best,
Tom

 From 825fe69d493dd2e7eef414b85340e8e27400f78d Mon Sep 17 00:00:00 2001
From: Tom Dye <tsd@tsdye.com>
Date: Thu, 5 May 2011 08:24:24 -1000
Subject: [PATCH] Refer to language specific Babel header arguments

---
  doc/org.texi |    3 +++
  1 files changed, 3 insertions(+), 0 deletions(-)

diff --git a/doc/org.texi b/doc/org.texi
index 7142ce0..98842ba 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11885,6 +11885,9 @@ The following header arguments are defined:
  * eval::                        Limit evaluation of specific code  
blocks
  @end menu

+Additional header arguments are defined on a language-specific basis,  
see
+@ref{Languages}.
+
  @node var, results, Specific header arguments, Specific header  
arguments
  @subsubsection @code{:var}
  The @code{:var} header argument is used to pass arguments to code  
blocks.
-- 
1.7.1



On May 5, 2011, at 9:09 AM, Nick Dokos wrote:

> Thomas S. Dye <tsd@tsdye.com> wrote:
>
>> Hi Nick,
>>
>> Thanks for fixing the documentation link.
>>
>> Here is a patch that adds a reference to language-specific header
>> arguments.
>>
>
> I think it's still the case that attachments of MIME type
> application/octet-stream will not be recorded in patchwork.  Please  
> use
> one of the types that patchwork will recognize (text/plain is the  
> best -
> remember the Orgmode motto!) or just insert it inline.
>
> See http://thread.gmane.org/gmane.emacs.orgmode/25727.
>
> I'll add a note to that effect to org-contribute.html on Worg
> unless somebody tells me otherwise.
>
> Nick
>
>

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Nick Dokos]

Thomas S. Dye <tsd@tsdye.com> wrote:

> Ack.  There were problems earlier with my Mac Mail client and line
> breaks, IIRC, but here is the patch in-line.  I'm not sure how to make
> attachments follow specific MIME requirements.
> 

And as you feared, the line-break ogre struck again. They add all these
shiny knobs on the dashboard and make the wheels square: that's progress...

Nick

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Eric Schulte]

Applied, Thanks -- Eric

"Thomas S. Dye" <tsd@tsdye.com> writes:

> Hi Nick,
>
> Thanks for fixing the documentation link.
>
> Here is a patch that adds a reference to language-specific header
> arguments.
>
> All the best,
> Tom
>
>
>
>
>
> On May 5, 2011, at 7:45 AM, Nick Dokos wrote:
>
>> Thomas S. Dye <tsd@tsdye.com> wrote:
>>
>>> Hi Nick,
>>>
>>> Without claiming to be a babel expert, :results graphics is a
>>> language-
>>> specific option used for e.g. R code blocks.  You can find it
>>> documented in the appropriate language-specific sections.
>>>
>>
>> OK - thanks for the clarification! It might be a good idea to note
>> (perhaps in section 14.8.2, "Specific header arguments", or perhaps
>> its
>> parent?) that individual languages might provide extensions to the
>> standard header args. Also, the link in the manual (section 14.7,
>> "Languages")
>> to language-specific documentation should probably be changed to
>>
>>   http://orgmode.org/worg/org-contrib/babel/languages.html
>>
>> which provides some useful context. The current link just takes you to
>> the directory listing. Trivial patch for the latter problem is
>> appended.
>>
>> Thanks,
>> Nick
>>
>> diff --git a/doc/org.texi b/doc/org.texi
>> index a0f6638..8cf5535 100644
>> --- a/doc/org.texi
>> +++ b/doc/org.texi
>> @@ -11639,7 +11639,7 @@ Code blocks in the following languages are
>> supported.
>>
>> Language-specific documentation is available for some languages.  If
>> available, it can be found at
>> -@uref{http://orgmode.org/worg/org-contrib/babel/languages}.
>> +@uref{http://orgmode.org/worg/org-contrib/babel/languages.html}.
>>
>> The @code{org-babel-load-languages} controls which languages are
>> enabled for
>> evaluation (by default only @code{emacs-lisp} is enabled).  This
>> variable can
>

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

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Nick Dokos]

Nick Dokos <nicholas.dokos@hp.com> wrote:

> Thomas S. Dye <tsd@tsdye.com> wrote:
> 
> > Hi Nick,
> > 
> > Thanks for fixing the documentation link.
> > 
> > Here is a patch that adds a reference to language-specific header
> > arguments.
> > 
> 
> I think it's still the case that attachments of MIME type
> application/octet-stream will not be recorded in patchwork.  Please use
> one of the types that patchwork will recognize (text/plain is the best -
> remember the Orgmode motto!) or just insert it inline.
> 
> See http://thread.gmane.org/gmane.emacs.orgmode/25727.
> 
> I'll add a note to that effect to org-contribute.html on Worg
> unless somebody tells me otherwise.
> 

Note added: http://orgmode.org/worg/org-contribute.html#sec-4

Nick

Re: [Patch] Documentation, was Re: Spurious source-code output?

[Nick Dokos]

[-- Attachment #1: Type: text/plain, Size: 186 bytes --]

Here is Tom's patch as a text/plain attachment (I can't get to the
patchwork server right now - anybody? - but note that the version on
patchwork is probably line-break damaged).

Nick


[-- Attachment #2: Doc patch for language-specific code block headers --]
[-- Type: text/plain, Size: 834 bytes --]

From 825fe69d493dd2e7eef414b85340e8e27400f78d Mon Sep 17 00:00:00 2001
From: Tom Dye <tsd@tsdye.com>
Date: Thu, 5 May 2011 08:24:24 -1000
Subject: [PATCH] Refer to language specific Babel header arguments

---
 doc/org.texi |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

diff --git a/doc/org.texi b/doc/org.texi
index 7142ce0..98842ba 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11885,6 +11885,9 @@ The following header arguments are defined:
 * eval::                        Limit evaluation of specific code blocks
 @end menu
 
+Additional header arguments are defined on a language-specific basis, see
+@ref{Languages}. 
+
 @node var, results, Specific header arguments, Specific header arguments
 @subsubsection @code{:var}
 The @code{:var} header argument is used to pass arguments to code blocks.
-- 
1.7.1