org-babel-tangle-w-comments has no effect in R?

org-babel-tangle-w-comments has no effect in R?

[Rainer M Krug]

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Hi

I am trying to use "tangle with comments". Based on a previous thread, I
set org-babel-tangle-w-comments to t with
 (setq org-babel-tangle-w-comments t)
in my emacs.org file.

The variable is actually set to 1 - I checked vie C-h - v

But nothing is changing in the tangled file? Am I doing something wrong? Or
are comments not supported in R in org-babel?

I attach a small testfile.

Cheers,

Rainer

-- 
NEW GERMAN FAX NUMBER!!!

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:           +27 - (0)83 9479 042
Fax:            +27 - (0)86 516 2782
Fax:            +49 - (0)321 2125 2244
email:          Rainer@krugs.de

Skype:          RMkrug
Google:         R.M.Krug@gmail.com

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#+TITLE:     test.org
#+AUTHOR:    Rainer M Krug
#+EMAIL:     rkrug@ecolmod
#+DATE:      2010-06-30 Wed
#+DESCRIPTION: 
#+KEYWORDS: 
#+LANGUAGE:  en
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS:   TeX:t LaTeX:nil skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js
#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+LINK_UP:   
#+LINK_HOME: 
#+XSLT: 

* TODO first
#+begin_src R :tangle test.R
  x <- 1:10
  y <- runif(10)
  print(x)
  plot(x,y)
#+end_src

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Re: org-babel-tangle-w-comments has no effect in R?

[Eric Schulte]

Hi Rainer,

There is one more requirement for tangling with comments, that is the
presence of a :comments header argument.  If this argument is not set
for a code block then that code block *will not* be tangled with
comments regardless of the value of `org-babel-tangle-w-comments'.

You can set this variable to default to true for R code blocks with the
following

  (add-to-list 'org-babel-default-header-args:R '(:comments . "yes"))

Hope this helps.

I think that moving forward it might make sense to remove the
org-babel-tangle-w-comments variable, as it's confusing to have two
points of control for comments during tangling.  Also, it looks like I
need to add the :comments header argument to the babel documentation.

Thanks for helping to sort some of these issues out!

Best -- Eric

Rainer M Krug <r.m.krug@gmail.com> writes:

> Hi
>
> I am trying to use "tangle with comments". Based on a previous thread, I
> set org-babel-tangle-w-comments to t with
>  (setq org-babel-tangle-w-comments t)
> in my emacs.org file.
>
> The variable is actually set to 1 - I checked vie C-h - v
>
> But nothing is changing in the tangled file? Am I doing something wrong? Or
> are comments not supported in R in org-babel?
>
> I attach a small testfile.
>
> Cheers,
>
> Rainer

Re: org-babel-tangle-w-comments has no effect in R?

[Rainer M Krug]

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On Thu, Jul 1, 2010 at 5:41 PM, Eric Schulte <schulte.eric@gmail.com> wrote:

> Hi Rainer,
>

Hi Eric


>
> There is one more requirement for tangling with comments, that is the
> presence of a :comments header argument.  If this argument is not set
> for a code block then that code block *will not* be tangled with
> comments regardless of the value of `org-babel-tangle-w-comments'.
>

That explains.


>
> You can set this variable to default to true for R code blocks with the
> following
>
>  (add-to-list 'org-babel-default-header-args:R '(:comments . "yes"))
>

OK - it is working.
What I actually did, was to add

   #+BABEL: :comments yes

to the headers of the file, so I can control it on a file basis.


> Hope this helps.
>

Definitely.


>
> I think that moving forward it might make sense to remove the
> org-babel-tangle-w-comments variable, as it's confusing to have two
> points of control for comments during tangling.  Also, it looks like I
> need to add the :comments header argument to the babel documentation.
>

Both points agreed.

In addition: is it possible to customize the format for all comments (on a
per file basis and / or a per block basis)? i.e. I don't need the file name,
as all blocks are coming from one file. I know about

  #+srcname: <name>

but is there a variable for the line number (I guess that is covered by the
request posted in another thread) one could use?

Also, would it be possible to include a link in the comment block, so that
clicking on that link actually opens the org-file file at the location of
the source block? That would make editing the code really easy.

Thanks for helping to sort some of these issues out!
>

Pleasure - I use them and I profit when they are sorted out. In addition: I
think org-mode and babel deserve it - they are great tools for programming
in R.

Cheers,

Rainer



>
> Best -- Eric
>
> Rainer M Krug <r.m.krug@gmail.com> writes:
>
> > Hi
> >
> > I am trying to use "tangle with comments". Based on a previous thread, I
> > set org-babel-tangle-w-comments to t with
> >  (setq org-babel-tangle-w-comments t)
> > in my emacs.org file.
> >
> > The variable is actually set to 1 - I checked vie C-h - v
> >
> > But nothing is changing in the tangled file? Am I doing something wrong?
> Or
> > are comments not supported in R in org-babel?
> >
> > I attach a small testfile.
> >
> > Cheers,
> >
> > Rainer
>



-- 
NEW GERMAN FAX NUMBER!!!

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:           +27 - (0)83 9479 042
Fax:            +27 - (0)86 516 2782
Fax:            +49 - (0)321 2125 2244
email:          Rainer@krugs.de

Skype:          RMkrug
Google:         R.M.Krug@gmail.com

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Re: org-babel-tangle-w-comments has no effect in R?

[Eric Schulte]

Hi Rainer,

Rainer M Krug <r.m.krug@gmail.com> writes:

[...]
>>
>> I think that moving forward it might make sense to remove the
>> org-babel-tangle-w-comments variable, as it's confusing to have two
>> points of control for comments during tangling.  Also, it looks like I
>> need to add the :comments header argument to the babel documentation.
>>
>
> Both points agreed.
>

Great, I'll put together a patch removing this variable.

>
> In addition: is it possible to customize the format for all comments
> (on a per file basis and / or a per block basis)? i.e. I don't need
> the file name, as all blocks are coming from one file. I know about
>
>   #+srcname: <name>
>
> but is there a variable for the line number (I guess that is covered by the
> request posted in another thread) one could use?
>

We could very easily introduce a customizable
`org-babel-tangle-comment-format-string', in fact I think this would be
a very good idea.

>
> Also, would it be possible to include a link in the comment block, so
> that clicking on that link actually opens the org-file file at the
> location of the source block? That would make editing the code really
> easy.
>

That was the goal of the current comment syntax, unfortunately I don't
know of a good way to activate Org-mode style links in the comments of
source code files.  Rest assured once that feature exists (and I know
about it) we'll have such links.

Best -- Eric

Re: org-babel-tangle-w-comments has no effect in R?

[Rainer M Krug]

Hi Eric

On Friday, July 2, 2010, Eric Schulte <schulte.eric@gmail.com> wrote:
> Hi Rainer,
>
> Rainer M Krug <r.m.krug@gmail.com> writes:
>
> [...]
>>>
>>> I think that moving forward it might make sense to remove the
>>> org-babel-tangle-w-comments variable, as it's confusing to have two
>>> points of control for comments during tangling.  Also, it looks like I
>>> need to add the :comments header argument to the babel documentation.
>>>
>>
>> Both points agreed.
>>
>
> Great, I'll put together a patch removing this variable.

Great.

>
>>
>> In addition: is it possible to customize the format for all comments
>> (on a per file basis and / or a per block basis)? i.e. I don't need
>> the file name, as all blocks are coming from one file. I know about
>>
>>   #+srcname: <name>
>>
>> but is there a variable for the line number (I guess that is covered by the
>> request posted in another thread) one could use?
>>
>
> We could very easily introduce a customizable
> `org-babel-tangle-comment-format-string', in fact I think this would be
> a very good idea.

Yes -  that would make the comment feature much more useful.

>
>>
>> Also, would it be possible to include a link in the comment block, so
>> that clicking on that link actually opens the org-file file at the
>> location of the source block? That would make editing the code really
>> easy.
>>
>
> That was the goal of the current comment syntax, unfortunately I don't
> know of a good way to activate Org-mode style links in the comments of
> source code files.  Rest assured once that feature exists (and I know
> about it) we'll have such links.

Sound great. That would actually make it perfect.

Cheers,

Rainer

>
> Best -- Eric
>

-- 
NEW GERMAN FAX NUMBER!!!

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:           +27 - (0)83 9479 042
Fax:            +27 - (0)86 516 2782
Fax:            +49 - (0)321 2125 2244
email:          Rainer@krugs.de

Skype:          RMkrug
Google:         R.M.Krug@gmail.com