[babel] Evaluating all source blocks in a document?

[babel] Evaluating all source blocks in a document?

[Rainer M Krug]

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Hi

I use Org-babel for literate programming in R, but the tangling takes quite
long. Therefore my question: as it is possible to evaluate a single code
block, is it possible to evaluate ALL code blocks i a document? that would
make debugging much easier.

Also: is it possible, to get some kind of automatic headings for the tangled
code blocks? That would make it easier to identify in which code block the
source code in the tangled file comes from.

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: [babel] Evaluating all source blocks in a document?

[Russell Adams]

On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
> Hi
> 
> I use Org-babel for literate programming in R, but the tangling takes quite
> long. Therefore my question: as it is possible to evaluate a single code
> block, is it possible to evaluate ALL code blocks i a document? that would
> make debugging much easier.

M-x org-babel-execute-buffer

OTOH this may not make it easier to debug, the babel error window
doesn't list line numbers or blocks where the error occurred. Perhaps
that should be a feature request to log what src block or org file
line number the errors occurred in.

> Also: is it possible, to get some kind of automatic headings for the tangled
> code blocks? That would make it easier to identify in which code block the
> source code in the tangled file comes from.

I haven't tried tangling yet, is there a good tutorial somewhere?

Thanks.

------------------------------------------------------------------
Russell Adams                            RLAdams@AdamsInfoServ.com

PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/

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Re: [babel] Evaluating all source blocks in a document?

[Rainer M Krug]

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Hi Russel

On Wed, Jun 30, 2010 at 3:33 PM, Russell Adams <RLAdams@adamsinfoserv.com>wrote:

> On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
> > Hi
> >
> > I use Org-babel for literate programming in R, but the tangling takes
> quite
> > long. Therefore my question: as it is possible to evaluate a single code
> > block, is it possible to evaluate ALL code blocks i a document? that
> would
> > make debugging much easier.
>
> M-x org-babel-execute-buffer
>

Thanks - that  seems to be what I am looking for, but after trying it out, I
realized the following: for each block, e new R session is opened. This does
not work for literate programming, as different blocks belong to each other,
i.e. one block opens a function, the next one closes it. In addition, I want
to evaluate the results, i.e. created objects, in R - therefore the session
should stay open. So my guess: tangle and debug.

OTOH this may not make it easier to debug, the babel error window
> doesn't list line numbers or blocks where the error occurred.


True.


> Perhaps that should be a feature request to log what src block or org file
> line number the errors occurred in.
>

That would be nice.


> > Also: is it possible, to get some kind of automatic headings for the
> tangled
> > code blocks? That would make it easier to identify in which code block
> the
> > source code in the tangled file comes from.
>
> I haven't tried tangling yet, is there a good tutorial somewhere?
>

No idea - sorry. But it works really nice, If each block (in the tangled
file) would have a commented header specifying the line number of the
org-mode file where the block is located.

Thanks,

Rainer



>
> Thanks.
>
> ------------------------------------------------------------------
> Russell Adams                            RLAdams@AdamsInfoServ.com
>
> PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/
>
> Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3
>
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> Please use `Reply All' to send replies to the list.
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> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>



-- 
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: [babel] Evaluating all source blocks in a document?

[Erik Iverson]

Hello,

>     On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
>      > Hi
>      >
>      > I use Org-babel for literate programming in R, but the tangling
>     takes quite
>      > long. Therefore my question: as it is possible to evaluate a
>     single code
>      > block, is it possible to evaluate ALL code blocks i a document?
>     that would
>      > make debugging much easier.
> 
>     M-x org-babel-execute-buffer
> 

C-c C-v C-b should be a shortcut for that in org-mode now, according to 
my reference card.

>  
> Thanks - that  seems to be what I am looking for, but after trying it 
> out, I realized the following: for each block, e new R session is 
> opened. This does not work for literate programming, as different blocks 
> belong to each other, i.e. one block opens a function, the next one 
> closes it. In addition, I want to evaluate the results, i.e. created 
> objects, in R - therefore the session should stay open. So my guess: 
> tangle and debug.
> 
>     OTOH this may not make it easier to debug, the babel error window
>     doesn't list line numbers or blocks where the error occurred. 
> 

Have you tried the :session argument?  It submits the code block to a 
running R session.  I use it for what you're doing with success.  You 
can set it per code block, or buffer-wide, try for example:

#+PROPERTY: session *R*

> 
>     Perhaps that should be a feature request to log what src block or
>     org file
>     line number the errors occurred in.
> 
> 
> That would be nice.
> 
> 
>      > Also: is it possible, to get some kind of automatic headings for
>     the tangled
>      > code blocks? That would make it easier to identify in which code
>     block the
>      > source code in the tangled file comes from.

Try

(setq org-babel-tangle-w-comments t)

and see if that does what you're thinking.  It will give headings for 
the source block, but I don't recall  what information they contain.

Re: [babel] Evaluating all source blocks in a document?

[Eric Schulte]

Russell Adams <RLAdams@AdamsInfoServ.Com> writes:

[...]
>
> OTOH this may not make it easier to debug, the babel error window
> doesn't list line numbers or blocks where the error occurred. Perhaps
> that should be a feature request to log what src block or org file
> line number the errors occurred in.
>

I think most of the questions in the original e-mail have been addressed
(thanks Erik), however this raises a good point which I have just added
as a PROPOSED task on the Babel development log.

http://eschulte.github.com/babel-dev/PROPOSED-mention-block-name-or-number-in-error-windows.html

Thanks -- Eric

Re: [babel] Evaluating all source blocks in a document?

[Rainer M Krug]

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Hi Eric

On Wed, Jun 30, 2010 at 4:55 PM, Erik Iverson <eriki@ccbr.umn.edu> wrote:

> Hello,
>
>
>     On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
>>     > Hi
>>     >
>>     > I use Org-babel for literate programming in R, but the tangling
>>    takes quite
>>     > long. Therefore my question: as it is possible to evaluate a
>>    single code
>>     > block, is it possible to evaluate ALL code blocks i a document?
>>    that would
>>     > make debugging much easier.
>>
>>    M-x org-babel-execute-buffer
>>
>>
> C-c C-v C-b should be a shortcut for that in org-mode now, according to my
> reference card.


Thanks - I was looking for that one.


>
>   Thanks - that  seems to be what I am looking for, but after trying it
>> out, I realized the following: for each block, e new R session is opened.
>> This does not work for literate programming, as different blocks belong to
>> each other, i.e. one block opens a function, the next one closes it. In
>> addition, I want to evaluate the results, i.e. created objects, in R -
>> therefore the session should stay open. So my guess: tangle and debug.
>>
>>    OTOH this may not make it easier to debug, the babel error window
>>    doesn't list line numbers or blocks where the error occurred.
>>
>
> Have you tried the :session argument?  It submits the code block to a
> running R session.  I use it for what you're doing with success.  You can
> set it per code block, or buffer-wide, try for example:
>
> #+PROPERTY: session *R*


No - I actually have not looked at that one before, but that is exactly what
I was looking for.

I'll come back if I have any further questions.

Thanks a lot,

Rainer


>
>
>
>>    Perhaps that should be a feature request to log what src block or
>>    org file
>>    line number the errors occurred in.
>>
>>
>> That would be nice.
>>
>>
>>     > Also: is it possible, to get some kind of automatic headings for
>>    the tangled
>>     > code blocks? That would make it easier to identify in which code
>>    block the
>>     > source code in the tangled file comes from.
>>
>
> Try
>
> (setq org-babel-tangle-w-comments t)
>
> and see if that does what you're thinking.  It will give headings for the
> source block, but I don't recall  what information they contain.
>



-- 
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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