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.