Re: [BABEL] html export for R not working, but for sh and others

From: Rainer M Krug <r.m.krug@gmail.com>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode <emacs-orgmode@gnu.org>
Subject: Re: [BABEL] html export for R not working, but for sh and others
Date: Fri, 2 Jul 2010 09:44:23 +0200	[thread overview]
Message-ID: <AANLkTilnzm8tuDgnbQdR8q9dsqge9DuB0iLdb3H7AgSy@mail.gmail.com> (raw)
In-Reply-To: <87mxubqjrm.fsf@gmail.com>

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On Thu, Jul 1, 2010 at 5:55 PM, Eric Schulte <schulte.eric@gmail.com> wrote:

> Hi Rainer,
>

Hi Eric,

>
> Rainer M Krug <r.m.krug@gmail.com> writes:
>
> > Hi
> >
> > I am trying to export the attached test.org file to HTML, but I can only
> > export it, when I change the source block language to anything different
> > from R.
> >
> > I also attach my emacs.org file, but I am not doing any customisations
> to R.
> >
>
> I've just started up a minimal Emacs instance and loaded the babel
> portion of your attached config, but I am able to export your attached
> org file w/o error.  A couple of questions.
>
> 1) are you able to export to latex?  If so, then maybe the issue has to
>   do with fontification of R code by htmlize-buffer
>

Yes - export to latex (and from there to pdf) are working.

>
> 2) could you send in the actual error being reported by Emacs, or a
>   stack trace?
>
These are the messages in emacs:

Select command:
Exporting...
org-babel-exp processing...
Fontifying  *temp*... (regexps.............)
org-babel-exp processing...
font-lock-fontify-keywords-region: Invalid regexp: "Regular expression too
big"

How can I get a stack trace?

One more thing: if I start emacs with the -Q option, it works. So I assume
it is something in my emacs.org file. What is the easiest way to avoid that
source blocks under a heading in the emacs.org file are executed?

> >
> > In addition: if I specify :session *R* in #:BABEL: , the code is
> > evaluated, even though I specified :exports code. Is this intended?
> >
>
> Yes, this is for Sweave like behavior.
>
> If you have a session specified for every block in the buffer, and you
> are exporting the buffer, there are cases when you need a block to be
> executed (e.g. because it sets the value of a variable used by a
> subsequent block) even though you *do not* want the results of the block
> included in the final document.  To support these use cases, on export
> every block with a session is executed so that it's effects on the
> persist session takes place.
>

OK - that makes sense.
If you need any further info, please let me know.

Thanks,

Rainer

>
> Cheers -- Eric
>
> >
> > Thanks,
> >
> > Rainer
>

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Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
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