From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: [babel] Evaluating all source blocks in a document? Date: Wed, 30 Jun 2010 16:03:44 +0200 Message-ID: References: <20100630133310.GG25163@thinkpad.adamsinfoserv.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1761290650==" Return-path: Received: from [140.186.70.92] (port=53682 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1OTxtf-0005kt-3e for emacs-orgmode@gnu.org; Wed, 30 Jun 2010 10:04:22 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1OTxtU-0002Hm-6n for emacs-orgmode@gnu.org; Wed, 30 Jun 2010 10:04:12 -0400 Received: from mail-wy0-f169.google.com ([74.125.82.169]:47394) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1OTxtT-0002Ha-WE for emacs-orgmode@gnu.org; Wed, 30 Jun 2010 10:04:04 -0400 Received: by wyb39 with SMTP id 39so995365wyb.0 for ; Wed, 30 Jun 2010 07:04:00 -0700 (PDT) In-Reply-To: <20100630133310.GG25163@thinkpad.adamsinfoserv.com> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org --===============1761290650== Content-Type: multipart/alternative; boundary=0016367d674e7ea1ae048a3fd223 --0016367d674e7ea1ae048a3fd223 Content-Type: text/plain; charset=ISO-8859-1 Hi Russel On Wed, Jun 30, 2010 at 3:33 PM, Russell Adams 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 > > _______________________________________________ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > 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 --0016367d674e7ea1ae048a3fd223 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
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 w= rote:
> 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 co= de
> block, is it possible to evaluate ALL code blocks i a document? that w= ould
> make debugging much easier.

M-x org-babel-execute-buffer
=A0
Thank= s - that =A0seems to be what I am looking for, but after trying it out, I r= ealized the following: for each block, e new R session is opened. This does= not work for literate programming, as different blocks belong to each othe= r, 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 se= ssion 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.
=A0
Perhaps=A0that should be a feature request to log what src block or org fil= e
line number the errors occurred in.

Tha= t would be nice.


> Also: is it possible, to get some kind of automatic headings for the t= angled
> 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 n= ice, If each block (in the tangled file) would have a commented header spec= ifying the line number of the org-mode file where the block is located.=A0<= /div>

Thanks,

Rainer

<= /div>
=A0

Thanks.

------------------------------------------------------------------
Russell Adams =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0RLAdam= s@AdamsInfoServ.com

PGP Key ID: =A0 =A0 0x1160DCB3 =A0 =A0 =A0 =A0 =A0 http://www.adamsinfoserv.com/

Fingerprint: =A0 =A01723 D8CA 4280 1EC9 557F =A066E8 1154 E018 1160 DCB3

_______________________________________________
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Please use `Reply All' to send replies to the list.
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--
NEW GERMAN = FAX NUMBER!!!

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

Centre of Excellen= ce for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch UniversityMain Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:= =A0 =A0 =A0 =A0 =A0 +27 - (0)83 9479 042
Fax: =A0 =A0 =A0 =A0 =A0 =A0+2= 7 - (0)86 516 2782
Fax: =A0 =A0 =A0 =A0 =A0 =A0+49 - (0)321 2125 2244
email: =A0 =A0 =A0 = =A0 =A0Rainer@krugs.de

Skype:= =A0 =A0 =A0 =A0 =A0RMkrug
Google: =A0 =A0 =A0 =A0 R.M.Krug@gmail.com

--0016367d674e7ea1ae048a3fd223-- --===============1761290650== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode --===============1761290650==--