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: Thu, 1 Jul 2010 09:05:15 +0200 Message-ID: References: <20100630133310.GG25163@thinkpad.adamsinfoserv.com> <4C2B5AD9.1080202@ccbr.umn.edu> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1537419529==" Return-path: Received: from [140.186.70.92] (port=48522 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1OUDpo-0006Dr-2W for emacs-orgmode@gnu.org; Thu, 01 Jul 2010 03:05:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1OUDpl-0003ZR-92 for emacs-orgmode@gnu.org; Thu, 01 Jul 2010 03:05:19 -0400 Received: from mail-ww0-f49.google.com ([74.125.82.49]:36787) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1OUDpk-0003ZE-SN for emacs-orgmode@gnu.org; Thu, 01 Jul 2010 03:05:17 -0400 Received: by wwi14 with SMTP id 14so1189960wwi.30 for ; Thu, 01 Jul 2010 00:05:16 -0700 (PDT) In-Reply-To: <4C2B5AD9.1080202@ccbr.umn.edu> 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: Erik Iverson Cc: emacs-orgmode@gnu.org --===============1537419529== Content-Type: multipart/alternative; boundary=000e0cd61d84abcb0e048a4e1757 --000e0cd61d84abcb0e048a4e1757 Content-Type: text/plain; charset=ISO-8859-1 Hi Eric On Wed, Jun 30, 2010 at 4:55 PM, Erik Iverson 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 --000e0cd61d84abcb0e048a4e1757 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Eric

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


=A0 =A0On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
=A0 =A0 > Hi
=A0 =A0 >
=A0 =A0 > I use Org-babel for literate programming in R, but the tangli= ng
=A0 =A0takes quite
=A0 =A0 > long. Therefore my question: as it is possible to evaluate a<= br> =A0 =A0single code
=A0 =A0 > block, is it possible to evaluate ALL code blocks i a documen= t?
=A0 =A0that would
=A0 =A0 > make debugging much easier.

=A0 =A0M-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.=A0



=A0Thanks - that =A0seems 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. T= his does not work for literate programming, as different blocks belong to e= ach other, i.e. one block opens a function, the next one closes it. In addi= tion, I want to evaluate the results, i.e. created objects, in R - therefor= e the session should stay open. So my guess: tangle and debug.

=A0 =A0OTOH this may not make it easier to debug, the babel error window =A0 =A0doesn't list line numbers or blocks where the error occurred. <= br>

Have you tried the :session argument? =A0It submits the code block to a run= ning R session. =A0I use it for what you're doing with success. =A0You = can set it per code block, or buffer-wide, try for example:

#+PROPERTY: session *R*

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

I'll come back if I have any further questio= ns.

Thanks a lot,

Rainer
=A0



=A0 =A0Perhaps that should be a feature request to log what src block or =A0 =A0org file
=A0 =A0line number the errors occurred in.


That would be nice.


=A0 =A0 > Also: is it possible, to get some kind of automatic headings = for
=A0 =A0the tangled
=A0 =A0 > code blocks? That would make it easier to identify in which c= ode
=A0 =A0block the
=A0 =A0 > 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. =A0It will give headings for= the source block, but I don't recall =A0what 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 Invas= ion 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

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