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