* [babel] Evaluating all source blocks in a document? @ 2010-06-30 11:35 Rainer M Krug 2010-06-30 13:33 ` Russell Adams 0 siblings, 1 reply; 6+ messages in thread From: Rainer M Krug @ 2010-06-30 11:35 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1.1: Type: text/plain, Size: 976 bytes --] 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. 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. Cheers, Rainer -- 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 [-- Attachment #1.2: Type: text/html, Size: 1245 bytes --] [-- Attachment #2: Type: text/plain, Size: 201 bytes --] _______________________________________________ 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 ^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [babel] Evaluating all source blocks in a document? 2010-06-30 11:35 [babel] Evaluating all source blocks in a document? Rainer M Krug @ 2010-06-30 13:33 ` Russell Adams 2010-06-30 14:03 ` Rainer M Krug 2010-06-30 16:35 ` Eric Schulte 0 siblings, 2 replies; 6+ messages in thread From: Russell Adams @ 2010-06-30 13:33 UTC (permalink / raw) To: emacs-orgmode 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 OTOH this may not make it easier to debug, the babel error window doesn't list line numbers or blocks where the error occurred. Perhaps that should be a feature request to log what src block or org file line number the errors occurred in. > 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? 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 ^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [babel] Evaluating all source blocks in a document? 2010-06-30 13:33 ` Russell Adams @ 2010-06-30 14:03 ` Rainer M Krug 2010-06-30 14:55 ` Erik Iverson 2010-06-30 16:35 ` Eric Schulte 1 sibling, 1 reply; 6+ messages in thread From: Rainer M Krug @ 2010-06-30 14:03 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1.1: Type: text/plain, Size: 2698 bytes --] 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 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 [-- Attachment #1.2: Type: text/html, Size: 4192 bytes --] [-- Attachment #2: Type: text/plain, Size: 201 bytes --] _______________________________________________ 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 ^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [babel] Evaluating all source blocks in a document? 2010-06-30 14:03 ` Rainer M Krug @ 2010-06-30 14:55 ` Erik Iverson 2010-07-01 7:05 ` Rainer M Krug 0 siblings, 1 reply; 6+ messages in thread From: Erik Iverson @ 2010-06-30 14:55 UTC (permalink / raw) To: Rainer M Krug; +Cc: emacs-orgmode 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 - 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* > > 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. ^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [babel] Evaluating all source blocks in a document? 2010-06-30 14:55 ` Erik Iverson @ 2010-07-01 7:05 ` Rainer M Krug 0 siblings, 0 replies; 6+ messages in thread From: Rainer M Krug @ 2010-07-01 7:05 UTC (permalink / raw) To: Erik Iverson; +Cc: emacs-orgmode [-- Attachment #1.1: Type: text/plain, Size: 2793 bytes --] Hi Eric 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. > -- 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 [-- Attachment #1.2: Type: text/html, Size: 4153 bytes --] [-- Attachment #2: Type: text/plain, Size: 201 bytes --] _______________________________________________ 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 ^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [babel] Evaluating all source blocks in a document? 2010-06-30 13:33 ` Russell Adams 2010-06-30 14:03 ` Rainer M Krug @ 2010-06-30 16:35 ` Eric Schulte 1 sibling, 0 replies; 6+ messages in thread From: Eric Schulte @ 2010-06-30 16:35 UTC (permalink / raw) To: emacs-orgmode Russell Adams <RLAdams@AdamsInfoServ.Com> writes: [...] > > OTOH this may not make it easier to debug, the babel error window > doesn't list line numbers or blocks where the error occurred. Perhaps > that should be a feature request to log what src block or org file > line number the errors occurred in. > I think most of the questions in the original e-mail have been addressed (thanks Erik), however this raises a good point which I have just added as a PROPOSED task on the Babel development log. http://eschulte.github.com/babel-dev/PROPOSED-mention-block-name-or-number-in-error-windows.html Thanks -- Eric ^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2010-07-01 7:05 UTC | newest] Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2010-06-30 11:35 [babel] Evaluating all source blocks in a document? Rainer M Krug 2010-06-30 13:33 ` Russell Adams 2010-06-30 14:03 ` Rainer M Krug 2010-06-30 14:55 ` Erik Iverson 2010-07-01 7:05 ` Rainer M Krug 2010-06-30 16:35 ` Eric Schulte
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