* [BABEL] Bugin :session? Export html - works --- export pdf not @ 2010-07-08 10:42 Rainer M Krug 2010-07-08 18:40 ` Eric Schulte 0 siblings, 1 reply; 5+ messages in thread From: Rainer M Krug @ 2010-07-08 10:42 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1.1: Type: text/plain, Size: 921 bytes --] Hi I have the attached org file. It seems that when exporting to a pdf, the :session argument is ignored, as I get a Org-Babel Error Output buffer with: Error: object 'x' not found Execution halted and an Org-Babel Error buffer with the same text, and the resulting pdf does only show the code.. HTML export, works as expected. If I put :session *R_test* behind #+begin_src (R2.org) it works. 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: 1310 bytes --] [-- Attachment #2: R.org --] [-- Type: application/octet-stream, Size: 644 bytes --] #+TITLE: R.org #+AUTHOR: Rainer M Krug #+EMAIL: rkrug@ecolmod #+DATE: 2010-07-08 Thu #+DESCRIPTION: #+KEYWORDS: #+LANGUAGE: en #+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t #+OPTIONS: TeX:t LaTeX:nil skip:nil d:nil todo:t pri:nil tags:not-in-toc #+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js #+EXPORT_SELECT_TAGS: export #+EXPORT_EXCLUDE_TAGS: noexport #+LINK_UP: #+LINK_HOME: #+XSLT: #+BABEL: :session *R_test* * test 1 #+begin_src R :exports both x <- log(1:10) #+end_src #+begin_src R :exports both :results output x + x #+end_src [-- Attachment #3: R2.org --] [-- Type: application/octet-stream, Size: 682 bytes --] #+TITLE: R.org #+AUTHOR: Rainer M Krug #+EMAIL: rkrug@ecolmod #+DATE: 2010-07-08 Thu #+DESCRIPTION: #+KEYWORDS: #+LANGUAGE: en #+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t #+OPTIONS: TeX:t LaTeX:nil skip:nil d:nil todo:t pri:nil tags:not-in-toc #+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js #+EXPORT_SELECT_TAGS: export #+EXPORT_EXCLUDE_TAGS: noexport #+LINK_UP: #+LINK_HOME: #+XSLT: #+BABEL: :session *R_test* * test 1 #+begin_src R :exports both :session *R_test* x <- log(1:10) #+end_src #+begin_src R :exports both :results output :session *R_test* x + x #+end_src [-- Attachment #4: 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] 5+ messages in thread
* Re: [BABEL] Bugin :session? Export html - works --- export pdf not 2010-07-08 10:42 [BABEL] Bugin :session? Export html - works --- export pdf not Rainer M Krug @ 2010-07-08 18:40 ` Eric Schulte 2010-07-09 7:21 ` Rainer M Krug 0 siblings, 1 reply; 5+ messages in thread From: Eric Schulte @ 2010-07-08 18:40 UTC (permalink / raw) To: Rainer M Krug; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1392 bytes --] Hi Rainer, I am aware of this problem, and although I don't know any a good solution, I do have a good workaround (example attached [1]). The problem is that org-latex removes all of the #+ lines from the beginning of any Org-mode file which has headlines as part of the export process. This means that by the time it's Babel's turn to run code blocks, the #+BABEL line has been removed, and the session is not set. If there are no headlines, then this problem does not arise. I sent in a patch last week, [2] but it's application would have broken other features of the latex export, I've yet to work out a good solution to this. There is a decent work-around. Whenever there are no headlines, then the #+BABEL: line works fine on LaTeX export, when there are headlines, then header arguments can be placed as properties in the headlines to the same effect. Cheers -- Eric Rainer M Krug <r.m.krug@gmail.com> writes: > Hi > > I have the attached org file. > > It seems that when exporting to a pdf, the :session argument is ignored, as > I get a > Org-Babel Error Output buffer with: > Error: object 'x' not found > Execution halted > > and an Org-Babel Error buffer with the same text, and the resulting pdf does > only show the code.. > > HTML export, works as expected. > > If I put :session *R_test* behind #+begin_src (R2.org) it works. > > Cheers, > > Rainer Footnotes: [1] [-- Attachment #2: R.3.org --] [-- Type: application/octet-stream, Size: 661 bytes --] #+TITLE: R.org #+AUTHOR: Rainer M Krug #+EMAIL: rkrug@ecolmod #+DATE: 2010-07-08 Thu #+DESCRIPTION: #+KEYWORDS: #+LANGUAGE: en #+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t #+OPTIONS: TeX:t LaTeX:nil skip:nil d:nil todo:t pri:nil tags:not-in-toc #+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js #+EXPORT_SELECT_TAGS: export #+EXPORT_EXCLUDE_TAGS: noexport #+LINK_UP: #+LINK_HOME: #+XSLT: * test 1 :PROPERTIES: :session: *R_test* :END: #+begin_src R :exports both x <- log(1:10) #+end_src #+begin_src R :exports both :results output x + x #+end_src [-- Attachment #3: Type: text/plain, Size: 58 bytes --] [2] http://thread.gmane.org/gmane.emacs.orgmode/27081 [-- Attachment #4: 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] 5+ messages in thread
* Re: [BABEL] Bugin :session? Export html - works --- export pdf not 2010-07-08 18:40 ` Eric Schulte @ 2010-07-09 7:21 ` Rainer M Krug 2010-07-09 8:00 ` Carsten Dominik 0 siblings, 1 reply; 5+ messages in thread From: Rainer M Krug @ 2010-07-09 7:21 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode [-- Attachment #1.1: Type: text/plain, Size: 2539 bytes --] On Thu, Jul 8, 2010 at 8:40 PM, Eric Schulte <schulte.eric@gmail.com> wrote: > Hi Rainer, > Hi Eric > > I am aware of this problem, and although I don't know any a good > solution, I do have a good workaround (example attached [1]). > That workaround looks really good - thanks. Much better then putting :session at the beginning of each source block. > > The problem is that org-latex removes all of the #+ lines from the > beginning of any Org-mode file which has headlines as part of the export > process. This means that by the time it's Babel's turn to run code > blocks, the #+BABEL line has been removed, and the session is not set. > If there are no headlines, then this problem does not arise. > OK - that explains. > > I sent in a patch last week, [2] but it's application would have broken > other features of the latex export, I've yet to work out a good solution > to this. > > There is a decent work-around. Whenever there are no headlines, then > the #+BABEL: line works fine on LaTeX export, when there are headlines, > then header arguments can be placed as properties in the headlines to > the same effect. > Would it be possible to issue a warning if a #+BABEL line is stripped by LaTeX? If I think back, this stripping cost me quite some time to figure out why things are working differently when exporting to LaTeX then html. > > Cheers -- Eric > Cheers, Rainer > > Rainer M Krug <r.m.krug@gmail.com> writes: > > > Hi > > > > I have the attached org file. > > > > It seems that when exporting to a pdf, the :session argument is ignored, > as > > I get a > > Org-Babel Error Output buffer with: > > Error: object 'x' not found > > Execution halted > > > > and an Org-Babel Error buffer with the same text, and the resulting pdf > does > > only show the code.. > > > > HTML export, works as expected. > > > > If I put :session *R_test* behind #+begin_src (R2.org) it works. > > > > Cheers, > > > > Rainer > > Footnotes: > [1] > > > [2] http://thread.gmane.org/gmane.emacs.orgmode/27081 > > > -- 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: 4179 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] 5+ messages in thread
* Re: [BABEL] Bugin :session? Export html - works --- export pdf not 2010-07-09 7:21 ` Rainer M Krug @ 2010-07-09 8:00 ` Carsten Dominik 2010-07-09 15:54 ` Eric Schulte 0 siblings, 1 reply; 5+ messages in thread From: Carsten Dominik @ 2010-07-09 8:00 UTC (permalink / raw) To: Rainer M Krug; +Cc: emacs-orgmode On Jul 9, 2010, at 9:21 AM, Rainer M Krug wrote: > > > On Thu, Jul 8, 2010 at 8:40 PM, Eric Schulte > <schulte.eric@gmail.com> wrote: > Hi Rainer, > > Hi Eric > > > I am aware of this problem, and although I don't know any a good > solution, I do have a good workaround (example attached [1]). > > That workaround looks really good - thanks. Much better then > putting :session at the beginning of each source block. > > > The problem is that org-latex removes all of the #+ lines from the > beginning of any Org-mode file which has headlines as part of the > export > process. This means that by the time it's Babel's turn to run code > blocks, the #+BABEL line has been removed, and the session is not set. > If there are no headlines, then this problem does not arise. > > OK - that explains. > > > I sent in a patch last week, [2] but it's application would have > broken > other features of the latex export, I've yet to work out a good > solution > to this. > > There is a decent work-around. Whenever there are no headlines, then > the #+BABEL: line works fine on LaTeX export, when there are > headlines, > then header arguments can be placed as properties in the headlines to > the same effect. > > Would it be possible to issue a warning if a #+BABEL line is > stripped by LaTeX? If I think back, this stripping cost me quite > some time to figure out why things are working differently when > exporting to LaTeX then html. No, we really need to fix this. Can someone please try if the following patch does fix this issue? diff --git a/lisp/org-latex.el b/lisp/org-latex.el index 70298fd..3cfa36c 100644 --- a/lisp/org-latex.el +++ b/lisp/org-latex.el @@ -1221,9 +1221,16 @@ If END is non-nil, it is the end of the region." :timestamps (plist-get opt-plist :timestamps) :footnotes (plist-get opt-plist :footnotes))) (org-unmodified - (let ((inhibit-read-only t)) - (add-text-properties pt (max pt (1- end)) - '(:org-license-to-kill t)))))))) + (let ((inhibit-read-only t) + (limit (max pt (1- end)))) + (add-text-properties pt limit + '(:org-license-to-kill t)) + (save-excursion + (goto-char pt) + (while (re-search-forward "^[ \t]*#+.*\n?" limit t) + (remove-text-properties (match-beginning 0) (match-end 0) + '(:org-license-to-kill t)))))))))) + (defvar org-export-latex-header-defs nil "The header definitions that might be used in the LaTeX body.") Thanks - Carsten > > > > Cheers -- Eric > > Cheers, > > Rainer > > > Rainer M Krug <r.m.krug@gmail.com> writes: > > > Hi > > > > I have the attached org file. > > > > It seems that when exporting to a pdf, the :session argument is > ignored, as > > I get a > > Org-Babel Error Output buffer with: > > Error: object 'x' not found > > Execution halted > > > > and an Org-Babel Error buffer with the same text, and the > resulting pdf does > > only show the code.. > > > > HTML export, works as expected. > > > > If I put :session *R_test* behind #+begin_src (R2.org) it works. > > > > Cheers, > > > > Rainer > > Footnotes: > [1] > > > [2] http://thread.gmane.org/gmane.emacs.orgmode/27081 > > > > > > -- > 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 > > _______________________________________________ > 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 - Carsten ^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [BABEL] Bugin :session? Export html - works --- export pdf not 2010-07-09 8:00 ` Carsten Dominik @ 2010-07-09 15:54 ` Eric Schulte 0 siblings, 0 replies; 5+ messages in thread From: Eric Schulte @ 2010-07-09 15:54 UTC (permalink / raw) To: Carsten Dominik; +Cc: emacs-orgmode, Rainer M Krug Carsten Dominik <carsten.dominik@gmail.com> writes: [...] > > No, we really need to fix this. > > Can someone please try if the following patch does fix this issue? > Hi Carsten, I've just tested your patch against the following minimal example, and it does fix the problem, in that both of the R blocks now use the session from the #+BABEL: header. --8<---------------cut here---------------start------------->8--- #+Title: testing preservation of babel header #+Author: Eric #+BABEL: :session *R* * top header #+begin_src R :exports code x <- 1 #+end_src The result from the above block + 1 should be src_R{x+1}. --8<---------------cut here---------------end--------------->8--- Additionally I tested it against the in example which my previous patch was causing errors, namely --8<---------------cut here---------------start------------->8--- #+OPTIONS: skip:nil text before first * Test \begin{equation} E=mc^2 \end{equation} --8<---------------cut here---------------end--------------->8--- and this exported without problem. So it looks to me like this patch should be applied. Thanks for implementing a solution here. Best -- Eric ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2010-07-09 15:54 UTC | newest] Thread overview: 5+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2010-07-08 10:42 [BABEL] Bugin :session? Export html - works --- export pdf not Rainer M Krug 2010-07-08 18:40 ` Eric Schulte 2010-07-09 7:21 ` Rainer M Krug 2010-07-09 8:00 ` Carsten Dominik 2010-07-09 15:54 ` Eric Schulte
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