From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: [BABEL] html export for R not working, but for sh and others Date: Sat, 3 Jul 2010 20:42:55 +0200 Message-ID: References: <87mxubqjrm.fsf@gmail.com> <87r5jlts2w.fsf@gmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Return-path: Received: from [140.186.70.92] (port=55650 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1OV7g2-0006fz-Sk for emacs-orgmode@gnu.org; Sat, 03 Jul 2010 14:43:00 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1OV7g1-0001p7-1M for emacs-orgmode@gnu.org; Sat, 03 Jul 2010 14:42:58 -0400 Received: from mail-ww0-f49.google.com ([74.125.82.49]:53441) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1OV7g0-0001ot-KU for emacs-orgmode@gnu.org; Sat, 03 Jul 2010 14:42:57 -0400 Received: by wwi14 with SMTP id 14so3856568wwi.30 for ; Sat, 03 Jul 2010 11:42:55 -0700 (PDT) In-Reply-To: <87r5jlts2w.fsf@gmail.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: Eric Schulte Cc: emacs-orgmode Hi Eric On Saturday, July 3, 2010, Eric Schulte wrote: > Hi Rainer, > > My guess would be that the `htmlize-buffer' command which is used to > fontify code in html export is choking because the elisp below is > defining new fonts for R code. =A0If htmlize-buffer can't find the > definitions for these fonts then it will throw an error. > > I'm not sure what the solution would be, but I'm pretty sure that's the > source of the problem. If I find Time,I'll look into it and contact the original author. For the time being,i'll disable that Code Section. Thanks, Rainer > > Best -- Eric > > Rainer M Krug writes: > >> Hi Eric >> >> I traced the problem to the following section in my emacs.org file: >> >> * Syntax highlighting for functions in R >> =A0 based on https://mail.google.com/mail/#label/Lists%2FESS/125131ed246= 88970 >> =A0 The following code needs to be run in R: >> >> =A0 obj <- do.call("c", sapply(c("package:base", "package:stats", >> =A0 "package:utils"), objects, all.names=3DTRUE)) >> =A0 re <- "(^[^.[:alpha:][:digit:]]|<-|__)" =A0# to remove "weird" funct= ions >> =A0 obj <- obj[-grep(re, obj)] >> =A0 fpath <- file.path(Sys.getenv("HOME"), ".emacs.d", "R-function-names= .txt") >> =A0 write.table(obj, fpath, quote=3DFALSE, row.names=3DFALSE, col.names= =3DFALSE) >> >> =A0 Read a whole file into list of lines >> =A0 Author: Xah Lee >> =A0 see http://xahlee.org/emacs/elisp_process_lines.html >> #+begin_src emacs-lisp >> =A0 (defun read-lines (file) >> =A0 "Return a list of lines in FILE." >> =A0 (with-temp-buffer >> =A0 (insert-file-contents file) >> =A0 (split-string >> =A0 (buffer-string) "\n" t) >> =A0 ) >> =A0 ) >> >> =A0 (add-hook 'ess-mode-hook >> =A0 '(lambda() >> =A0 (setq ess-my-extra-R-function-keywords >> =A0 (read-lines "~/.emacs.d/R-function-names.txt")) >> =A0 (setq ess-R-mode-font-lock-keywords >> =A0 (append ess-R-mode-font-lock-keywords >> =A0 (list (cons (concat "\\<" (regexp-opt >> =A0 ess-my-extra-R-function-keywords 'enc-paren) "\\>") >> =A0 'font-lock-function-name-face)))))) >> >> If I disable that section, it works. Do you have any ideas if it could b= e >> changes? I don't know anything about emacs-lisp. >> >> Thanks, >> >> Rainer >> >> On Fri, Jul 2, 2010 at 9:44 AM, Rainer M Krug wrote= : >> >>> >>> >>> On Thu, Jul 1, 2010 at 5:55 PM, Eric Schulte wr= ote: >>> >>>> Hi Rainer, >>>> >>> >>> Hi Eric, >>> >>> >>>> >>>> Rainer M Krug writes: >>>> >>>> > Hi >>>> > >>>> > I am trying to export the attached test.org file to HTML, but I can >>>> only >>>> > export it, when I change the source block language to anything diffe= rent >>>> > from R. >>>> > >>>> > I also attach my emacs.org file, but I am not doing any customisatio= ns >>>> to R. >>>> > >>>> >>>> I've just started up a minimal Emacs instance and loaded the babel >>>> portion of your attached config, but I am able to export your attached >>>> org file w/o error. =A0A couple of questions. >>>> >>>> 1) are you able to export to latex? =A0If so, then maybe the issue has= to >>>> =A0 do with fontification of R code by htmlize-buffer >>>> >>> >>> Yes - export to latex (and from there to pdf) are working. >>> >>>> >>>> 2) could you send in the actual error being reported by Emacs, or a >>>> =A0 stack trace? >>>> >>> These are the messages in emacs: >>> >>> Select command: >>> Exporting... >>> org-babel-exp processing... >>> Fontifying =A0*temp*... (regexps.............) >>> org-babel-exp processing... >>> font-lock-fontify-keywords-region: Invalid regexp: "Regular expression = too >>> big" >>> >>> How can I get a stack trace? >>> >>> One more thing: if I start emacs with --=20 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