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: Fri, 2 Jul 2010 14:37:54 +0200 Message-ID: References: <87mxubqjrm.fsf@gmail.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1435353209==" Return-path: Received: from [140.186.70.92] (port=42202 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1OUfVH-0000Ce-NH for emacs-orgmode@gnu.org; Fri, 02 Jul 2010 08:38:01 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1OUfVF-0006hw-Kf for emacs-orgmode@gnu.org; Fri, 02 Jul 2010 08:37:59 -0400 Received: from mail-px0-f169.google.com ([209.85.212.169]:37981) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1OUfVF-0006hm-9d for emacs-orgmode@gnu.org; Fri, 02 Jul 2010 08:37:57 -0400 Received: by pxi17 with SMTP id 17so3051860pxi.0 for ; Fri, 02 Jul 2010 05:37:55 -0700 (PDT) In-Reply-To: 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 --===============1435353209== Content-Type: multipart/alternative; boundary=001636417d4d1edebc048a66db97 --001636417d4d1edebc048a66db97 Content-Type: text/plain; charset=ISO-8859-1 Hi Eric I traced the problem to the following section in my emacs.org file: * Syntax highlighting for functions in R based on https://mail.google.com/mail/#label/Lists%2FESS/125131ed24688970 The following code needs to be run in R: obj <- do.call("c", sapply(c("package:base", "package:stats", "package:utils"), objects, all.names=TRUE)) re <- "(^[^.[:alpha:][:digit:]]|<-|__)" # to remove "weird" functions obj <- obj[-grep(re, obj)] fpath <- file.path(Sys.getenv("HOME"), ".emacs.d", "R-function-names.txt") write.table(obj, fpath, quote=FALSE, row.names=FALSE, col.names=FALSE) Read a whole file into list of lines Author: Xah Lee see http://xahlee.org/emacs/elisp_process_lines.html #+begin_src emacs-lisp (defun read-lines (file) "Return a list of lines in FILE." (with-temp-buffer (insert-file-contents file) (split-string (buffer-string) "\n" t) ) ) (add-hook 'ess-mode-hook '(lambda() (setq ess-my-extra-R-function-keywords (read-lines "~/.emacs.d/R-function-names.txt")) (setq ess-R-mode-font-lock-keywords (append ess-R-mode-font-lock-keywords (list (cons (concat "\\<" (regexp-opt ess-my-extra-R-function-keywords 'enc-paren) "\\>") 'font-lock-function-name-face)))))) If I disable that section, it works. Do you have any ideas if it could be 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 wrote: > >> 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 different >> > from R. >> > >> > I also attach my emacs.org file, but I am not doing any customisations >> 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. A couple of questions. >> >> 1) are you able to export to latex? If so, then maybe the issue has to >> 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 >> stack trace? >> > These are the messages in emacs: > > Select command: > Exporting... > org-babel-exp processing... > Fontifying *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 the -Q option, it works. So I assume > it is something in my emacs.org file. What is the easiest way to avoid > that source blocks under a heading in the emacs.org file are executed? > > >> > >> > In addition: if I specify :session *R* in #:BABEL: , the code is >> > evaluated, even though I specified :exports code. Is this intended? >> > >> >> Yes, this is for Sweave like behavior. >> >> If you have a session specified for every block in the buffer, and you >> are exporting the buffer, there are cases when you need a block to be >> executed (e.g. because it sets the value of a variable used by a >> subsequent block) even though you *do not* want the results of the block >> included in the final document. To support these use cases, on export >> every block with a session is executed so that it's effects on the >> persist session takes place. >> > > OK - that makes sense. > If you need any further info, please let me know. > > Thanks, > > Rainer > >> >> Cheers -- Eric >> >> > >> > Thanks, >> > >> > 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 > > -- 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 --001636417d4d1edebc048a66db97 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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/125131ed24688970
=A0 The following code = needs to be run in R:
=A0
=A0 obj <- do.call(&= quot;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.pa= th(Sys.getenv("HOME"), ".emacs.d", "R-function-nam= es.txt")
=A0 write.table(obj, fpath, = quote=3DFALSE, row.names=3DFALSE, col.names=3DFALSE)
=A0
=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<= /span>
=A0 (defun read-lines (file)
=A0 "Return a list= of lines in FILE."
=A0 (with-temp-bu= ffer
=A0 (insert-file-conten= ts file)
=A0 (split-string
=A0 (buffer-string) &qu= ot;\n" t)
=A0 )
=A0 )

=A0 (ad= d-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-func= tion-keywords 'enc-paren) "\\>")
=A0 'font-lock-function-name-face))))))

If I disable that section, it works. Do you have any ideas if it could = be changes? I don't know anything about emacs-lisp.

Thanks,
<= br>Rainer

On Fri, Jul 2, 2010 at 9:44 AM,= Rainer M Krug <= r.m.krug@gmail.com> wrote:


On Thu, Jul 1, 2010 at 5:55 PM, Eric Schulte <schul= te.eric@gmail.com> wrote:
Hi Rainer,

Hi Eric,
=A0

Rainer M Krug <r= .m.krug@gmail.com> 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 differe= nt
> from R.
>
> I also attach my emacs.= org file, but I am not doing any customisations to R.
>

I've just started up a minimal Emacs instance and loaded the babe= l
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.
<= /div>

2) could you send in the actual error being reported by Emacs, or a
=A0 stack trace?
These are the messages in emac= s:
=A0
Select com= mand:
Exporting...
org-babel-exp processin= g...
Fontifying=A0 *temp*... (regexps.....= ........)
org-babel-exp processin= g...
font-lock-fontify-keywords-region: In= valid regexp: "Regular expression too big"

How can I get a stack trace?

One more thing: if I start emacs wi= th the -Q option, it works. So I assume it is something in my emacs.org file. What is the easiest w= ay to avoid that source blocks under a heading in the emacs.org file are executed?


>
> In addition: if I specify :session *R* in #:BABEL: , the code is
> evaluated, even though I specified :exports code. Is this intended? >

Yes, this is for Sweave like behavior.

If you have a session specified for every block in the buffer, and you
are exporting the buffer, there are cases when you need a block to be
executed (e.g. because it sets the value of a variable used by a
subsequent block) even though you *do not* want the results of the block included in the final document. =A0To support these use cases, on export every block with a session is executed so that it's effects on the
persist session takes place.

OK - that makes= sense.
If you need any further info, please let me know.

Thanks,=

Rainer

Cheers -- Eric

>
> Thanks,
>
> Rainer


=
--
NEW GERMAN FAX NUMBER!!!

Rainer M. Krug, PhD (Conservatio= n Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion 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=




--
NEW GERMAN = FAX NUMBER!!!

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (= Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellen= ce for Invasion 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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