Re: [Orgmode] [BABEL] html export for R not working, but for sh and others

[Rainer M Krug]

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 <address@hidden> wrote:

On Thu, Jul 1, 2010 at 5:55 PM, Eric Schulte <address@hidden> wrote:

Hi Rainer,

Hi Eric,
 

Rainer M Krug <address@hidden> 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

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

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-- 
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:          address@hidden

Skype:          RMkrug
Google:         address@hidden