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* Problems with Org-Mode export
@ 2011-09-16 17:50 Michael Hannon
  2011-09-16 20:04 ` Michael Hannon
                   ` (2 more replies)
  0 siblings, 3 replies; 11+ messages in thread
From: Michael Hannon @ 2011-09-16 17:50 UTC (permalink / raw)
  To: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 2189 bytes --]

Greetings.  I've been having problems lately in exporting Org-Mode source-code
documents to HTML and/or PDF.

I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).

I've appended a document that exhibits at least some of the problem.  The
problems are similar to the problem described at:

    http://comments.gmane.org/gmane.emacs.orgmode/45316

and can *sometimes* be circumvented by executing org-reload.

In the particular example shown below, the HTML export works as expected, but
the PDF export fails with message:

    org-export-latex-preprocess: Wrong type argument: stringp, nil

By the way, everything worked fine in the example until I added the last
source block:

    #+begin_src R

      x

    #+end_src

I tried using what I take to be the latest version of Org-Mode:

    Org-mode version 7.7 (release_7.7.290.g65d05)

but that only made things worse.  I tried an HTML export with this version, and
it generated a horrendous-looking message that begins with:

org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
result-params column-names-p row-names-p) Æ=}...

followed by a bunch of stuff containing enough non-printing characters that
it's hard to reproduce in email, and ending with:

...org-mode/lisp/ob-R.elc" . 9734)], 5

I'd welcome any help/advice that anybody can provide.

Thanks,

-- Mike

########## Sample file that exhibits some export problems

#+TITLE: This is a test

#+AUTHOR: Michael Hannon
#+email: jm_hannon@yahoo.com

#+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes

* Getting Started

** Batch Mode


#+begin_src R :exports code

pdf("xh.pdf") # set graphical output file
hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
dev.off() # close the graphical output file

#+end_src

If we put the code above in a file called =z.R=, we can execute the
code from the command line via: =R CMD BATCH z.R=


#+begin_src R
  
  x <- c(1, 3, 5)
  
#+end_src

#+begin_src R

  x[3]

#+end_src

#+begin_src R

  q <- c(x,x,8)

#+end_src

#+begin_src R

  x

#+end_src

[-- Attachment #2: Type: text/html, Size: 2687 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-16 17:50 Problems with Org-Mode export Michael Hannon
@ 2011-09-16 20:04 ` Michael Hannon
  2011-09-17  4:59 ` David Maus
  2011-09-20 19:31 ` Problems with Org-Mode export Michael Hannon
  2 siblings, 0 replies; 11+ messages in thread
From: Michael Hannon @ 2011-09-16 20:04 UTC (permalink / raw)
  To: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 2641 bytes --]

FYI: the problem described below is worse with:

    Org-mode version 7.7 (release_7.7.298.gbf3e9)

-- Mike




>________________________________
>From: Michael Hannon <jm_hannon@yahoo.com>
>To: Org-Mode List <emacs-orgmode@gnu.org>
>Sent: Friday, September 16, 2011 10:50 AM
>Subject: [O] Problems with Org-Mode export
>
>
>Greetings.  I've been having problems lately in exporting Org-Mode source-code
>documents to HTML and/or PDF.
>
>I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).
>
>I've appended a document that exhibits at least some of the problem.  The
>problems are similar to the problem described at:
>
>    http://comments.gmane.org/gmane.emacs.orgmode/45316
>
>and can *sometimes* be circumvented by executing org-reload.
>
>In the particular example shown below, the HTML export works as expected, but
>the PDF export fails with message:
>
>    org-export-latex-preprocess: Wrong type argument: stringp, nil
>
>By the way, everything worked fine in the example until I added the last
>source block:
>
>    #+begin_src
 R
>
>      x
>
>    #+end_src
>
>I tried using what I take to be the latest version of Org-Mode:
>
>    Org-mode version 7.7 (release_7.7.290.g65d05)
>
>but that only made things worse.  I tried an HTML export with this version, and
>it generated a horrendous-looking message that begins with:
>
>org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>result-params column-names-p row-names-p) Æ=}...
>
>followed by a bunch of stuff containing enough non-printing characters that
>it's hard to reproduce in email, and ending with:
>
>...org-mode/lisp/ob-R.elc" . 9734)], 5
>
>I'd welcome any help/advice that anybody can provide.
>
>Thanks,
>
>-- Mike
>
>########## Sample file that exhibits some export problems
>
>#+TITLE: This is a test
>
>#+AUTHOR: Michael Hannon
>#+email: jm_hannon@yahoo.com
>
>#+BABEL:
 :session *R* :cache yes :results output graphics :exports both :tangle yes
>
>* Getting Started
>
>** Batch Mode
>
>
>#+begin_src R :exports code
>
>pdf("xh.pdf") # set graphical output file
>hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
>dev.off() # close the graphical output file
>
>#+end_src
>
>If we put the code above in a file called =z.R=, we can execute the
>code from the command line via: =R CMD BATCH z.R=
>
>
>#+begin_src R
>  
>  x <- c(1, 3, 5)
>  
>#+end_src
>
>#+begin_src R
>
>  x[3]
>
>#+end_src
>
>#+begin_src R
>
>  q <- c(x,x,8)
>
>#+end_src
>
>#+begin_src R
>
>  x
>
>#+end_src
>
>
>
>

[-- Attachment #2: Type: text/html, Size: 3807 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-16 17:50 Problems with Org-Mode export Michael Hannon
  2011-09-16 20:04 ` Michael Hannon
@ 2011-09-17  4:59 ` David Maus
  2011-09-19 21:17   ` Michael Hannon
  2011-09-20 19:31 ` Problems with Org-Mode export Michael Hannon
  2 siblings, 1 reply; 11+ messages in thread
From: David Maus @ 2011-09-17  4:59 UTC (permalink / raw)
  To: Michael Hannon; +Cc: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 1941 bytes --]

At Fri, 16 Sep 2011 10:50:01 -0700 (PDT),
Michael Hannon wrote:
> Greetings.  I've been having problems lately in exporting Org-Mode source-code
> documents to HTML and/or PDF.
> 
> I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).
> 
> I've appended a document that exhibits at least some of the problem.  The
> problems are similar to the problem described at:
> 
>     http://comments.gmane.org/gmane.emacs.orgmode/45316
> 
> and can *sometimes* be circumvented by executing org-reload.
> 
> In the particular example shown below, the HTML export works as expected, but
> the PDF export fails with message:
> 
>     org-export-latex-preprocess: Wrong type argument: stringp, nil
> 
> By the way, everything worked fine in the example until I added the last
> source block:
> 
>     #+begin_src R
> 
>       x
> 
>     #+end_src
> 
> I tried using what I take to be the latest version of Org-Mode:
> 
>     Org-mode version 7.7 (release_7.7.290.g65d05)
> 
> but that only made things worse.  I tried an HTML export with this version, and
> it generated a horrendous-looking message that begins with:
> 
> org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
> result-params column-names-p row-names-p) Æ=}...
> 
> followed by a bunch of stuff containing enough non-printing characters that
> it's hard to reproduce in email, and ending with:
> 
> ...org-mode/lisp/ob-R.elc" . 9734)], 5
> 
> I'd welcome any help/advice that anybody can provide.


Could I ask you to provide the entire backtrace for both errors?

M-x toggle-debug-on-error RET

The backtrace might contain information about the exact place where a
string is expected. If you can't copy it into the email program save
to disk + gzip + attach should do the trick.

Best,
  -- David
-- 
OpenPGP... 0x99ADB83B5A4478E6
Jabber.... dmjena@jabber.org
Email..... dmaus@ictsoc.de

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^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-17  4:59 ` David Maus
@ 2011-09-19 21:17   ` Michael Hannon
  2011-09-19 23:20     ` [PATCH] Check argument is a string before calling string-match Bernt Hansen
  0 siblings, 1 reply; 11+ messages in thread
From: Michael Hannon @ 2011-09-19 21:17 UTC (permalink / raw)
  To: David Maus; +Cc: Org-Mode List


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>> Greetings.  I've been having problems lately in exporting Org-Mode
>> source-code documents to HTML and/or PDF.

>> 
>> I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).

>> I've appended a document that exhibits at least some of the problem.  The
>> problems are similar to the problem described at:

>>    http://comments.gmane.org/gmane.emacs.orgmode/45316

>> and can *sometimes* be circumvented by executing org-reload.

>> In the particular example shown below, the HTML export works as expected,
>> but the PDF export fails with message:

>>    org-export-latex-preprocess: Wrong type argument: stringp, nil

>> By the way, everything worked fine in the example until I added the last
>> source block:

>>    #+begin_src R
>> 
>>      x
>> 
>>    #+end_src
>> 
>> I tried using what I take to be the latest version of Org-Mode:
>> 
>>    Org-mode version 7.7 (release_7.7.290.g65d05)
>> 
>> but that only made things worse.  I tried an HTML export with this version,
>> and
>> it generated a horrendous-looking message that begins with:
>> 
>> org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>> result-params column-names-p row-names-p) Æ=}...
>> 
>> followed by a bunch of stuff containing enough non-printing characters that
>> it's hard to reproduce in email, and ending with:
>> 
>> ...org-mode/lisp/ob-R.elc" . 9734)], 5
>> 
>> I'd welcome any help/advice that anybody can provide.
>
>
> Could I ask you to provide the entire backtrace for both errors?
> 
> M-x toggle-debug-on-error RET
> 
> The backtrace might contain information about the exact place where a
> string is expected. If you can't copy it into the email program save
> to disk + gzip + attach should do the trick.

Hi, David.  I've attached the backtrace for:

    Org-mode version 7.7 (release_7.7.304.g9da4)

(I was traveling when I worked on this previously, and my environment has now
changed.  The version I'm using now exhibits the same kind of error.)

Thanks,

-- Mike

[-- Attachment #1.2: Type: text/html, Size: 3282 bytes --]

[-- Attachment #2: backtrace.txt.gz --]
[-- Type: application/x-gzip, Size: 3319 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* [PATCH] Check argument is a string before calling string-match
  2011-09-19 21:17   ` Michael Hannon
@ 2011-09-19 23:20     ` Bernt Hansen
  2011-10-04 12:36       ` [Accepted] " Carsten Dominik
  0 siblings, 1 reply; 11+ messages in thread
From: Bernt Hansen @ 2011-09-19 23:20 UTC (permalink / raw)
  To: emacs-orgmode; +Cc: Bernt Hansen

* lisp/org-html.el (org-export-as-html): Check string-match argument
(org-html-handle-time-stamps): Check string-match argument

Avoid wrong-type-argument errors during exporting.
---

This may or may not be the same error you are getting - but I ran into 
this during exporting back in August and it was sitting in my queue.

Please report if this fixes your issue or not.

-Bernt

 lisp/org-html.el |   30 ++++++++++++++++--------------
 1 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/lisp/org-html.el b/lisp/org-html.el
index fde563b..6492c2f 100644
--- a/lisp/org-html.el
+++ b/lisp/org-html.el
@@ -1598,7 +1598,8 @@ lang=\"%s\" xml:lang=\"%s\">
 	  (setq line (org-html-handle-links line opt-plist))
 
 	  ;; TODO items
-	  (if (and (string-match org-todo-line-regexp line)
+	  (if (and org-todo-line-regexp
+		   (string-match org-todo-line-regexp line)
 		   (match-beginning 2))
 
 	      (setq line
@@ -2213,19 +2214,20 @@ for further information."
   "Format time stamps in string S, or remove them."
   (catch 'exit
     (let (r b)
-      (while (string-match org-maybe-keyword-time-regexp s)
-	(or b (setq b (substring s 0 (match-beginning 0))))
-	(setq r (concat
-		 r (substring s 0 (match-beginning 0))
-		 " @<span class=\"timestamp-wrapper\">"
-		 (if (match-end 1)
-		     (format "@<span class=\"timestamp-kwd\">%s @</span>"
-			     (match-string 1 s)))
-		 (format " @<span class=\"timestamp\">%s@</span>"
-			 (substring
-			  (org-translate-time (match-string 3 s)) 1 -1))
-		 "@</span>")
-	      s (substring s (match-end 0))))
+      (when org-maybe-keyword-time-regexp
+	(while (string-match org-maybe-keyword-time-regexp s)
+	  (or b (setq b (substring s 0 (match-beginning 0))))
+	  (setq r (concat
+		   r (substring s 0 (match-beginning 0))
+		   " @<span class=\"timestamp-wrapper\">"
+		   (if (match-end 1)
+		       (format "@<span class=\"timestamp-kwd\">%s @</span>"
+			       (match-string 1 s)))
+		   (format " @<span class=\"timestamp\">%s@</span>"
+			   (substring
+			    (org-translate-time (match-string 3 s)) 1 -1))
+		   "@</span>")
+		s (substring s (match-end 0)))))
       ;; Line break if line started and ended with time stamp stuff
       (if (not r)
 	  s
-- 
1.7.7.rc1.3.g5593

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-16 17:50 Problems with Org-Mode export Michael Hannon
  2011-09-16 20:04 ` Michael Hannon
  2011-09-17  4:59 ` David Maus
@ 2011-09-20 19:31 ` Michael Hannon
  2011-09-20 20:29   ` Nick Dokos
  2 siblings, 1 reply; 11+ messages in thread
From: Michael Hannon @ 2011-09-20 19:31 UTC (permalink / raw)
  To: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 3311 bytes --]

Another bit of information about this:  if I remove:

    :session *R*

from the line starting with:

    #+BABEL

then I don't see any error message.

OTOH, this isn't much of a workaround, because without a "session", the values of the variables are not preserved between source-code blocks, so that, for instance, the combination:

    x <- c(1, 3, 5)    #### defined in one block

and

    q <- c(x, 8, 8)    #### defined in another block

raises an R error ('x' is not defined when the assignment to 'q' is made).

Also, in grasping at straws, I've tried renaming the R session, as:

    ... :session mTest

(on the theory that the '*' is used for emphasis in Org-Mode markup and might, therefore, somehow confuse things).  That didn't help.

-- Mike




>________________________________
>From: Michael Hannon <jm_hannon@yahoo.com>
>To: Org-Mode List <emacs-orgmode@gnu.org>
>Sent: Friday, September 16, 2011 10:50 AM
>Subject: [O] Problems with Org-Mode export
>
>
>Greetings.  I've been having problems lately in exporting Org-Mode source-code
>documents to HTML and/or PDF.
>
>I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).
>
>I've appended a document that exhibits at least some of the problem.  The
>problems are similar to the problem described at:
>
>    http://comments.gmane.org/gmane.emacs.orgmode/45316
>
>and can *sometimes* be circumvented by executing org-reload.
>
>In the particular example shown below, the HTML export works as expected, but
>the PDF export fails with message:
>
>    org-export-latex-preprocess: Wrong type argument: stringp, nil
>
>By the way, everything worked fine in the example until I added the last
>source block:
>
>    #+begin_src
 R
>
>      x
>
>    #+end_src
>
>I tried using what I take to be the latest version of Org-Mode:
>
>    Org-mode version 7.7 (release_7.7.290.g65d05)
>
>but that only made things worse.  I tried an HTML export with this version, and
>it generated a horrendous-looking message that begins with:
>
>org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>result-params column-names-p row-names-p) Æ=}...
>
>followed by a bunch of stuff containing enough non-printing characters that
>it's hard to reproduce in email, and ending with:
>
>...org-mode/lisp/ob-R.elc" . 9734)], 5
>
>I'd welcome any help/advice that anybody can provide.
>
>Thanks,
>
>-- Mike
>
>########## Sample file that exhibits some export problems
>
>#+TITLE: This is a test
>
>#+AUTHOR: Michael Hannon
>#+email: jm_hannon@yahoo.com
>
>#+BABEL:
 :session *R* :cache yes :results output graphics :exports both :tangle yes
>
>* Getting Started
>
>** Batch Mode
>
>
>#+begin_src R :exports code
>
>pdf("xh.pdf") # set graphical output file
>hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
>dev.off() # close the graphical output file
>
>#+end_src
>
>If we put the code above in a file called =z.R=, we can execute the
>code from the command line via: =R CMD BATCH z.R=
>
>
>#+begin_src R
>  
>  x <- c(1, 3, 5)
>  
>#+end_src
>
>#+begin_src R
>
>  x[3]
>
>#+end_src
>
>#+begin_src R
>
>  q <- c(x,x,8)
>
>#+end_src
>
>#+begin_src R
>
>  x
>
>#+end_src
>
>
>
>

[-- Attachment #2: Type: text/html, Size: 5095 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-20 19:31 ` Problems with Org-Mode export Michael Hannon
@ 2011-09-20 20:29   ` Nick Dokos
  2011-09-21  1:09     ` Michael Hannon
  0 siblings, 1 reply; 11+ messages in thread
From: Nick Dokos @ 2011-09-20 20:29 UTC (permalink / raw)
  To: Michael Hannon; +Cc: nicholas.dokos, Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 4333 bytes --]

Michael Hannon <jm_hannon@yahoo.com> wrote:

> Another bit of information about this:  if I remove:
> 
>     :session *R*
> 
> from the line starting with:
> 
>     #+BABEL
> 
> then I don't see any error message.
> 
> OTOH, this isn't much of a workaround, because without a "session", the values of the variables are
> not preserved between source-code blocks, so that, for instance, the combination:
> 
>     x <- c(1, 3, 5)    #### defined in one block
> 
> and
> 
>     q <- c(x, 8, 8)    #### defined in another block
> 
> raises an R error ('x' is not defined when the assignment to 'q' is made).
> 
> Also, in grasping at straws, I've tried renaming the R session, as:
> 
>     ... :session mTest
> 
> (on the theory that the '*' is used for emphasis in Org-Mode markup and might, therefore, somehow
> confuse things).  That didn't help.
> 

FWIW, I don't get any error messages. I have no idea what the exported
file should look like: I attach both the exported pdf and the exported
html below (as well as the org file, which is just cut-n-pasted from
what you posted).

Versions:

Org-mode version 7.7 (release_7.7.224.g6e14)
GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13

I'll pull the newest bits and try again.

Nick

> 
>     -------------------------------------------------------------------------------------------------
>     From: Michael Hannon <jm_hannon@yahoo.com>
>     To: Org-Mode List <emacs-orgmode@gnu.org>
>     Sent: Friday, September 16, 2011 10:50 AM
>     Subject: [O] Problems with Org-Mode export
>    
>     Greetings.  I've been having problems lately in exporting Org-Mode source-code
>     documents to HTML and/or PDF.
>    
>     I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).
>    
>     I've appended a document that exhibits at least some of the problem.  The
>     problems are similar to the problem described at:
>    
>         http://comments.gmane.org/gmane.emacs.orgmode/45316
>    
>     and can *sometimes* be circumvented by executing org-reload.
>    
>     In the particular example shown below, the HTML export works as expected, but
>     the PDF export fails with message:
>    
>         org-export-latex-preprocess: Wrong type argument: stringp, nil
>    
>     By the way, everything worked fine in the example until I added the last
>     source block:
>    
>         #+begin_src R
>    
>           x
>    
>         #+end_src
>    
>     I tried using what I take to be the latest version of Org-Mode:
>    
>         Org-mode version 7.7 (release_7.7.290.g65d05)
>    
>     but that only made things worse.  I tried an HTML export with this version, and
>     it generated a horrendous-looking message that begins with:
>    
>     org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>     result-params column-names-p row-names-p) Æ=}...
>    
>     followed by a bunch of stuff containing enough non-printing characters that
>     it's hard to reproduce in email, and ending with:
>    
>     ...org-mode/lisp/ob-R.elc" . 9734)], 5
>    
>     I'd welcome any help/advice that anybody can provide.
>    
>     Thanks,
>    
>     -- Mike
>    
>     ########## Sample file that exhibits some export problems
>    
>     #+TITLE: This is a test
>    
>     #+AUTHOR: Michael Hannon
>     #+email: jm_hannon@yahoo.com
>    
>     #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes
>    
>     * Getting Started
>    
>     ** Batch Mode
> 
>     #+begin_src R :exports code
>    
>     pdf("xh.pdf") # set graphical output file
>     hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
>     dev.off() # close the graphical output file
>    
>     #+end_src
>    
>     If we put the code above in a file called =z.R=, we can execute the
>     code from the command line via: =R CMD BATCH z.R=
> 
>     #+begin_src R
>      
>       x <- c(1, 3, 5)
>      
>     #+end_src
>    
>     #+begin_src R
>    
>       x[3]
>    
>     #+end_src
>    
>     #+begin_src R
>    
>       q <- c(x,x,8)
>    
>     #+end_src
>    
>     #+begin_src R
>    
>       x
>    
>     #+end_src


[-- Attachment #2: org file --]
[-- Type: text/plain, Size: 673 bytes --]

#+TITLE: This is a test

#+AUTHOR: Michael Hannon
#+email: jm_hannon@yahoo.com

#+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes

* Getting Started

** Batch Mode

#+begin_src R :exports code

pdf("xh.pdf") # set graphical output file
hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
dev.off() # close the graphical output file

#+end_src

If we put the code above in a file called =z.R=, we can execute the
code from the command line via: =R CMD BATCH z.R=

#+begin_src R

  x <- c(1, 3, 5)

#+end_src


#+begin_src R

  x[3]

#+end_src


#+begin_src R

  q <- c(x,x,8)

#+end_src


#+begin_src R

  x

#+end_src

[-- Attachment #3: html file --]
[-- Type: application/xml, Size: 4775 bytes --]

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
               "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"
lang="en" xml:lang="en">
<head>
<title>This is a test</title>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
<meta name="generator" content="Org-mode"/>
<meta name="generated" content="2011-09-20 16:28:20 EDT"/>
<meta name="author" content="Michael Hannon"/>
<meta name="description" content=""/>
<meta name="keywords" content=""/>
<style type="text/css">
 <!--/*--><![CDATA[/*><!--*/
  html { font-family: Times, serif; font-size: 12pt; }
  .title  { text-align: center; }
  .todo   { color: red; }
  .done   { color: green; }
  .tag    { background-color: #add8e6; font-weight:normal }
  .target { }
  .timestamp { color: #bebebe; }
  .timestamp-kwd { color: #5f9ea0; }
  .right  {margin-left:auto; margin-right:0px;  text-align:right;}
  .left   {margin-left:0px;  margin-right:auto; text-align:left;}
  .center {margin-left:auto; margin-right:auto; text-align:center;}
  p.verse { margin-left: 3% }
  pre {
	border: 1pt solid #AEBDCC;
	background-color: #F3F5F7;
	padding: 5pt;
	font-family: courier, monospace;
        font-size: 90%;
        overflow:auto;
  }
  table { border-collapse: collapse; }
  td, th { vertical-align: top;  }
  th.right  { text-align:center;  }
  th.left   { text-align:center;   }
  th.center { text-align:center; }
  td.right  { text-align:right;  }
  td.left   { text-align:left;   }
  td.center { text-align:center; }
  dt { font-weight: bold; }
  div.figure { padding: 0.5em; }
  div.figure p { text-align: center; }
  div.inlinetask {
    padding:10px;
    border:2px solid gray;
    margin:10px;
    background: #ffffcc;
  }
  textarea { overflow-x: auto; }
  .linenr { font-size:smaller }
  .code-highlighted {background-color:#ffff00;}
  .org-info-js_info-navigation { border-style:none; }
  #org-info-js_console-label { font-size:10px; font-weight:bold;
                               white-space:nowrap; }
  .org-info-js_search-highlight {background-color:#ffff00; color:#000000;
                                 font-weight:bold; }
  /*]]>*/-->
</style>
<script type="text/javascript">
<!--/*--><![CDATA[/*><!--*/
 function CodeHighlightOn(elem, id)
 {
   var target = document.getElementById(id);
   if(null != target) {
     elem.cacheClassElem = elem.className;
     elem.cacheClassTarget = target.className;
     target.className = "code-highlighted";
     elem.className   = "code-highlighted";
   }
 }
 function CodeHighlightOff(elem, id)
 {
   var target = document.getElementById(id);
   if(elem.cacheClassElem)
     elem.className = elem.cacheClassElem;
   if(elem.cacheClassTarget)
     target.className = elem.cacheClassTarget;
 }
/*]]>*///-->
</script>

</head>
<body>

<div id="preamble">

</div>

<div id="content">
<h1 class="title">This is a test</h1>




<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1 Getting Started </a>
<ul>
<li><a href="#sec-1-1">1.1 Batch Mode </a></li>
</ul>
</li>
</ul>
</div>
</div>

<div id="outline-container-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Getting Started </h2>
<div class="outline-text-2" id="text-1">



</div>

<div id="outline-container-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> Batch Mode </h3>
<div class="outline-text-3" id="text-1-1">





<pre class="src src-R">pdf(<span style="color: #ffa07a;">"xh.pdf"</span>) <span style="color: #f4a460;"># </span><span style="color: #f4a460;">set graphical output file</span>
hist(rnorm(100)) <span style="color: #f4a460;"># </span><span style="color: #f4a460;">generate 100 N(0,1) variates and plot their histogram</span>
dev.off() <span style="color: #f4a460;"># </span><span style="color: #f4a460;">close the graphical output file</span>

</pre>


<p>
If we put the code above in a file called <code>z.R</code>, we can execute the
code from the command line via: <code>R CMD BATCH z.R</code>
</p>



<pre class="src src-R">  x <span style="color: #7fffd4;">&lt;-</span> c(1, 3, 5)

</pre>





<pre class="src src-R">  x[3]

</pre>


<pre class="example">
[1] 5
</pre>






<pre class="src src-R">  q <span style="color: #7fffd4;">&lt;-</span> c(x,x,8)

</pre>





<pre class="src src-R">  x

</pre>


<pre class="example">
[1] 1 3 5
</pre>


</div>
</div>
</div>
</div>

<div id="postamble">
<p class="date">Date: 2011-09-20 16:28:20 EDT</p>
<p class="author">Author: Michael Hannon</p>
<p class="creator">Org version 7.7 with Emacs version 24</p>
<a href="http://validator.w3.org/check?uri=referer">Validate XHTML 1.0</a>

</div>
</body>
</html>

[-- Attachment #4: pdf file --]
[-- Type: application/pdf, Size: 51751 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-20 20:29   ` Nick Dokos
@ 2011-09-21  1:09     ` Michael Hannon
  2011-09-21 14:37       ` Nick Dokos
  0 siblings, 1 reply; 11+ messages in thread
From: Michael Hannon @ 2011-09-21  1:09 UTC (permalink / raw)
  To: nicholas.dokos; +Cc: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 2698 bytes --]

Nick Dokos <nicholas.dokos@hp.com> wrote:

> [...]

> FWIW, I don't get any error messages. I have no idea what the exported file
> should look like: I attach both the exported pdf and the exported html below
> (as well as the org file, which is just cut-n-pasted from what you posted).
 
> Versions:

> Org-mode version 7.7 (release_7.7.224.g6e14) GNU Emacs 24.0.50.2
> (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13

> I'll pull the newest bits and try again.

Thanks, Nick.  This is getting curiouser and curiouser.  I can now reliably
get documents exported using the vanilla 7.7 Org-Mode, but not with the
development version I currently have installed:

    Org-mode version 7.7 (release_7.7.304.g9da4)

I suspect that the following bit of the error message is the relevant one:

    org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
    result-params column-names-p row-names-p

but I don't know what to make of it.

In order to simplify the discussion, I've been working with some Org code that
I took from the "worg" web site.  Please see below for details.

I've also appended the pieces of my .emacs file that relate to finding Org
files.

At this point I guess I'm ready to declare victory and slink away, but it
WOULD be interesting to know what's going on.

-- Mike


----------

#+TITLE: Test 
#+AUTHOR: Michael Hannon
#+EMAIL: jm_hannon@yahoo.com
#+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes 

#### Example taken from:
####    http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html

* Example of Org-Babel for R Literate Programming
** R text output
A simple summary. 
#+begin_src R 
  x <- rnorm(10)
  summary(x)
#+end_src

** R graphics output
Note we use the object =x= generated in previous code block, thanks to
the header option =:session *R*=.  The output graphics file is
=a.png=. 

#+begin_src R  :file a.png
  y <- rnorm(10)
  plot(x, y)
#+end_src

Same plot with larger dimension:

#+begin_src R  :file b.png :width 800 :height 800
  plot(x, y)
#+end_src


---------- Org-Mode path variables, standard and devel versions

(setq load-path (cons "/usr/local/emacs.d/ssh" load-path))
(require 'ssh)

;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/lisp" load-path))

;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/contrib/lisp" load-path))

(setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/lisp" load-path))

(setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp" load-path))

(require 'org-install)

[-- Attachment #2: Type: text/html, Size: 4194 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-21  1:09     ` Michael Hannon
@ 2011-09-21 14:37       ` Nick Dokos
  2011-09-21 19:10         ` Michael Hannon
  0 siblings, 1 reply; 11+ messages in thread
From: Nick Dokos @ 2011-09-21 14:37 UTC (permalink / raw)
  To: Michael Hannon; +Cc: nicholas.dokos, Org-Mode List

Michael Hannon <jm_hannon@yahoo.com> wrote:

> Nick Dokos <nicholas.dokos@hp.com> wrote:
> 
> > Org-mode version 7.7 (release_7.7.224.g6e14) GNU Emacs 24.0.50.2
> > (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13
> 
> > I'll pull the newest bits and try again.
> 

I pulled from latest and reran both the original test file and the test
file below. I get no errors either with my standard config or with a
minimal .emacs in either case.

Version info for reference:

Org-mode version 7.7 (release_7.7.311.g0c099)

GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13

This is on Ubuntu 10.10.

Nick

> Thanks, Nick.  This is getting curiouser and curiouser.  I can now reliably
> get documents exported using the vanilla 7.7 Org-Mode, but not with the
> development version I currently have installed:
> 
>     Org-mode version 7.7 (release_7.7.304.g9da4)
> 
> I suspect that the following bit of the error message is the relevant one:
> 
>     org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>     result-params column-names-p row-names-p
> 
> but I don't know what to make of it.
> 
> In order to simplify the discussion, I've been working with some Org code that
> I took from the "worg" web site.  Please see below for details.
> 
> I've also appended the pieces of my .emacs file that relate to finding Org
> files.
> 
> At this point I guess I'm ready to declare victory and slink away, but it
> WOULD be interesting to know what's going on.
> 
> -- Mike
> 
> ----------
> 
> #+TITLE: Test 
> #+AUTHOR: Michael Hannon
> #+EMAIL: jm_hannon@yahoo.com
> #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes 
> 
> #### Example taken from:
> ####    http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html
> 
> * Example of Org-Babel for R Literate Programming
> ** R text output
> A simple summary. 
> #+begin_src R 
>   x <- rnorm(10)
>   summary(x)
> #+end_src
> 
> ** R graphics output
> Note we use the object =x= generated in previous code block, thanks to
> the header option =:session *R*=.  The output graphics file is
> =a.png=. 
> 
> #+begin_src R  :file a.png
>   y <- rnorm(10)
>   plot(x, y)
> #+end_src
> 
> Same plot with larger dimension:
> 
> #+begin_src R  :file b.png :width 800 :height 800
>   plot(x, y)
> #+end_src
> 
> ---------- Org-Mode path variables, standard and devel versions
> 
> (setq load-path (cons "/usr/local/emacs.d/ssh" load-path))
> (require 'ssh)
> 
> ;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/lisp" load-path))
> 
> ;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/contrib/lisp" load-path))
> 
> (setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/lisp" load-path))
> 
> (setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp" load-path))
> 
> (require 'org-install)
> 
> 

^ permalink raw reply	[flat|nested] 11+ messages in thread

* Re: Problems with Org-Mode export
  2011-09-21 14:37       ` Nick Dokos
@ 2011-09-21 19:10         ` Michael Hannon
  0 siblings, 0 replies; 11+ messages in thread
From: Michael Hannon @ 2011-09-21 19:10 UTC (permalink / raw)
  To: nicholas.dokos; +Cc: Org-Mode List

[-- Attachment #1: Type: text/plain, Size: 3563 bytes --]

Thanks, Nick.  I just grabbed:

    Org-mode version 7.7 (release_7.7.314.g12f0)

and don't seem to have the problem any more.

-- Mike



>________________________________
>From: Nick Dokos <nicholas.dokos@hp.com>
>To: Michael Hannon <jm_hannon@yahoo.com>
>Cc: nicholas.dokos@hp.com; Org-Mode List <emacs-orgmode@gnu.org>
>Sent: Wednesday, September 21, 2011 7:37 AM
>Subject: Re: [O] Problems with Org-Mode export
>
>Michael Hannon <jm_hannon@yahoo.com> wrote:
>
>> Nick Dokos <nicholas.dokos@hp.com> wrote:
>> 
>> > Org-mode version 7.7 (release_7.7.224.g6e14) GNU Emacs 24.0.50.2
>> > (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13
>> 
>> > I'll pull the newest bits and try again.
>> 
>
>I pulled from latest and reran both the original test file and the test
>file below. I get no errors either with my standard config or with a
>minimal .emacs in either case.
>
>Version info for reference:
>
>Org-mode version 7.7 (release_7.7.311.g0c099)
>
>GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13
>
>This is on Ubuntu 10.10.
>
>Nick
>
>> Thanks, Nick.  This is getting curiouser and curiouser.  I can now reliably
>> get documents exported using the vanilla 7.7 Org-Mode, but not with the
>> development version I currently have installed:
>> 
>>     Org-mode version 7.7 (release_7.7.304.g9da4)
>> 
>> I suspect that the following bit of the error message is the relevant one:
>> 
>>     org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type
>>     result-params column-names-p row-names-p
>> 
>> but I don't know what to make of it.
>> 
>> In order to simplify the discussion, I've been working with some Org code that
>> I took from the "worg" web site.  Please see below for details.
>> 
>> I've also appended the pieces of my .emacs file that relate to finding Org
>> files.
>> 
>> At this point I guess I'm ready to declare victory and slink away, but it
>> WOULD be interesting to know what's going on.
>> 
>> -- Mike
>> 
>> ----------
>> 
>> #+TITLE: Test 
>> #+AUTHOR: Michael Hannon
>> #+EMAIL: jm_hannon@yahoo.com
>> #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes 
>> 
>> #### Example taken from:
>> ####    http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html
>> 
>> * Example of Org-Babel for R Literate Programming
>> ** R text output
>> A simple summary. 
>> #+begin_src R 
>>   x <- rnorm(10)
>>   summary(x)
>> #+end_src
>> 
>> ** R graphics output
>> Note we use the object =x= generated in previous code block, thanks to
>> the header option =:session *R*=.  The output graphics file is
>> =a.png=. 
>> 
>> #+begin_src R  :file a.png
>>   y <- rnorm(10)
>>   plot(x, y)
>> #+end_src
>> 
>> Same plot with larger dimension:
>> 
>> #+begin_src R  :file b.png :width 800 :height 800
>>   plot(x, y)
>> #+end_src
>> 
>> ---------- Org-Mode path variables, standard and devel versions
>> 
>> (setq load-path (cons "/usr/local/emacs.d/ssh" load-path))
>> (require 'ssh)
>> 
>> ;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/lisp" load-path))
>> 
>> ;;;;;;(setq load-path (cons "/usr/local/emacs.d/org-mode/org-7.7/contrib/lisp" load-path))
>> 
>> (setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/lisp" load-path))
>> 
>> (setq load-path (cons "/usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp" load-path))
>> 
>> (require 'org-install)
>> 
>> 
>
>
>
>

[-- Attachment #2: Type: text/html, Size: 5266 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

* [Accepted] Check argument is a string before calling string-match
  2011-09-19 23:20     ` [PATCH] Check argument is a string before calling string-match Bernt Hansen
@ 2011-10-04 12:36       ` Carsten Dominik
  0 siblings, 0 replies; 11+ messages in thread
From: Carsten Dominik @ 2011-10-04 12:36 UTC (permalink / raw)
  To: emacs-orgmode

Patch 952 (http://patchwork.newartisans.com/patch/952/) is now "Accepted".

Maintainer comment: none

This relates to the following submission:

http://mid.gmane.org/%3C1316474402-26292-1-git-send-email-bernt%40norang.ca%3E

Here is the original message containing the patch:

> Content-Type: text/plain; charset="utf-8"
> MIME-Version: 1.0
> Content-Transfer-Encoding: 7bit
> Subject: [O] Check argument is a string before calling string-match
> Date: Tue, 20 Sep 2011 04:20:02 -0000
> From: Bernt Hansen <bernt@norang.ca>
> X-Patchwork-Id: 952
> Message-Id: <1316474402-26292-1-git-send-email-bernt@norang.ca>
> To: emacs-orgmode@gnu.org
> Cc: Bernt Hansen <bernt@norang.ca>
> 
> * lisp/org-html.el (org-export-as-html): Check string-match argument
> (org-html-handle-time-stamps): Check string-match argument
> 
> Avoid wrong-type-argument errors during exporting.
> 
> ---
> This may or may not be the same error you are getting - but I ran into 
> this during exporting back in August and it was sitting in my queue.
> 
> Please report if this fixes your issue or not.
> 
> -Bernt
> 
>  lisp/org-html.el |   30 ++++++++++++++++--------------
>  1 files changed, 16 insertions(+), 14 deletions(-)
> 
> diff --git a/lisp/org-html.el b/lisp/org-html.el
> index fde563b..6492c2f 100644
> --- a/lisp/org-html.el
> +++ b/lisp/org-html.el
> @@ -1598,7 +1598,8 @@ lang=\"%s\" xml:lang=\"%s\">
>  	  (setq line (org-html-handle-links line opt-plist))
>  
>  	  ;; TODO items
> -	  (if (and (string-match org-todo-line-regexp line)
> +	  (if (and org-todo-line-regexp
> +		   (string-match org-todo-line-regexp line)
>  		   (match-beginning 2))
>  
>  	      (setq line
> @@ -2213,19 +2214,20 @@ for further information."
>    "Format time stamps in string S, or remove them."
>    (catch 'exit
>      (let (r b)
> -      (while (string-match org-maybe-keyword-time-regexp s)
> -	(or b (setq b (substring s 0 (match-beginning 0))))
> -	(setq r (concat
> -		 r (substring s 0 (match-beginning 0))
> -		 " @<span class=\"timestamp-wrapper\">"
> -		 (if (match-end 1)
> -		     (format "@<span class=\"timestamp-kwd\">%s @</span>"
> -			     (match-string 1 s)))
> -		 (format " @<span class=\"timestamp\">%s@</span>"
> -			 (substring
> -			  (org-translate-time (match-string 3 s)) 1 -1))
> -		 "@</span>")
> -	      s (substring s (match-end 0))))
> +      (when org-maybe-keyword-time-regexp
> +	(while (string-match org-maybe-keyword-time-regexp s)
> +	  (or b (setq b (substring s 0 (match-beginning 0))))
> +	  (setq r (concat
> +		   r (substring s 0 (match-beginning 0))
> +		   " @<span class=\"timestamp-wrapper\">"
> +		   (if (match-end 1)
> +		       (format "@<span class=\"timestamp-kwd\">%s @</span>"
> +			       (match-string 1 s)))
> +		   (format " @<span class=\"timestamp\">%s@</span>"
> +			   (substring
> +			    (org-translate-time (match-string 3 s)) 1 -1))
> +		   "@</span>")
> +		s (substring s (match-end 0)))))
>        ;; Line break if line started and ended with time stamp stuff
>        (if (not r)
>  	  s
> 

^ permalink raw reply	[flat|nested] 11+ messages in thread

end of thread, other threads:[~2011-10-04 12:36 UTC | newest]

Thread overview: 11+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2011-09-16 17:50 Problems with Org-Mode export Michael Hannon
2011-09-16 20:04 ` Michael Hannon
2011-09-17  4:59 ` David Maus
2011-09-19 21:17   ` Michael Hannon
2011-09-19 23:20     ` [PATCH] Check argument is a string before calling string-match Bernt Hansen
2011-10-04 12:36       ` [Accepted] " Carsten Dominik
2011-09-20 19:31 ` Problems with Org-Mode export Michael Hannon
2011-09-20 20:29   ` Nick Dokos
2011-09-21  1:09     ` Michael Hannon
2011-09-21 14:37       ` Nick Dokos
2011-09-21 19:10         ` Michael Hannon

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