* 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
[-- Attachment #2: Type: application/pgp-signature, Size: 230 bytes --]
^ 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
[-- Attachment #1.1: Type: text/plain, Size: 2070 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.
>
>
> 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 related [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">
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</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;"><-</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;"><-</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@hp.com; +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@hp.com; +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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