Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Andreas Leha
t...@tsdye.com (Thomas S. Dye) writes:

 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Hi all,

 attached is a patch that enhances org-babel-goto-named-src-block (bound
 to C-c C-v g by default).  Included are two enhancements:

  1. the point is pushed to the org-mark-ring, such that returning with
 C-c  becomes possible
  2. the target src block is guessed from
  a) noweb-reference
  b) #+call:
  c) #+results:
  d) symbol-at-point
 if one of these is found (in that order)

 - Andreas


 Hi all,

 Should C-c  be included in Key Bindings and Useful Functions, Section
 14.11 of the Org Mode manual?  Or, is this a general Emacs thing
 documented elsewhere?

 Tom

In my opinion, it would be nice to have this listed in the Org Mode
manual.

- Andreas




Re: [O] Bug in odt export of org files with footnotes

2012-02-29 Thread Jambunathan K
Martin Gürtler martin.guert...@gmx.de writes:

 Hi,

 I started using the new odt export feature of org mode, and it turns out
 to be very useful, and I am very pleased with the results. I am using
 the latest version available with the package manager of emacs-snapshot
 in debian (20120216).

I am not sure what version of Orgmode this corresponds to...What does
M-x org-version RET say.

If Debian picks from Emacs-24.1 bzr repo then the Orgmode there is
atleast 2 months old.

If they are picking up from GNU ELPA, http://elpa.gnu.org/packages/ then
it is likely to be fairly recent.

 There, the export of documents with footnotes seems to be broken. 

Footnote export in ODT was known to be broken[1] with the following is
true:

,
|   (setq org-footnote-section nil)
`

May I know what value do you use one your end?

[1] http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg00124.html


 A minimal document is provided at end. It exports without problems . 

 As soon as I add a footnote (say, at the end of The software
 system...numbers:, the exported document breaks. It can still be
 opened in libreoffice, but a complete section is missing. 

Could you please try out the earlier suggestions?

Providing a complete Org file (with footnotes) is necessary so that
there is no confusion on what we are looking at.

With a footnotes added, I was able to export just fine with the version
of Org in the git repo.

 In a more complex document, libreoffice crashed when trying to open
 the document, and I recognised missing closing xml tags in
 content.xml.

To debug such issues see FAQ and Org manual.
- http://orgmode.org/worg/org-faq.html#debugging-org-odt
- (info (org) Validating OpenDocument XML)

You most likely need OpenDocument schema files available for validation
to proceed. This you can confirm by checking the value of:

C-h v org-export-odt-schema-dir

or visiting the directory

C-h v org-odt-data-dir

ODF schema files are available from the git repo. See link below. Make
sure you download the files in raw form.

http://orgmode.org/w/?p=org-mode.git;a=tree;f=contrib/odt/etc/schema;hb=HEAD

Let me know how things go.

-- 



Re: [O] Agenda custom command problems

2012-02-29 Thread James Harkins
At Mon, 27 Feb 2012 18:45:05 +0800,
James Harkins wrote:
 
 Hi,
 
 Two questions about agenda custom commands.

Hi,

Any ideas on these?

Short versions of the questions:

1. Why does Emacs ignore 2 out of 3 agenda custom commands, which I defined 
through the customize interface and appear in correct syntax in my ~/.emacs?

2. Why does (org-agenda-sorting-strategy (quote (time-up))) have no effect in a 
tags-todo search?

James

Details, for context:

 1. I've defined a few custom agenda commands, but the only one that actually 
 appears in the agenda dispatcher is 'z'. If I open Emacs and immediately C-h 
 v org-agenda-custom-commands, it says:
 
 Its value is 
 ((z tags-todo -ExamFdbk))
 
 But... The following block is one of the arguments to custom-set-variables in 
 my ~/.emacs. I used the customize interface to create the custom commands.
 
  '(org-agenda-custom-commands (quote ((z tags-todo -ExamFdbk nil) (1 
 Course-related TODOs tags-todo 
 +AudioClass|Lesson|MyConcert|Workshop11-Wk11plugs-Wk11Docs nil) (2 
 Spring semester TODOs tags-todo -Wk11plugs-Wk11Docs ((org-agenda-files 
 (quote (~/Documents/xinghai/11-12-spring/semester-spr.org))) 
 (org-agenda-sorting-strategy (quote (time-up
 
 If I manually execute the entire custom-set-variables block, after that, C-h 
 v shows the complete value.
 
 Quite funny... it's all there, but Emacs doesn't process it during 
 startup...? I've never seen that before with any other customize variable. 
 All the other customize variables are set correctly.
 
 Any ideas how to fix?
 
 2. I would like command 2 to show a subset of the TODOs (based on tags) in 
 one given file, sorted in order of time stamp. Everything is working except 
 the sorting: (org-agenda-sorting-strategy '(time-up)) is so far not having 
 any effect. The TODOs appear in the order of appearance in the file.
 
 I need time stamp order to see at a glance what I need to do today vs 
 tomorrow, etc.
 
 (2 Spring semester TODOs tags-todo -Wk11plugs-Wk11Docs
   ((org-agenda-files
 '(~/Documents/xinghai/11-12-spring/semester-spr.org))
(org-agenda-sorting-strategy
 '(time-up
 
 How to make the sorting strategy apply to a tags-todo search?
 
 (Sorry if these are boring questions... I'm not as deep into org as people 
 who are contributing emacs-lisp on list :)  These are just things that seem 
 like they should be working, according to the documentation, but they aren't.)


--
James Harkins /// dewdrop world
jamshar...@dewdrop-world.net
http://www.dewdrop-world.net

Come said the Muse,
Sing me a song no poet has yet chanted,
Sing me the universal.  -- Whitman

blog: http://www.dewdrop-world.net/words
audio clips: http://www.dewdrop-world.net/audio
more audio: http://soundcloud.com/dewdrop_world/tracks



Re: [O] Agenda custom command problems

2012-02-29 Thread James Harkins
At Wed, 29 Feb 2012 17:22:34 +0800,
James Harkins wrote:
 1. Why does Emacs ignore 2 out of 3 agenda custom commands, which I defined 
 through the customize interface and appear in correct syntax in my ~/.emacs?
 
 2. Why does (org-agenda-sorting-strategy (quote (time-up))) have no effect in 
 a tags-todo search?

Question #1 has a stupid answer. I had forgotten to remove another setq for 
org-agenda-custom commands later in my .emacs -- so this one is solved now.

Question #2 is open. Is there any way at all to change the sorting of a to-do 
list?

  2. I would like command 2 to show a subset of the TODOs (based on tags) 
  in one given file, sorted in order of time stamp. Everything is working 
  except the sorting: (org-agenda-sorting-strategy '(time-up)) is so far not 
  having any effect. The TODOs appear in the order of appearance in the file.
  
  I need time stamp order to see at a glance what I need to do today vs 
  tomorrow, etc.
  
  (2 Spring semester TODOs tags-todo -Wk11plugs-Wk11Docs
((org-agenda-files
  '(~/Documents/xinghai/11-12-spring/semester-spr.org))
 (org-agenda-sorting-strategy
  '(time-up

James


--
James Harkins /// dewdrop world
jamshar...@dewdrop-world.net
http://www.dewdrop-world.net

Come said the Muse,
Sing me a song no poet has yet chanted,
Sing me the universal.  -- Whitman

blog: http://www.dewdrop-world.net/words
audio clips: http://www.dewdrop-world.net/audio
more audio: http://soundcloud.com/dewdrop_world/tracks



Re: [O] Bug in odt export of org files with footnotes

2012-02-29 Thread Martin Gürtler
Hi,

thanks for quick response.

Am Mittwoch, den 29.02.2012, 14:51 +0530 schrieb Jambunathan K:
 Martin Gürtler martin.guert...@gmx.de writes:
 
 I am not sure what version of Orgmode this corresponds to...What does
 M-x org-version RET say.
7.8.03, I use elpa.

  There, the export of documents with footnotes seems to be broken. 
 
 Footnote export in ODT was known to be broken[1] with the following is
 true:
 
 ,
 |   (setq org-footnote-section nil)
 `
 
 May I know what value do you use one your end?
C-h v says org-footnote-section's value is Footnotes which seems to
be default and not the case you mention.
 Providing a complete Org file (with footnotes) is necessary so that
 there is no confusion on what we are looking at.
 
 With a footnotes added, I was able to export just fine with the version
 of Org in the git repo.
In my case, section 1.1 is missing. I attach the org file with footnote
and the resulting odt.

Cheers,

Martin


test.odt
Description: application/vnd.oasis.opendocument.text
#+TITLE: test.org
#+AUTHOR:Martin G�rtler
#+EMAIL: none@none
#+DATE:  2012-02-29 Wed
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  de
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t :nil
#+OPTIONS:   TeX:t LaTeX:dvipng skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 
path:http://orgmode.org/org-info.js
#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+LINK_UP:   
#+LINK_HOME: 
#+XSLT:
* Protocol
** System description
   The software system provides the following numbers:[fn:1]
   - 1
   - 2
   - 3
   - 4
   - 5
   - 6
   - 7
   - 8
   It also provides letters:
   - q
   - w
   - e
   - r
   - t
   - z
   - u
   - i

** Another subsection
   Just to have some more words...

* Footnotes

[fn:1] footnote



[O] Is it possible to refer to section numbers in links?

2012-02-29 Thread Martin Gürtler
Hi,

I wonder whether there is an easy way to refer to section numbers in ODT
export. TOCs including these numbers can be produced automatically
during export. Does anybody have an idea how one could access that
information inside the org file?

Thanks,

Martin




Re: [O] Bug in odt export of org files with footnotes

2012-02-29 Thread Jambunathan K

Martin

I am attaching a patch that should fix this issue. I will let Nicolas
review/apply it.

ps: If you are not comfortable applying patches, the best way to get
things working again, is to force a blank line before the first
non-commented line in your Org file i.e., replace

--8---cut here---start-8---
[snip]
#+XSLT:
* Protocol
--8---cut here---end---8---

with 

--8---cut here---start-8---
[snip]
#+XSLT:

* Protocol
--8---cut here---end---8---

in the test file that you circulated.

#+TITLE: test.org
#+AUTHOR:Martin Gürtler
#+EMAIL: none@none
#+DATE:  2012-02-29 Wed
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  de
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t :nil
#+OPTIONS:   TeX:t LaTeX:dvipng skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js
#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+LINK_UP:   
#+LINK_HOME: 
#+XSLT:
* Protocol
** System description
   The software system provides the following numbers:[fn:1]
   - 1
   - 2
   - 3
   - 4
   - 5
   - 6
   - 7
   - 8
   It also provides letters[fn:2]:
   - q
   - w
   - e
   - r
   - t
   - z
   - u
   - i

** Another subsection
   Just to have some more words...

* Footnotes

[fn:1] footnote

[fn:2] testing

From d09cc7bb3bdb1b32b32fae14b722f4d4c8b0ef79 Mon Sep 17 00:00:00 2001
From: Jambunathan K kjambunat...@gmail.com
Date: Wed, 29 Feb 2012 20:09:44 +0530
Subject: [PATCH] org-footnote: Workaround a limitation in the ODT exporter

* lisp/org-footnote.el (org-footnote-normalize): Force a paragraph
break after the last footnote definition.  This is an an
implicit assumption made by the org-lparse.el library.  With
this change, footnote definitions can reliably be exported
with ODT backend.  See
http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg01013.html.
---
 lisp/org-footnote.el |2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/lisp/org-footnote.el b/lisp/org-footnote.el
index c848bae..f4ea7ff 100644
--- a/lisp/org-footnote.el
+++ b/lisp/org-footnote.el
@@ -810,7 +810,7 @@ Additional note on `org-footnote-insert-pos-for-preprocessor':
 	  (lambda (x)
 	(format \n[%s] %s (nth (if sort-only 0 1) x) (nth 2 x)))
 	  ref-table \n))
-	(unless (eobp) (insert \n))
+	(unless (eobp) (insert \n\n))
 	;; When exporting, add newly inserted markers along with their
 	;; associated definition to `org-export-footnotes-seen'.
 	(when export-props (setq org-export-footnotes-seen ref-table)))
-- 
1.7.5.1


Martin Gürtler martin.guert...@gmx.de writes:

 Hi,

 thanks for quick response.

 Am Mittwoch, den 29.02.2012, 14:51 +0530 schrieb Jambunathan K:
 Martin Gürtler martin.guert...@gmx.de writes:
 
 I am not sure what version of Orgmode this corresponds to...What does
 M-x org-version RET say.
 7.8.03, I use elpa.

  There, the export of documents with footnotes seems to be broken. 
 
 Footnote export in ODT was known to be broken[1] with the following is
 true:
 
 ,
 |   (setq org-footnote-section nil)
 `
 
 May I know what value do you use one your end?
 C-h v says org-footnote-section's value is Footnotes which seems to
 be default and not the case you mention.
 Providing a complete Org file (with footnotes) is necessary so that
 there is no confusion on what we are looking at.
 
 With a footnotes added, I was able to export just fine with the version
 of Org in the git repo.
 In my case, section 1.1 is missing. I attach the org file with footnote
 and the resulting odt.

 Cheers,

 Martin


Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Thomas S. Dye
Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 t...@tsdye.com (Thomas S. Dye) writes:

 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Hi all,

 attached is a patch that enhances org-babel-goto-named-src-block (bound
 to C-c C-v g by default).  Included are two enhancements:

  1. the point is pushed to the org-mark-ring, such that returning with
 C-c  becomes possible
  2. the target src block is guessed from
  a) noweb-reference
  b) #+call:
  c) #+results:
  d) symbol-at-point
 if one of these is found (in that order)

 - Andreas


 Hi all,

 Should C-c  be included in Key Bindings and Useful Functions, Section
 14.11 of the Org Mode manual?  Or, is this a general Emacs thing
 documented elsewhere?

 Tom

 In my opinion, it would be nice to have this listed in the Org Mode
 manual.

 - Andreas



Hi Andreas,

Is C-c  correct here?  On my system I can jump back following the
instructions:
Position saved to mark ring, go back with M-x org-mark-ring-goto.

But C-c  waits for more input.

Tom
-- 
Thomas S. Dye
http://www.tsdye.com



Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

2012-02-29 Thread Eric Schulte
Moving forward on this point, many of the existing tests explicitly
`require' new Org-mode functionality (mainly language support for
testing code blocks execution).  I do not think that tests should ever
be activating new packages changing a users global environment.

For this reason I have just pushed up a commit which changes all

  (require 'org-foo)

to

  (unless (featurep 'org-foo)
(signal 'missing-test-dependency Org support for doing foo.))

so that those tests simple aren't run on the users system.  Please let
me know if anyone thinks this is a mistake and we can discuss.  The only
drawback I see is that batch-mode scripts will have to explicitly
activate the features which they would like to test, by evaluating forms
like (require 'org-foo) before the call to the test suite -- and I would
argue that being explicit about such things is a benefit.

Cheers,

Achim Gratz strom...@nexgo.de writes:

 Tests for experimental org features (e.g. from contrib/ ) should expect
 to fail when the user has not configured their inclusion into the
 current setup.  In other words, things like (require org-element)
 should not break the test run, but instead just note that this test has
 failed expectedly and continue testing.


 Regards,
 Achim.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
t...@tsdye.com (Thomas S. Dye) writes:

 cbe...@tajo.ucsd.edu writes:

 I sometimes create large documents with many dozens of src blocks and
 associated #+RESULTS.

 I'd like to be able to grab some of these results blocks and export them
 into a document. Since revisions of the src blocks can change the
 results, I do not want to just and to copy and paste the results in case
 I need to revise the sub-document(s).

 And with long running blocks, I do not want to use a noweb strategy to
 rerun the code in the src blocks.

 As an example, I might have this in a file with many other headlines
 and src blocks:

 ,
 | * Selectively Export Some Results
 |   :PROPERTIES:
 |   :EXPORT_FILE_NAME: Selected_Results.pdf
 |   :EXPORT_TITLE: Selected Results
 |   :END:
 | 
 | Here are the results from block named Ablock:
 | 
 | #+CALL: show-results(Ablock)
 | 
 | and here they are for a block named Bblock:
 | 
 | #+CALL: show-results(Bblock)
 `

 and if I put point on the headline and type C-c @ C-c C-e d, I'd like
 to have a document that includes the two results blocks in it after each 
 CALL line.

 It looks like many of the pieces I need are available, but I don't see
 how to stitch them together to create the show-results() function.

 TIA,

 Chuck

 Hi Chuck,


Thanks for the reply.

 Does this do what you want?

No. 

When I put point under the headline and type C-c @ C-c C-e d, it prompts
me to evaluate each of the blocks, and when I answer 'no' to each, it
produces a document that omits the previously computed results.

What I want is to grab *existing* results blocks and use them. 

And if at a later date some of those results blocks have changed, when I
again put point under the headline and type C-c @ C-c C-e d, I'd like
the newer blocks to be updated.

The computations in some blocks run for many minutes, so it is
impractical to recompute them every time I want to tweak the format of a
document that depends on them.


Chuck


  * Selectively Export Some Results
:PROPERTIES:
:EXPORT_FILE_NAME: Selected_Results.pdf
:EXPORT_TITLE: Selected Results
:END:
  
  Here are the results from block named Ablock:
  
  #+CALL: Ablock() :exports results
  
  and here they are for a block named Bblock:
  
  #+CALL: Bblock() :exports results

 All the best,
 Tom

-- 
Charles C. BerryDept of Family/Preventive Medicine
cberry at ucsd edu  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901




Re: [O] Selectively export RESULTS

2012-02-29 Thread Eric Schulte
 Does this do what you want?

 No. 

 When I put point under the headline and type C-c @ C-c C-e d, it prompts
 me to evaluate each of the blocks, and when I answer 'no' to each, it
 produces a document that omits the previously computed results.

 What I want is to grab *existing* results blocks and use them. 

 And if at a later date some of those results blocks have changed, when I
 again put point under the headline and type C-c @ C-c C-e d, I'd like
 the newer blocks to be updated.

 The computations in some blocks run for many minutes, so it is
 impractical to recompute them every time I want to tweak the format of a
 document that depends on them.


Hi Chuck,

Have you looked at the :cache header argument [1], from my understanding
of your use case it should be exactly what you are after.

Best,

Footnotes: 
[1]  http://orgmode.org/manual/cache.html

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] [PATCH] Option for clock and timer to be displayed in frame-title

2012-02-29 Thread George Kettleborough
On Tue, Feb 28 2012, Bernt Hansen wrote:
 This patch needs a changelog entry in the commit text and a long
 description would also be appreciated.  The long description allows us
 to see the purpose of the patch and how to use it without the necessity
 to read and parse any of the code changes.

Ok, I've done a changelog entry.  I hope this is what is expected.
(Also fixed a minor bug in original patch and added better documentation
to the new custom variable).

The patch adds options to both org-clock and org-timer regarding how the
current clock/timer is displayed.  Currently they are both displayed in
the mode line.  This is not ideal since if you split your window
horizontally then the mode line becomes quite short so often the clock
is truncated and the timer might not even be visible.

The new options control whether the clock/timer is displayed in the mode
line and/or frame title.  The frame title is usually wasted space for
people running a graphical version of emacs so it is quite useful there
I think.

From 23b45a824a6118a6aa51ae1ad734747b54ee2f08 Mon Sep 17 00:00:00 2001
From: George Kettleborough g.kettleboro...@member.fsf.org
Date: Wed, 29 Feb 2012 17:04:22 +
Subject: [PATCH] Option for clock and timer to be displayed in frame-title

* lisp/org-clock.el: Add variable org-clock-clocked-in-display which controls
whether the current clock is displayed in the mode line and/or frame title.

* lisp/org-timer.el: Add variable org-timer-display which controls whether the
current timer is displayed in the mode line and/or frame title.

This allows the clock and timer to be displayed in the frame title instead of,
or as well as, the mode line.  This is useful for people with limited space in
the mode line but with ample space in the frame title.
---
 lisp/org-clock.el |   52 
 lisp/org-timer.el |   50 ++
 2 files changed, 86 insertions(+), 16 deletions(-)

diff --git a/lisp/org-clock.el b/lisp/org-clock.el
index 9206608..b5a9a1b 100644
--- a/lisp/org-clock.el
+++ b/lisp/org-clock.el
@@ -323,6 +323,22 @@ play with them.
   :version 24.1
   :type 'boolean)
 
+(defcustom org-clock-clocked-in-display 'mode-line
+  When clocked in for a task, org-mode can display the current
+task and accumulated time in the mode line and/or frame title.
+Allowed values are:
+
+both displays in both mode line and frame title
+mode-linedisplays only in mode line (default)
+frame-title  displays only in frame title
+nil  current clock is not displayed
+  :group 'org-clock
+  :type '(choice
+	  (const :tag Mode line mode-line)
+	  (const :tag Frame title frame-title)
+	  (const :tag Both both)
+	  (const :tag None nil)))
+
 (defvar org-clock-in-prepare-hook nil
   Hook run when preparing the clock.
 This hook is run before anything happens to the task that
@@ -345,6 +361,8 @@ to add an effort property.)
 (defvar org-mode-line-string )
 (put 'org-mode-line-string 'risky-local-variable t)
 
+(defvar org-frame-title-string '(  org-mode-line-string))
+
 (defvar org-clock-mode-line-timer nil)
 (defvar org-clock-idle-timer nil)
 (defvar org-clock-heading) ; defined in org.el
@@ -1170,18 +1188,28 @@ the clocking selection, associated with the letter `d'.
 			 (save-excursion (org-back-to-heading t) (point))
 			 (buffer-base-buffer))
 	(setq org-clock-has-been-used t)
-	(or global-mode-string (setq global-mode-string '()))
-	(or (memq 'org-mode-line-string global-mode-string)
-		(setq global-mode-string
-		  (append global-mode-string '(org-mode-line-string
+	;; add to mode line
+	(when (or (eq org-clock-clocked-in-display 'mode-line)
+		  (eq org-clock-clocked-in-display 'both))
+	  (or global-mode-string (setq global-mode-string '()))
+	  (or (memq 'org-mode-line-string global-mode-string)
+		  (setq global-mode-string
+			(append global-mode-string '(org-mode-line-string)
+	;; add to frame title
+	(when (or (eq org-clock-clocked-in-display 'frame-title)
+		  (eq org-clock-clocked-in-display 'both))
+	  (or (memq 'org-frame-title-string frame-title-format)
+		  (setq frame-title-format
+			(append frame-title-format '(org-frame-title-string)
 	(org-clock-update-mode-line)
 	(when org-clock-mode-line-timer
 	  (cancel-timer org-clock-mode-line-timer)
 	  (setq org-clock-mode-line-timer nil))
-	(setq org-clock-mode-line-timer
-		  (run-with-timer org-clock-update-period
-  org-clock-update-period
-  'org-clock-update-mode-line))
+	(when org-clock-clocked-in-display
+	  (setq org-clock-mode-line-timer
+		(run-with-timer org-clock-update-period
+org-clock-update-period
+'org-clock-update-mode-line)))
 	(when org-clock-idle-timer
 	  (cancel-timer org-clock-idle-timer)
 	  (setq org-clock-idle-timer nil))
@@ -1329,6 +1357,8 @@ If there is no running clock, throw an error, unless 

[O] Rebased to the latest tip

2012-02-29 Thread Max Mikhanosha
At Tue, 28 Feb 2012 10:57:11 -0600,
Marcelo de Moraes Serpa wrote:
 
 Anyway, I can't emphasize enough how useful this feature is. Having
 different agenda filtered views at the same time is a
 timesaver. This should be in the main org branch! 


Thanks for the kind words, I think you are the only person who
seriously tried it.

As for merging its up to the maintainers. If there are any objections
or code needs to be cleaned up or such, I have not heard anything.

Anyway I had re-based multiple-agenda-buffers branch to the latest
origin/master, and it seems to have went smoothly, and pushed to
https://github.com/7max/org-mode

Regards,
  Max




Re: [O] Is it possible to refer to section numbers in links?

2012-02-29 Thread Jambunathan K
Martin Gürtler martin.guert...@gmx.de writes:

 Hi,

 I wonder whether there is an easy way to refer to section numbers in ODT
 export. TOCs including these numbers can be produced automatically
 during export. Does anybody have an idea how one could access that
 information inside the org file?

What you ask for, is currently not possible. It is easily doable
though. I will add your request to my TODO list. I will let you know
once I am done with it.

For the sake of clarity and for my own later reference, does the
attached Org file/ODT file capture what you want? One of the links in
the ODT file is hand-edited with LibreOffice for the sake of
illustration.
-- 


xref.odt
Description: application/vnd.oasis.opendocument.text
#+TITLE: xref.org
#+AUTHOR:Jambunathan K
#+EMAIL: kjambunat...@gmail.com
#+DATE:  2012-02-29 Wed
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  en
#+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t :t
#+OPTIONS:   TeX:t LaTeX:dvipng skip:nil d:t todo:t pri:nil tags:t

#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+LINK_UP:   
#+LINK_HOME: 
#+XSLT:



* First Headline

* Second Headline

  This is what ODT exporter does right now - [[First%20Headline][First Headline]].This is
  what I want instead - .


[O] Org appt notifications with Growl (OSX)

2012-02-29 Thread Marcelo de Moraes Serpa
Hi folks,

What is the best way to setup notifications to work with Growl for orgmode?
I know org can work with emacs Appt system, but is anyone currently using
it with Growl for notifications?

If you could point me to the right direction, I'd be grateful.

- Marcelo.


Re: [O] Bug: ditaa breaks export [7.8.03]

2012-02-29 Thread Eric Schulte
Thomas Holst thomas.ho...@de.bosch.com writes:

 Hello orgers,

 · Ian Dalton iain.dal...@gmail.com wrote:

 When I run `emacs -q' and evaluate `(setq org-babel-load-languages
 '((ditaa . t)))', then try to export an org document to PDF, after
 answering yes to Evaluate this ditaa code block, I get:

 Wrong type argument: stringp, nil

 Emacs  : GNU Emacs 24.0.93.1 (i486-pc-linux-gnu, GTK+ Version 2.20.1)
  of 2012-02-22 on cw-bkp0, modified by Debian
 Package: Org-mode version 7.8.03

 I can confirm this.

 A little investigation shows that there are two definitions for
 `org-ditaa-jar-path':


Thanks for running down the cause of this problem and suggesting a fix.
I've just applied your suggestion.  The redundant definition is now
removed from ob-ditaa and ob-ditaa requires org-exp-blocks.

Cheers,


 - in =lisp/ob-ditaa.el=:
   #+begin_src emacs-lisp
 (defcustom org-ditaa-jar-path nil
   Path for the ditaa jar file.
   :group 'org-babel
   :type 'string)
   #+end_src

   This results in nil and so the error occurs.
   
 - in =lisp/org-exp-blocks.el=
   #+begin_src emacs-lisp
 (defvar org-ditaa-jar-path (expand-file-name
   ditaa.jar
   (file-name-as-directory
(expand-file-name
 scripts
 (file-name-as-directory
  (expand-file-name
   ../contrib
   (file-name-directory (or load-file-name 
 buffer-file-name)))
   Path to the ditaa jar executable.)
   #+end_src

   On my machine this results in the correct path.

 So the value of `org-ditaa-jar-path' depends on the loading sequence of
 el-files.

 A quick solution for OP would be to the set the path

 #+begin_src emacs-lisp
   (setq org-ditaa-jar-path path-to-ditaa-jar)
 #+end_src

 I am not too deep into dependencies of org files, but ob-ditaa.el could
 require org-exp-blocks and skip the definition of `org-ditaa-jar-path'.
 Or vice versa.

 HTH

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] Org appt notifications with Growl (OSX)

2012-02-29 Thread Nick Dokos
Marcelo de Moraes Serpa celose...@gmail.com wrote:

 Hi folks,
 
 What is the best way to setup notifications to work with Growl for orgmode? I 
 know org can work with
 emacs Appt system, but is anyone currently using it with Growl for 
 notifications? 
 
 If you could point me to the right direction, I'd be grateful.
 

Somebody asked the same question back in 2010:

   http://thread.gmane.org/gmane.emacs.orgmode/27530

Oh, wait - it was you :-)

There were a few replies back then: have you tried those
suggestions?

Nick




[O] bug: syntax corruption in link

2012-02-29 Thread Samuel Wales
In the following paragraph, the highlighted and active link
is Severity as expected and the link is correct.

If you remove the spaces after the period, the label and
link are both corrupted.

  If you are an advocate or want to be, the most important
  article is 
[[http://thekafkapandemic.blogspot.com/2011/06/severity.html][Severity]].
 If

If your goal is to separate the paragraph into two
paragraphs, a natural sequence is to put point at I, press
backspace twice, and press RET.

Unexpectedly, RET tries to follow a link.

Thanks.

Samuel

-- 
The Kafka Pandemic: http://thekafkapandemic.blogspot.com



Re: [O] Org appt notifications with Growl (OSX)

2012-02-29 Thread Shine Zhong
There is a good tool integrate with Growl, todochiku
http://www.emacswiki.org/emacs/ToDoChiKu


Here is the section of my .emacs
---
;; begin todochiku, enable the growlnotify
(load-file ~/.emacs.d/plugins/todochiku.el)
(setq todochiku-icons-directory ~/Downloads/todochiku-icons)
;; end todochiku


;; begin: orgmode + appt
; For org appointment reminders
;; Get appointments for today
(defun my-org-agenda-to-appt ()
  (interactive)
  (setq appt-time-msg-list nil)
  (org-agenda-to-appt))

;; Run once, activate and schedule refresh
(my-org-agenda-to-appt)
(appt-activate t)
(run-at-time 24:01 nil 'my-org-agenda-to-appt)

; Update appt each time agenda opened.
(add-hook 'org-finalize-agenda-hook 'my-org-agenda-to-appt)
;; end:   orgmode + appt
---


Regards,
Shine


On Wed, Feb 29, 2012 at 10:35 AM, Nick Dokos nicholas.do...@hp.com wrote:

 Marcelo de Moraes Serpa celose...@gmail.com wrote:

  Hi folks,
 
  What is the best way to setup notifications to work with Growl for
 orgmode? I know org can work with
  emacs Appt system, but is anyone currently using it with Growl for
 notifications?
 
  If you could point me to the right direction, I'd be grateful.
 

 Somebody asked the same question back in 2010:

   http://thread.gmane.org/gmane.emacs.orgmode/27530

 Oh, wait - it was you :-)

 There were a few replies back then: have you tried those
 suggestions?

 Nick





Re: [O] taskjuggler3 export

2012-02-29 Thread d . tchin
Hi, 

I use the following testtj3.org file that I export to taskjuggler 3.0 :

,
|#+TITLE: testtj3.org   
  
|#+PROPERTY: Effort_ALL 2d 5d 10d 20d 30d 35d 50d 
| 
|* Action list  :taskjuggler_project:  
|** TODO Test tj3 A   
|:PROPERTIES:
|:Effort:   1w
|:allocate: toA  
|:END:
|** TODO Test tj3 B   
|:PROPERTIES: 
|:Effort:   1w
|:allocate: toB   
|:BLOCKER:  previous-sibling  
|:END:
|** TODO Test 2 tj3 
|:PROPERTIES: 
|:Effort:   2w
|:allocate:  toA  
|:BLOCKER:  previous-sibling
|:END:
|** TODO Test 2 tj3 B
|:PROPERTIES: 
|:Effort:   2w   
|:allocate: toB 
|:BLOCKER: previous-sibling   
|:END:
|* Ressources  :taskjuggler_resource: 
|** A 
|:PROPERTIES: 
|:resource_id: toA
|:END:   
|** B 
|:PROPERTIES:   
|:resource_id: toB   
|:END:   
| 
|# Local Variables:   
|# org-export-taskjuggler-target-version: 3.0   
|# org-export-taskjuggler-default-reports: (include \gantexport.tji\)  
|# End:
`

As you can see, I define in the org-export-taskjuggler-default-reports 
variable at the end of the file that I want to use gantexport.tji where the 
gant output directives are defined. This file is in the same directory as org 
file.

The gantexport.tji is the following :

,-
|### begin report definition   
|  
|taskreport Gantt Chart {
|  headline Project Gantt Chart  
|  columns hierarchindex, name, start, end, effort, duration, completed, 
chart  
|  timeformat %Y-%m-%d   
|  hideresource 1  
|  formats html
|  loadunit shortauto  
|}
`-

Then the instruction tj3 testtj3.tjp generate the gant chart accessible 
in Gantt Chart.html file.

Hope that can help.






[O] [PATCH] org-agenda-list (from git) giving args-out-of-range error

2012-02-29 Thread Karl Fogel
Nick Dokos nicholas.do...@hp.com writes:
There have been a couple of recent reports on this problem (headlines
with just a timestamp cause this error) in addition to the ones you
found:

http://thread.gmane.org/gmane.emacs.orgmode/52621
http://thread.gmane.org/gmane.emacs.orgmode/52786

The first one contains a diagnosis and a (possibly wrong) suggested fix.

Thank you, Nick.  I eventually found the same cause, by doing a
binary-search reduction of the problematic .org file until I knew
exactly which headline was the source of the problem.  It was a
second-level headline with a date but no content...

  ** 2012-02-27 Mon

...as described in James Atwood's mail (the second one you list above).

It's relevant that the line ends immediately after the .  If there is
even one space after the , then the bug does not reproduce.  This
makes sense, given the code.  I have a tentative patch, which is
attached.  What's the typical way to submit such things for review?

From 8a4c65479b2f62cbffe32735c4afac5dd6a1ecae Mon Sep 17 00:00:00 2001
From: Karl Fogel kfo...@red-bean.com
Date: Wed, 29 Feb 2012 13:06:06 -0600
Subject: [PATCH] * lisp/org-agenda.el (org-agenda-highlight-todo): Handle the
 case of a heading that has a date but no todo keyword. 
 This is a fix for the args-out-of-range bug discussed in
 these threads

  http://thread.gmane.org/gmane.emacs.orgmode/52621
  http://thread.gmane.org/gmane.emacs.orgmode/52793
  http://thread.gmane.org/gmane.emacs.orgmode/52786
  http://thread.gmane.org/gmane.emacs.orgmode/52810

among Ilya Shlyakhter, James Atwood, Nick Dokos, and myself.  The subject 
headers are:

  bug report: agenda timeline crashes
  Bug report: weekly agenda and blank, timestamped headers
  org-agenda-list (from git) giving args-out-of-range error
---
 lisp/org-agenda.el |   12 +++-
 1 files changed, 11 insertions(+), 1 deletions(-)

diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index 98a2cc0..ac1b5b1 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -5889,8 +5889,18 @@ could bind the variable in the options section of a 
custom command.)
   (let ((pl (text-property-any 0 (length x) 'org-heading t x)))
(setq re (get-text-property 0 'org-todo-regexp x))
(when (and re
+  ;; Test `pl' because if there's no heading content,
+  ;; there's no point matching to highlight.  Note
+  ;; that if we didn't test `pl' first, and there
+  ;; happened to be no keyword from `org-todo-regexp'
+  ;; on this heading line, then the `equal' comparison
+  ;; afterwards would spuriously succeed in the case
+  ;; where `pl' is nil -- causing an args-out-of-range
+  ;; error when we try to add text properties to text
+  ;; that isn't there.
+  pl
   (equal (string-match (concat \\(\\.*\\) re \\( +\\))
-   x (or pl 0)) pl))
+   x pl) pl))
  (add-text-properties
   (or (match-end 1) (match-end 0)) (match-end 0)
   (list 'face (org-get-todo-face (match-string 2 x)))
-- 
1.7.9



Re: [O] [PATCH] org-agenda-list (from git) giving args-out-of-range error

2012-02-29 Thread Nick Dokos
Karl Fogel kfo...@red-bean.com wrote:

 Nick Dokos nicholas.do...@hp.com writes:
 There have been a couple of recent reports on this problem (headlines
 with just a timestamp cause this error) in addition to the ones you
 found:
 
 http://thread.gmane.org/gmane.emacs.orgmode/52621
 http://thread.gmane.org/gmane.emacs.orgmode/52786
 
 The first one contains a diagnosis and a (possibly wrong) suggested fix.
 
 Thank you, Nick.  I eventually found the same cause, by doing a
 binary-search reduction of the problematic .org file until I knew
 exactly which headline was the source of the problem.  It was a
 second-level headline with a date but no content...
 
   ** 2012-02-27 Mon
 
 ...as described in James Atwood's mail (the second one you list above).
 
 It's relevant that the line ends immediately after the .  If there is
 even one space after the , then the bug does not reproduce.  This
 makes sense, given the code.  I have a tentative patch, which is
 attached.  What's the typical way to submit such things for review?
 

Exactly what you've done: send the patch to the list.

Modulo possible changelog formatting issues (see
http://orgmode.org/worg/org-contribute.html#sec-5 for the gory details),
the patch looks good to me. Thanks for submitting it!

Nick


 From 8a4c65479b2f62cbffe32735c4afac5dd6a1ecae Mon Sep 17 00:00:00 2001
 From: Karl Fogel kfo...@red-bean.com
 Date: Wed, 29 Feb 2012 13:06:06 -0600
 Subject: [PATCH] * lisp/org-agenda.el (org-agenda-highlight-todo): Handle the
  case of a heading that has a date but no todo keyword. 
  This is a fix for the args-out-of-range bug discussed in
  these threads
 
   http://thread.gmane.org/gmane.emacs.orgmode/52621
   http://thread.gmane.org/gmane.emacs.orgmode/52793
   http://thread.gmane.org/gmane.emacs.orgmode/52786
   http://thread.gmane.org/gmane.emacs.orgmode/52810
 
 among Ilya Shlyakhter, James Atwood, Nick Dokos, and myself.  The subject 
 headers are:
 
   bug report: agenda timeline crashes
   Bug report: weekly agenda and blank, timestamped headers
   org-agenda-list (from git) giving args-out-of-range error
 ---
  lisp/org-agenda.el |   12 +++-
  1 files changed, 11 insertions(+), 1 deletions(-)
 
 diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
 index 98a2cc0..ac1b5b1 100644
 --- a/lisp/org-agenda.el
 +++ b/lisp/org-agenda.el
 @@ -5889,8 +5889,18 @@ could bind the variable in the options section of a 
 custom command.)
(let ((pl (text-property-any 0 (length x) 'org-heading t x)))
   (setq re (get-text-property 0 'org-todo-regexp x))
   (when (and re
 +;; Test `pl' because if there's no heading content,
 +;; there's no point matching to highlight.  Note
 +;; that if we didn't test `pl' first, and there
 +;; happened to be no keyword from `org-todo-regexp'
 +;; on this heading line, then the `equal' comparison
 +;; afterwards would spuriously succeed in the case
 +;; where `pl' is nil -- causing an args-out-of-range
 +;; error when we try to add text properties to text
 +;; that isn't there.
 +pl
  (equal (string-match (concat \\(\\.*\\) re \\( +\\))
 - x (or pl 0)) pl))
 + x pl) pl))
 (add-text-properties
  (or (match-end 1) (match-end 0)) (match-end 0)
  (list 'face (org-get-todo-face (match-string 2 x)))
 -- 
 1.7.9
 



Re: [O] [PATCH] org-agenda-list (from git) giving args-out-of-range error

2012-02-29 Thread Karl Fogel
Nick Dokos nicholas.do...@hp.com writes:
Exactly what you've done: send the patch to the list.

Modulo possible changelog formatting issues (see
http://orgmode.org/worg/org-contribute.html#sec-5 for the gory details),
the patch looks good to me. Thanks for submitting it!

Oh, thanks -- I should have looked for those guidelines first.  Here is
the same patch, but with a properly-done log message this time.

I already have copyright assignment papers on file at the FSF for Emacs
itself, by the way; does that cover us for Org Mode too?

From 7809b35a6e88640006753e28bcb87a6b66a80639 Mon Sep 17 00:00:00 2001
From: Karl Fogel kfo...@red-bean.com
Date: Wed, 29 Feb 2012 13:42:35 -0600
Subject: [PATCH] Fix bug whereby a date-only line caused an error when
 generating an agenda

* lisp/org-agenda.el (org-agenda-highlight-todo): Handle the case of a heading 
that has a date but no todo keyword.

This is a fix for the args-out-of-range bug discussed in these threads:

  http://thread.gmane.org/gmane.emacs.orgmode/52621
  http://thread.gmane.org/gmane.emacs.orgmode/52793
  http://thread.gmane.org/gmane.emacs.orgmode/52786
  http://thread.gmane.org/gmane.emacs.orgmode/52810

The discussions involved Ilya Shlyakhter, James Atwood, Nick Dokos,
and myself, and the subject headers are:

  bug report: agenda timeline crashes
  Bug report: weekly agenda and blank, timestamped headers
  org-agenda-list (from git) giving args-out-of-range error

TINYCHANGE
---
 lisp/org-agenda.el |   12 +++-
 1 files changed, 11 insertions(+), 1 deletions(-)

diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index 98a2cc0..ac1b5b1 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -5889,8 +5889,18 @@ could bind the variable in the options section of a 
custom command.)
   (let ((pl (text-property-any 0 (length x) 'org-heading t x)))
(setq re (get-text-property 0 'org-todo-regexp x))
(when (and re
+  ;; Test `pl' because if there's no heading content,
+  ;; there's no point matching to highlight.  Note
+  ;; that if we didn't test `pl' first, and there
+  ;; happened to be no keyword from `org-todo-regexp'
+  ;; on this heading line, then the `equal' comparison
+  ;; afterwards would spuriously succeed in the case
+  ;; where `pl' is nil -- causing an args-out-of-range
+  ;; error when we try to add text properties to text
+  ;; that isn't there.
+  pl
   (equal (string-match (concat \\(\\.*\\) re \\( +\\))
-   x (or pl 0)) pl))
+   x pl) pl))
  (add-text-properties
   (or (match-end 1) (match-end 0)) (match-end 0)
   (list 'face (org-get-todo-face (match-string 2 x)))
-- 
1.7.9



Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Jonathan Leech-Pepin
Hello Thomas,

I ran into exactly that question this morning and managed to figure it out.

If I use emacs -q then C-c  works as expected and is mapped to
(org-mark-ring-goto  optional N).  However when trying C-c  C-h I find
out that C-c  is a prefix for a few yasnippet commands:

,
| `yas/minor-mode' Minor Mode Bindings Starting With C-c :
| key binding
| --- ---
|
| C-c  C-f yas/find-snippets
| C-c  C-n yas/new-snippet
| C-c  C-s yas/insert-snippet
| C-c  C-v yas/visit-snippet-file
`

Seems this is another place where yas and org don't get along well together

On Wed, Feb 29, 2012 at 11:09, Thomas S. Dye t...@tsdye.com wrote:
 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 t...@tsdye.com (Thomas S. Dye) writes:

 Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Hi all,

 attached is a patch that enhances org-babel-goto-named-src-block (bound
 to C-c C-v g by default).  Included are two enhancements:

  1. the point is pushed to the org-mark-ring, such that returning with
 C-c  becomes possible
  2. the target src block is guessed from
  a) noweb-reference
  b) #+call:
  c) #+results:
  d) symbol-at-point
 if one of these is found (in that order)

 - Andreas


 Hi all,

 Should C-c  be included in Key Bindings and Useful Functions, Section
 14.11 of the Org Mode manual?  Or, is this a general Emacs thing
 documented elsewhere?

 Tom

 In my opinion, it would be nice to have this listed in the Org Mode
 manual.

 - Andreas



 Hi Andreas,

 Is C-c  correct here?  On my system I can jump back following the
 instructions:
 Position saved to mark ring, go back with M-x org-mark-ring-goto.

 But C-c  waits for more input.

 Tom
 --
 Thomas S. Dye
 http://www.tsdye.com



Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

2012-02-29 Thread Achim Gratz
Eric Schulte eric.schu...@gmx.com writes:
 Moving forward on this point, many of the existing tests explicitly
 `require' new Org-mode functionality (mainly language support for
 testing code blocks execution).  I do not think that tests should ever
 be activating new packages changing a users global environment.

Thanks.

I've had to deactivate the inclusion of ./testing/lisp/contrib into the
test flow due to a recent removal of said directory by Nicolas (he's
probably doing that patch himself) and now get this:

lisp/org-mode make test-dirty | grep failed
   failed5/109  ob-exp/export-from-a-temp-buffer
   failed   17/109  org-missing-dependency/test-ob-C
   failed   18/109  org-missing-dependency/test-ob-R
   failed   19/109  org-missing-dependency/test-ob-awk
   failed   20/109  org-missing-dependency/test-ob-fortran
   failed   21/109  org-missing-dependency/test-ob-lilypond
   failed   22/109  org-missing-dependency/test-ob-maxima
   failed   23/109  org-missing-dependency/test-ob-octave
   failed   24/109  org-missing-dependency/test-ob-python
   failed   25/109  org-missing-dependency/test-org-element
   failed   26/109  org-missing-dependency/test-org-export

This is expected, as my local configuration doesn't have any of these
packages activated.

lisp/org-mode make test-dirty |  grep FAILED
   FAILED   27/109  test-ob-exp/org-babel-exp-src-blocks/w-no-file
   FAILED   62/109  test-org-babel/get-src-block-info-body
   FAILED   63/109  test-org-babel/get-src-block-info-language
   FAILED   64/109  test-org-babel/get-src-block-info-tangle

This is unexpected and I don't really see where they are coming from.
The backtrace always starts at (regexp-quote org-test-file-ob-anchor).

 For this reason I have just pushed up a commit which changes all

   (require 'org-foo)

 to

   (unless (featurep 'org-foo)
 (signal 'missing-test-dependency Org support for doing foo.))

 so that those tests simple aren't run on the users system.  Please let
 me know if anyone thinks this is a mistake and we can discuss.  The only
 drawback I see is that batch-mode scripts will have to explicitly
 activate the features which they would like to test, by evaluating forms
 like (require 'org-foo) before the call to the test suite -- and I would
 argue that being explicit about such things is a benefit.

Well, currently all testing runs under my user settings, which is not
ideal for testing anyway.  I suppose it would not be difficult to just
inject a different (minimal) startup file specifically for testing to
separate these issues.


Regards,
Achim.
-- 
+[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+

SD adaptations for KORG EX-800 and Poly-800MkII V0.9:
http://Synth.Stromeko.net/Downloads.html#KorgSDada




Re: [O] Is it possible to refer to section numbers in links?

2012-02-29 Thread Martin Gürtler
Am Mittwoch, den 29.02.2012, 23:26 +0530 schrieb Jambunathan K:
 Martin Gürtler martin.guert...@gmx.de writes:
 
  Hi,
 
  I wonder whether there is an easy way to refer to section numbers in ODT
  export. TOCs including these numbers can be produced automatically
  during export. Does anybody have an idea how one could access that
  information inside the org file?
 
 What you ask for, is currently not possible. It is easily doable
 though. I will add your request to my TODO list. I will let you know
 once I am done with it.
 
 For the sake of clarity and for my own later reference, does the
 attached Org file/ODT file capture what you want? One of the links in
 the ODT file is hand-edited with LibreOffice for the sake of
 illustration.
Yes. I think of 

As explained in Sec. [[*some_chapter]] it is highly desirable to be able
to refer to section numbers.

resulting in

As explained in Sec. 2.1.3. it is highly desirable to be able to refer
to section numbers.
 
Probably we need some option that tells the exporter to export section
numbers for description-less links referring to org-mode headlines.
I could also imagine  the word Sec. to trigger the insertion of a
section number, but then the thing becomes language dependent.

Thanks,

Martin 




Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
Eric Schulte eric.schu...@gmx.com writes:

 Does this do what you want?

 No. 

 When I put point under the headline and type C-c @ C-c C-e d, it prompts
 me to evaluate each of the blocks, and when I answer 'no' to each, it
 produces a document that omits the previously computed results.

 What I want is to grab *existing* results blocks and use them. 

 And if at a later date some of those results blocks have changed, when I
 again put point under the headline and type C-c @ C-c C-e d, I'd like
 the newer blocks to be updated.

 The computations in some blocks run for many minutes, so it is
 impractical to recompute them every time I want to tweak the format of a
 document that depends on them.


 Hi Chuck,

Thanks for your reply.


 Have you looked at the :cache header argument [1], from my understanding
 of your use case it should be exactly what you are after.


Its a step in the right direction.

It seems I have to set :cache yes on every block I use before I invoke
it. My attempt to use a buffer-wide PROPERTY setting for cache did not
pan out. 

With org-confirm-babel-evaluate set to t, it prompts for confirmation of
each and every block/call it encounters, which is a bit tiresome. I can
set this to nil, but the potential for causing mischief by
unintenionally evaluating blocks whose results were OK and needed for a
quick report worries me.

Its pretty clear that the machinery needed to capture results is all
there. If I can find time, I'll trace thru what is going on when cache
yes is set and see if I can  do so more directly.

Chuck
 Best,

 Footnotes: 
 [1]  http://orgmode.org/manual/cache.html

-- 
Charles C. BerryDept of Family/Preventive Medicine
cberry at ucsd edu  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901




[O] babel, executing code in background process

2012-02-29 Thread Erik Garrison
Hi,

I'm just starting to use org-mode and babel to structure exploratory data
analysis which I do for my work.

One issue that I've run into is that many of the queries I have to issue
will take a very long time to complete.

Is there any method I could use to execute them in a background process?

Thanks,
Erik


Re: [O] Is it possible to refer to section numbers in links?

2012-02-29 Thread Nicolas Goaziou
Hello,

Martin Gürtler martin.guert...@gmx.de writes:

 Probably we need some option that tells the exporter to export section
 numbers for description-less links referring to org-mode headlines.

It will be standard across all major back-ends in the next export engine
(which is actually experimental).


Regards,

-- 
Nicolas Goaziou



Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

2012-02-29 Thread Eric Schulte
Achim Gratz strom...@nexgo.de writes:

 Eric Schulte eric.schu...@gmx.com writes:
 Moving forward on this point, many of the existing tests explicitly
 `require' new Org-mode functionality (mainly language support for
 testing code blocks execution).  I do not think that tests should ever
 be activating new packages changing a users global environment.

 Thanks.

 I've had to deactivate the inclusion of ./testing/lisp/contrib into the
 test flow due to a recent removal of said directory by Nicolas (he's
 probably doing that patch himself) and now get this:


Yes,

I talked with Nicolas this morning, and at my urging he moved everything
from ./testing/lisp/contrib into ./testing/lisp and removed the contrib
directory.  I think moving forward we are best served by a single test
directory, especially given that we already have good methods of
conditionally loading only those tests appropriate for the users
environment.


 lisp/org-mode make test-dirty | grep failed
failed5/109  ob-exp/export-from-a-temp-buffer
failed   17/109  org-missing-dependency/test-ob-C
failed   18/109  org-missing-dependency/test-ob-R
failed   19/109  org-missing-dependency/test-ob-awk
failed   20/109  org-missing-dependency/test-ob-fortran
failed   21/109  org-missing-dependency/test-ob-lilypond
failed   22/109  org-missing-dependency/test-ob-maxima
failed   23/109  org-missing-dependency/test-ob-octave
failed   24/109  org-missing-dependency/test-ob-python
failed   25/109  org-missing-dependency/test-org-element
failed   26/109  org-missing-dependency/test-org-export

 This is expected, as my local configuration doesn't have any of these
 packages activated.


Yes, I assume that the lower case failed means expected failure.


 lisp/org-mode make test-dirty |  grep FAILED
FAILED   27/109  test-ob-exp/org-babel-exp-src-blocks/w-no-file
FAILED   62/109  test-org-babel/get-src-block-info-body
FAILED   63/109  test-org-babel/get-src-block-info-language
FAILED   64/109  test-org-babel/get-src-block-info-tangle

 This is unexpected and I don't really see where they are coming from.
 The backtrace always starts at (regexp-quote org-test-file-ob-anchor).


My guess is that when I removed require statements for org-html and
org-ascii from from test-org-html and test-org-exp, they removed some
functionality not loaded by default in the test scripts.  These should
probably be added into the Makefile.


 For this reason I have just pushed up a commit which changes all

   (require 'org-foo)

 to

   (unless (featurep 'org-foo)
 (signal 'missing-test-dependency Org support for doing foo.))

 so that those tests simple aren't run on the users system.  Please let
 me know if anyone thinks this is a mistake and we can discuss.  The only
 drawback I see is that batch-mode scripts will have to explicitly
 activate the features which they would like to test, by evaluating forms
 like (require 'org-foo) before the call to the test suite -- and I would
 argue that being explicit about such things is a benefit.

 Well, currently all testing runs under my user settings, which is not
 ideal for testing anyway.  I suppose it would not be difficult to just
 inject a different (minimal) startup file specifically for testing to
 separate these issues.


Yea, I also run most tests from my normal Emacs session, which is part
of the motivation for removing these embedded require statements.

Cheers,



 Regards,
 Achim.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] taskjuggler3 export

2012-02-29 Thread Thorsten
d.tchin d.tc...@voila.fr writes:

Hi, 

 |
 |# Local Variables:
 |# org-export-taskjuggler-target-version: 3.0 
 |# org-export-taskjuggler-default-reports: (include
 | \gantexport.tji\)
 |# End:
 `

 As you can see, I define in the org-export-taskjuggler-default-reports 
 variable at the end of the file that I want to use gantexport.tji
 where the
 gant output directives are defined. This file is in the same directory
 as org
 file.
 The gantexport.tji is the following :

 ,-
 |### begin report definition
 |
 |taskreport Gantt Chart {
 |  headline Project Gantt Chart
 |  columns hierarchindex, name, start, end, effort, duration, completed, 
 chart  
 |  timeformat %Y-%m-%d   
 |  hideresource 1
 |  formats html
 |  loadunit shortauto
 |}
 `-

 Then the instruction tj3 testtj3.tjp generate the gant chart accessible 
 in Gantt Chart.html file.

 Hope that can help.

Great, thats exactly what I was looking for!
Thanks a lot

-- 
cheers,
Thorsten




Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

2012-02-29 Thread Achim Gratz
Eric Schulte eric.schu...@gmx.com writes:
 My guess is that when I removed require statements for org-html and
 org-ascii from from test-org-html and test-org-exp, they removed some
 functionality not loaded by default in the test scripts.  These should
 probably be added into the Makefile.

Unless someone can give me a hint, I'll have a look at this
later... it'll probably become weekend before I get to this.

 Yea, I also run most tests from my normal Emacs session, which is part
 of the motivation for removing these embedded require statements.

I'll see that I create a minimal config and use that just for testing
from the Makefile (in my Makefile fork of course).  If somebody has a
good template to work from, please post, otherwise I should be able to
scrape it together from the parts that have just been removed.  BTW,
where should that startup file go, directly under testing?


Regards,
Achim.
-- 
+[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+

Samples for the Waldorf Blofeld:
http://Synth.Stromeko.net/Downloads.html#BlofeldSamplesExtra




[O] Minimal example... Is this intended ?

2012-02-29 Thread Allen S. Rout
I've attached 'minimal.org',  which demonstrates (for me) an odd 
behavior in current git head (I encountered this just after doing a git 
pull).


There are two ls listings in this file, one after the 'foo' block, and 
prefixed by a results: tag.   The other is before the block, and not so 
prefixed.


The trailing, prefixed block was generated when I had no space after the 
string 'foo' in the NAME: line.   If I add one space, then the results 
block which comes before is generated.


I can't think this is a deliberate feature;  can anyone else duplicate 
these results?


- Allen S. Rout


| total  | 324 | | |||   |  
 |
| -rw-rw-r-- |   1 | asr | asr |   1323 | 2012-02-15 | 15:40 | db-data  
 |
| -rw-r--r-- |   1 | asr | asr |   1632 | 2011-05-31 | 14:06 | dbsizing 
 |
| -rw-r--r-- |   1 | asr | asr |   3235 | 2011-05-31 | 14:05 | dbsizing~
 |
| -rw-rw-r-- |   1 | asr | asr | 50 | 2012-02-15 | 16:22 | dsmerror.log 
 |
| -rw-rw-r-- |   1 | asr | asr |157 | 2012-02-15 | 15:40 | Makefile 
 |
| -rw-rw-r-- |   1 | asr | asr |  3 | 2012-02-15 | 15:40 | Makefile~
 |
| -rw-rw-r-- |   1 | asr | asr |   1393 | 2012-02-29 | 16:01 | minimal.org  
 |
| -rw-rw-r-- |   1 | asr | asr |   1224 | 2012-02-29 | 15:53 | minimal.org~ 
 |
| -rw-r--r-- |   1 | asr | asr |   7929 | 2012-02-29 | 15:53 | notes.org
 |
| -rw-r--r-- |   1 | asr | asr |   6057 | 2012-02-29 | 15:21 | notes.org~   
 |
| -rw-r--r-- |   1 | asr | asr | 148474 | 2012-02-29 | 15:23 | notes.pdf
 |
| -rw-r--r-- |   1 | asr | asr |   6488 | 2012-02-29 | 15:23 | notes.tex
 |
| -rw-r--r-- |   1 | asr | asr |   6599 | 2012-02-29 | 15:18 | notes.tex~   
 |
| -rw-r--r-- |   1 | asr | asr | 106646 | 2011-11-02 | 13:46 | 
some_filename.png |
| drwxr-xr-x |   2 | asr | asr |   4096 | 2011-11-07 | 14:57 | upgrade-docs 
 |
#+NAME: foo 
#+BEGIN_SRC sh 
ls -l 
#+END_SRC

#+RESULTS: foo
| total  | 324 | | |||   |  
 |
| -rw-rw-r-- |   1 | asr | asr |   1323 | 2012-02-15 | 15:40 | db-data  
 |
| -rw-r--r-- |   1 | asr | asr |   1632 | 2011-05-31 | 14:06 | dbsizing 
 |
| -rw-r--r-- |   1 | asr | asr |   3235 | 2011-05-31 | 14:05 | dbsizing~
 |
| -rw-rw-r-- |   1 | asr | asr | 50 | 2012-02-15 | 16:22 | dsmerror.log 
 |
| -rw-rw-r-- |   1 | asr | asr |157 | 2012-02-15 | 15:40 | Makefile 
 |
| -rw-rw-r-- |   1 | asr | asr |  3 | 2012-02-15 | 15:40 | Makefile~
 |
| -rw-rw-r-- |   1 | asr | asr | 48 | 2012-02-29 | 15:55 | minimal.org  
 |
| -rw-rw-r-- |   1 | asr | asr |   1224 | 2012-02-29 | 15:53 | minimal.org~ 
 |
| -rw-r--r-- |   1 | asr | asr |   7929 | 2012-02-29 | 15:53 | notes.org
 |
| -rw-r--r-- |   1 | asr | asr |   6057 | 2012-02-29 | 15:21 | notes.org~   
 |
| -rw-r--r-- |   1 | asr | asr | 148474 | 2012-02-29 | 15:23 | notes.pdf
 |
| -rw-r--r-- |   1 | asr | asr |   6488 | 2012-02-29 | 15:23 | notes.tex
 |
| -rw-r--r-- |   1 | asr | asr |   6599 | 2012-02-29 | 15:18 | notes.tex~   
 |
| -rw-r--r-- |   1 | asr | asr | 106646 | 2011-11-02 | 13:46 | 
some_filename.png |
| drwxr-xr-x |   2 | asr | asr |   4096 | 2011-11-07 | 14:57 | upgrade-docs 
 |



Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Sebastien Vauban
Hi Jonathan,

Jonathan Leech-Pepin wrote:
 I ran into exactly that question this morning and managed to figure it out.

 If I use emacs -q then C-c  works as expected and is mapped to
 (org-mark-ring-goto  optional N).  However when trying C-c  C-h I find
 out that C-c  is a prefix for a few yasnippet commands:

 ,
 | `yas/minor-mode' Minor Mode Bindings Starting With C-c :
 | key binding
 | --- ---
 |
 | C-c  C-f yas/find-snippets
 | C-c  C-n yas/new-snippet
 | C-c  C-s yas/insert-snippet
 | C-c  C-v yas/visit-snippet-file
 `

 Seems this is another place where yas and org don't get along well together

Something along these lines should work:

#+begin_src emacs-lisp
  ;; remove the binding of `C-c '
  (add-hook 'yas/minor-mode-hook
(lambda ()
  (define-key global-map (kbd C-c  C-s) nil)
  (define-key global-map (kbd C-c  C-n) nil)
  (define-key global-map (kbd C-c  C-v) nil)
  (define-key global-map (kbd C-c  C-f) nil)
))
#+end_src

... but it doesn't. And I don't understand yet why. Maybe the hook in which
this is placed is not the right one?  If anyone sees an obvious reason for
it...

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] Bug in odt export of org files with footnotes

2012-02-29 Thread Nicolas Goaziou
Hello,

Jambunathan K kjambunat...@gmail.com writes:

 I am attaching a patch that should fix this issue. I will let Nicolas
 review/apply it.

Ok, I have applied it.


Regards,

-- 
Nicolas Goaziou



Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Andreas Leha
Sebastien Vauban
wxhgmqzgw...@spammotel.com writes:

 Hi Jonathan,

 Jonathan Leech-Pepin wrote:
 I ran into exactly that question this morning and managed to figure it out.

 If I use emacs -q then C-c  works as expected and is mapped to
 (org-mark-ring-goto  optional N).  However when trying C-c  C-h I find
 out that C-c  is a prefix for a few yasnippet commands:

 ,
 | `yas/minor-mode' Minor Mode Bindings Starting With C-c :
 | key binding
 | --- ---
 |
 | C-c  C-f yas/find-snippets
 | C-c  C-n yas/new-snippet
 | C-c  C-s yas/insert-snippet
 | C-c  C-v yas/visit-snippet-file
 `

 Seems this is another place where yas and org don't get along well together

 Something along these lines should work:

 #+begin_src emacs-lisp
   ;; remove the binding of `C-c '
   (add-hook 'yas/minor-mode-hook
 (lambda ()
   (define-key global-map (kbd C-c  C-s) nil)
   (define-key global-map (kbd C-c  C-n) nil)
   (define-key global-map (kbd C-c  C-v) nil)
   (define-key global-map (kbd C-c  C-f) nil)
 ))
 #+end_src

 ... but it doesn't. And I don't understand yet why. Maybe the hook in which
 this is placed is not the right one?  If anyone sees an obvious reason for
 it...

 Best regards,
   Seb

Thanks for looking into this.  I am not using yas myself - so I did not
notice.

@Tom: I think, if C-c  is documented, this issue (together with a
fix/work-around, as soon as found) should be mentioned there as well.
There will be more org- and yas-users.

Regards,
Andreas




Re: [O] babel, executing code in background process

2012-02-29 Thread Eric Schulte
Hi Erik,

Currently there is not (to my knowledge) any support for asynchronous
code block evaluation.  The one possible exception could be ob-screen
which I mention only because I don't really know anything about it.

This would certainly be a worthwhile feature to add to Org-mode code
blocks, however a good implementation (easy to use, robust and
cross-language) will be non-trivial to implement.

Best,

Erik Garrison erik.garri...@gmail.com writes:

 Hi,

 I'm just starting to use org-mode and babel to structure exploratory data
 analysis which I do for my work.

 One issue that I've run into is that many of the queries I have to issue
 will take a very long time to complete.

 Is there any method I could use to execute them in a background process?

 Thanks,
 Erik

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] Org appt notifications with Growl (OSX)

2012-02-29 Thread Marcelo de Moraes Serpa
Oh crap! I tried a google search but it didn't brought any results. I did
not remember. I'm sorry about that.

I will check it out, thanks!

On Wed, Feb 29, 2012 at 1:00 PM, Shine Zhong shineli...@gmail.com wrote:

 There is a good tool integrate with Growl, todochiku
 http://www.emacswiki.org/emacs/ToDoChiKu


 Here is the section of my .emacs
 ---
 ;; begin todochiku, enable the growlnotify
 (load-file ~/.emacs.d/plugins/todochiku.el)
 (setq todochiku-icons-directory ~/Downloads/todochiku-icons)
 ;; end todochiku


 ;; begin: orgmode + appt
 ; For org appointment reminders
 ;; Get appointments for today
 (defun my-org-agenda-to-appt ()
   (interactive)
   (setq appt-time-msg-list nil)
   (org-agenda-to-appt))

 ;; Run once, activate and schedule refresh
 (my-org-agenda-to-appt)
 (appt-activate t)
 (run-at-time 24:01 nil 'my-org-agenda-to-appt)

 ; Update appt each time agenda opened.
 (add-hook 'org-finalize-agenda-hook 'my-org-agenda-to-appt)
 ;; end:   orgmode + appt
 ---


 Regards,
 Shine



 On Wed, Feb 29, 2012 at 10:35 AM, Nick Dokos nicholas.do...@hp.comwrote:

 Marcelo de Moraes Serpa celose...@gmail.com wrote:

  Hi folks,
 
  What is the best way to setup notifications to work with Growl for
 orgmode? I know org can work with
  emacs Appt system, but is anyone currently using it with Growl for
 notifications?
 
  If you could point me to the right direction, I'd be grateful.
 

 Somebody asked the same question back in 2010:

   http://thread.gmane.org/gmane.emacs.orgmode/27530

 Oh, wait - it was you :-)

 There were a few replies back then: have you tried those
 suggestions?

 Nick






Re: [O] Org appt notifications with Growl (OSX)

2012-02-29 Thread Marcelo de Moraes Serpa
@Shine thanks! I'll try that.

On Wed, Feb 29, 2012 at 5:20 PM, Marcelo de Moraes Serpa 
celose...@gmail.com wrote:

 Oh crap! I tried a google search but it didn't brought any results. I did
 not remember. I'm sorry about that.

 I will check it out, thanks!


 On Wed, Feb 29, 2012 at 1:00 PM, Shine Zhong shineli...@gmail.com wrote:

 There is a good tool integrate with Growl, todochiku
 http://www.emacswiki.org/emacs/ToDoChiKu


 Here is the section of my .emacs
 ---
 ;; begin todochiku, enable the growlnotify
 (load-file ~/.emacs.d/plugins/todochiku.el)
 (setq todochiku-icons-directory ~/Downloads/todochiku-icons)
 ;; end todochiku


 ;; begin: orgmode + appt
 ; For org appointment reminders
 ;; Get appointments for today
 (defun my-org-agenda-to-appt ()
   (interactive)
   (setq appt-time-msg-list nil)
   (org-agenda-to-appt))

 ;; Run once, activate and schedule refresh
 (my-org-agenda-to-appt)
 (appt-activate t)
 (run-at-time 24:01 nil 'my-org-agenda-to-appt)

 ; Update appt each time agenda opened.
 (add-hook 'org-finalize-agenda-hook 'my-org-agenda-to-appt)
 ;; end:   orgmode + appt
 ---


 Regards,
 Shine



 On Wed, Feb 29, 2012 at 10:35 AM, Nick Dokos nicholas.do...@hp.comwrote:

 Marcelo de Moraes Serpa celose...@gmail.com wrote:

  Hi folks,
 
  What is the best way to setup notifications to work with Growl for
 orgmode? I know org can work with
  emacs Appt system, but is anyone currently using it with Growl for
 notifications?
 
  If you could point me to the right direction, I'd be grateful.
 

 Somebody asked the same question back in 2010:

   http://thread.gmane.org/gmane.emacs.orgmode/27530

 Oh, wait - it was you :-)

 There were a few replies back then: have you tried those
 suggestions?

 Nick







Re: [O] [babel] [PATCH] enhanced org-babel-goto-named-src-block

2012-02-29 Thread Thomas S. Dye
Andreas Leha andreas.l...@med.uni-goettingen.de writes:

 Sebastien Vauban
 wxhgmqzgw...@spammotel.com writes:

 Hi Jonathan,

 Jonathan Leech-Pepin wrote:
 I ran into exactly that question this morning and managed to figure it out.

 If I use emacs -q then C-c  works as expected and is mapped to
 (org-mark-ring-goto  optional N).  However when trying C-c  C-h I find
 out that C-c  is a prefix for a few yasnippet commands:

 ,
 | `yas/minor-mode' Minor Mode Bindings Starting With C-c :
 | key binding
 | --- ---
 |
 | C-c  C-f yas/find-snippets
 | C-c  C-n yas/new-snippet
 | C-c  C-s yas/insert-snippet
 | C-c  C-v yas/visit-snippet-file
 `

 Seems this is another place where yas and org don't get along well together

 Something along these lines should work:

 #+begin_src emacs-lisp
   ;; remove the binding of `C-c '
   (add-hook 'yas/minor-mode-hook
 (lambda ()
   (define-key global-map (kbd C-c  C-s) nil)
   (define-key global-map (kbd C-c  C-n) nil)
   (define-key global-map (kbd C-c  C-v) nil)
   (define-key global-map (kbd C-c  C-f) nil)
 ))
 #+end_src

 ... but it doesn't. And I don't understand yet why. Maybe the hook in which
 this is placed is not the right one?  If anyone sees an obvious reason for
 it...

 Best regards,
   Seb

 Thanks for looking into this.  I am not using yas myself - so I did not
 notice.

 @Tom: I think, if C-c  is documented, this issue (together with a
 fix/work-around, as soon as found) should be mentioned there as well.
 There will be more org- and yas-users.

 Regards,
 Andreas



Aloha Andreas,

IMO the manual should stick to describing Org Mode, and not get too
much into working around conflicts with other modes.  At the same time,
I tend to agree with your guess that there are lots of Org Mode users
who also use yas.

I wonder what others think about adding a babel key binding for
org-mark-ring-goto?  C-c C-v something.  This could be documented in the
babel key bindings, along with a reference there to the standard Org
Mode binding, C-c .

Assuming Seb's attempt finds a solution, then perhaps that could go
into the FAQ under something like Why doesn't C-c  work for me?

All the best,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com



Re: [O] Org appt notifications with Growl (OSX)

2012-02-29 Thread John Wiegley
 Marcelo de Moraes Serpa celose...@gmail.com writes:

 Hi folks, What is the best way to setup notifications to work with Growl for
 orgmode? I know org can work with emacs Appt system, but is anyone currently
 using it with Growl for notifications?

 If you could point me to the right direction, I'd be grateful.

I recommend adding support for alert.el to Org-mode, which was created for
just this purpose:

https://github.com/jwiegley/alert

It solves the general problem, not just sending alerts through Growl.  Once
a package uses alert.el, the user can customize what gets alert and how to
their heart's content, while keeping the changes to Org minimal.

John




Re: [O] [PATCH] Option for clock and timer to be displayed in frame-title

2012-02-29 Thread Bernt Hansen
George Kettleborough g.kettleboro...@uea.ac.uk writes:

 On Tue, Feb 28 2012, Bernt Hansen wrote:
 This patch needs a changelog entry in the commit text and a long
 description would also be appreciated.  The long description allows us
 to see the purpose of the patch and how to use it without the necessity
 to read and parse any of the code changes.

 Ok, I've done a changelog entry.  I hope this is what is expected.
 (Also fixed a minor bug in original patch and added better documentation
 to the new custom variable).

 The patch adds options to both org-clock and org-timer regarding how the
 current clock/timer is displayed.  Currently they are both displayed in
 the mode line.  This is not ideal since if you split your window
 horizontally then the mode line becomes quite short so often the clock
 is truncated and the timer might not even be visible.

 The new options control whether the clock/timer is displayed in the mode
 line and/or frame title.  The frame title is usually wasted space for
 people running a graphical version of emacs so it is quite useful there
 I think.

Thanks!  I use frames on Windows at work and no frames on Linux (in
xmonad) at home.  I tend to run with emacs full screen so I haven't
my modeline is long enough for me -- but it will be interesting to see
how the frame title clock works.

Regards,
Bernt



[O] problems with R graphics

2012-02-29 Thread Matthew Landis
Hello all,

I believe this is my first post on this list, and I'm very new to org-babel, so 
forgive me if I am posting nonsense.  However, I'm really enthused about the 
possibilities org-babel presents.  Unfortunately, I can't seem to get graphics 
to insert themselves properly on export.  I've included an example that 
reproduces my problem below.  For what it's worth, I am using Windows 7 with a 
freshly downloaded issue of Vincent Goulet's package.  Session info:

Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on MARVIN
Org mode version 7.8.03
ESS version 5.14
R version 2.14.1

Many thanks for any thoughts or requests for more info.

Matt

org example


#+TITLE: An attempt to make org-mode work with R

In this example, I want to fit a regression and plot it.  I'm
following the examples at the [[http://orgmode.org/worg/org-
contrib/babel/languages/ob-doc-R.html][org manual]] and Erik Iverson's 
[[https://github.com/erikriverson/org-mode-R-tutorial][tutorial]].

* A stand-alone code block

First, create some data, perform a regression, and plot it.  This
works great.
#+begin_src R :results graphics :file regress.png :exports both

  x - runif(n = 100, min = 0, max = 20)
  y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)

  f - lm(y ~ x)

  plot(x, y, bty = 'n')
  abline(f, lty = 'dashed')

#+end_src
Success.

* In code blocks using :session
Now do the same thing, but across an unnamed session

#+begin_src R :session :exports code :results silent

  x - runif(n = 100, min = 0, max = 20)
  y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)

#+end_src

Now, I would like to display the results of the regression as R output.

#+begin_src R :session :results output :exports both
  f - lm(y ~ x)
  summary(f)
#+end_src
Again, success!  This is really going to come in handy.

#+begin_src R :session :results graphics :file regress_session.png :exports both

 plot(x, y, bty = 'n')
 abline(f, lty = 'dashed')

#+end_src
This code block doesn't work. No error, but no file is created.
Also, if I press C-c C-c in the code block, in the org file I get

#+begin_example
#+results:
[[file:regress_session.png]]
#+end_example

But no file is actually created.  What could be going wrong?





Re: [O] babel, executing code in background process

2012-02-29 Thread Erik Garrison
Hi Eric,

Thanks for the background.  It looks like ob-screen may be very limited in
that it doesn't

It seems to me that a decent method would behave similarly to the way to
M-x compile works--- another buffer opens in which the compilation
progresses.  Is there any reason why this might not be applicable to the
way babel works?

Erik

On Wed, Feb 29, 2012 at 5:55 PM, Eric Schulte eric.schu...@gmx.com wrote:

 Hi Erik,

 Currently there is not (to my knowledge) any support for asynchronous
 code block evaluation.  The one possible exception could be ob-screen
 which I mention only because I don't really know anything about it.

 This would certainly be a worthwhile feature to add to Org-mode code
 blocks, however a good implementation (easy to use, robust and
 cross-language) will be non-trivial to implement.

 Best,

 Erik Garrison erik.garri...@gmail.com writes:

  Hi,
 
  I'm just starting to use org-mode and babel to structure exploratory data
  analysis which I do for my work.
 
  One issue that I've run into is that many of the queries I have to issue
  will take a very long time to complete.
 
  Is there any method I could use to execute them in a background process?
 
  Thanks,
  Erik

 --
 Eric Schulte
 http://cs.unm.edu/~eschulte/



Re: [O] problems with R graphics

2012-02-29 Thread Matthew Landis
Matthew Landis landis at isciences.com writes:

 
 Hello all,
...

 Unfortunately, I can't seem to get graphics 
 to insert themselves properly on export.  



 org example
 
...
 * A stand-alone code block
 
 First, create some data, perform a regression, and plot it.  This
 works great.
 #+begin_src R :results graphics :file regress.png :exports both
 
   x - runif(n = 100, min = 0, max = 20)
   y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)
 
   f - lm(y ~ x)
 
   plot(x, y, bty = 'n')
   abline(f, lty = 'dashed')
 
 #+end_src
 Success.
...

 #+begin_src R :session :results graphics :file regress_session.png :exports 
both
 
  plot(x, y, bty = 'n')
  abline(f, lty = 'dashed')
 
 #+end_src
 This code block doesn't work. No error, but no file is created.

...

I actually figured this one out just now.  If creating a file in a 'stand 
alone' 
code block, the default directory is the directory that the org file itself is 
in.  However, in a 'session' code block, the default directory is something 
else 
(R's default?).  If I specify the full path to the file in the 'session' code 
block, things work better.

Sorry for the noise!

M







[O] org-export-blocks-preprocess: Marker does not point anywhere

2012-02-29 Thread Matthew Landis

Hello orgmode fans,

Another issue with org and R giving me headaches tonight.

In the example below, using the :session header argument seems to cause 
problems with export to html.  On export, the *R* buffer is opened up, 
but no file is created.  in the *Messages* buffer, I see


org-export-blocks-preprocess: Marker does not point anywhere

however, if I try to export again, with the *R* buffer already open, 
then things work fine.  This is an OK work around I guess, but I thought 
someone ought to know about it.


Session info:
Windows 7, 64 bit.
Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on 
MARVIN

Org mode version 7.8.03
ESS version 5.14
R version 2.14.1

M

--
~~
Matthew Landis, Ph.D.
Research Scientist
ISciences, LLC
61 Main St. Suite 200
Burlington VT 05401
802.864.2999
www.isciences.com
~~




Re: [O] problems with R graphics

2012-02-29 Thread Nick Dokos
Matthew Landis lan...@isciences.com wrote:

 Matthew Landis landis at isciences.com writes:
 
 ...
 
  #+begin_src R :session :results graphics :file regress_session.png :exports 
 both
  
   plot(x, y, bty = 'n')
   abline(f, lty = 'dashed')
  
  #+end_src
  This code block doesn't work. No error, but no file is created.
 
 ...
 
 I actually figured this one out just now.  If creating a file in a 'stand 
 alone' 
 code block, the default directory is the directory that the org file itself 
 is 
 in.  However, in a 'session' code block, the default directory is something 
 else 
 (R's default?).  If I specify the full path to the file in the 'session' code 
 block, things work better.
 

Maybe Windows is doing something different, but on Linux, both plots are
produced with no problem, both in the current directory.

Nick



Re: [O] org-export-blocks-preprocess: Marker does not point anywhere

2012-02-29 Thread Nick Dokos
Matthew Landis lan...@isciences.com wrote:

 Hello orgmode fans,
 
 Another issue with org and R giving me headaches tonight.
 
 In the example below, using the :session header argument seems to

I guess you forgot to include the example?

Nick

 cause problems with export to html.  On export, the *R* buffer is
 opened up, but no file is created.  in the *Messages* buffer, I see
 
 org-export-blocks-preprocess: Marker does not point anywhere
 
 however, if I try to export again, with the *R* buffer already open,
 then things work fine.  This is an OK work around I guess, but I
 thought someone ought to know about it.
 
 Session info:
 Windows 7, 64 bit.
 Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04
 on MARVIN
 Org mode version 7.8.03
 ESS version 5.14
 R version 2.14.1
 
 M
 
 -- 
 ~~
 Matthew Landis, Ph.D.
 Research Scientist
 ISciences, LLC
 61 Main St. Suite 200
 Burlington VT 05401
 802.864.2999
 www.isciences.com
 ~~