Re: [Orgmode] org.texi patch for small typo

2010-08-31 Thread Carsten Dominik

Applied, thanks.

- Carsten

On Aug 30, 2010, at 4:13 PM, Stephen Eglen wrote:


diff --git a/doc/org.texi b/doc/org.texi
index 2e61ddf..4ce32ce 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -11176,10 +11176,10 @@ Include the code block in the tangled  
output to file @samp{filename}.

@kindex  C-c C-v t
@subsubheading Functions
@table @code
-...@item org-babel-tangle @kbd{C-c C-v t}
-Tangle the current file.
+...@item org-babel-tangle
+Tangle the current file.  Bound to @kbd{C-c C-v t}.
@item org-babel-tangle-file
-Choose a file to tangle.
+Choose a file to tangle.   Bound to @kbd{C-c C-v f}.
@end table

@subsubheading Hooks

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- Carsten




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[Accepted] [Orgmode] Make the number of printed weeks configureable

2010-08-31 Thread Carsten Dominik
Patch 248 (http://patchwork.newartisans.com/patch/248/) is now Accepted.

Maintainer comment: none

This relates to the following submission:

http://mid.gmane.org/%3C87iq2s9mg5.fsf%40saadawi.sbszh.ch%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: [Orgmode] Make the number of printed weeks configureable
 Date: Mon, 30 Aug 2010 19:58:34 -
 From: Christian Egli christian.e...@alumni.ethz.ch
 X-Patchwork-Id: 248
 Message-Id: 87iq2s9mg5@saadawi.sbszh.ch
 To: emacs-orgmode@gnu.org
 
 This is useful for the hipster PDA where you might want to print more
 weeks than just four.
 
 ---
 contrib/scripts/org2hpda |7 ++-
  1 files changed, 6 insertions(+), 1 deletions(-)
 
 diff --git a/contrib/scripts/org2hpda b/contrib/scripts/org2hpda
 index 1957aa9..6b308f3 100755
 --- a/contrib/scripts/org2hpda
 +++ b/contrib/scripts/org2hpda
 @@ -44,6 +44,11 @@ EMACS = emacs -batch -l ~/.emacs
  LATEX = latex
  DIARY = $($(EMACS) -eval diary-file)
  
 +# Number of weeks to be printed. Should be a multiple of 4, because 4
 +# of them are merged on one page. Can be set when invoking the script
 +# as follows: make NUMBER_OF_WEEKS=8 -f org2hpda
 +NUMBER_OF_WEEKS = 4 
 +
  hipsterFiles =  weekCalendar.pdf yearCalendar.pdf monthCalendar3.pdf 
 monthCalendar2.pdf monthCalendar1.pdf
  pocketModFiles =  weekCalendar.pdf yearCalendar-rotated.pdf \
   monthCalendar3-rotated.pdf monthCalendar2-rotated.pdf 
 monthCalendar1-rotated.pdf
 @@ -73,7 +78,7 @@ all: pocketMod.pdf hipsterPDA.pdf
   done
  
  weekCalendar.tex: $(DIARY)
 - $(EMACS) -eval (progn (calendar) (cal-tex-cursor-week-iso 4) 
 (with-current-buffer cal-tex-buffer (write-file \$...@\)))
 + $(EMACS) -eval (progn (calendar) (cal-tex-cursor-week-iso 
 $(NUMBER_OF_WEEKS)) (with-current-buffer cal-tex-buffer (write-file 
 \$...@\)))
  
  monthCalendar1.tex: $(DIARY)
$(EMACS) -eval (progn (calendar) (cal-tex-cursor-month-landscape 1) 
 (with-current-buffer cal-tex-buffer (write-file \$...@\)))
 

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[Orgmode] Archive to beginning of subtree?

2010-08-31 Thread Tom
Is there a setting like org-reverse-note-order for archiving, so that
the archived item goes to the beginning of the subtree instead of the
end? org-reverse-note-order  doesn't seem to affect it.

Shouldn't archiving honor the setting of org-reverse-note-order?



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Re: [Orgmode] a bit offtopic, fonts in exported PDF documents - oops

2010-08-31 Thread Carsten Dominik


On Aug 30, 2010, at 5:58 PM, Nick Dokos wrote:


Erik Iverson er...@ccbr.umn.edu wrote:


That would be my thought, too.  However, it appears that cm-super is
only suggested by texlive-fonts-extra, so in general
will not get installed with that package, unless you ask for
suggested packages also. (This is all Debian/Ubuntu by the way).



Right. I was wrong about texlive-fonts-extra: you need to install the
cm-super package to get the cm-super fonts. I am investigating the
various fonts right now and will update the org-dependencies.org  
file on

Worg later on this week. We can also add a FAQ entry to point back to
org-dependencies - that should take care of the documentation changes,
right?


Both this system and MikTeX
offer cm-super as a standalone package, so perhaps just recommending
that package (cm-super) would suffice?  I confirmed that cm-super is
not one of the default MikTeX packages in a standard install, so
Windows users may benefit from this advice, too.


Do windows users use evince? I'd think they mostly go with Acrobat  
Reader,

in which case they should have no problems with Type3 fonts.

The other possible change that Erik identified is the deletion of  
the
t1enc package from the list of packages that org includes in  
exported
LaTeX by default. I haven't tried without it, but it does indeed  
seem to

be an obsolete remnant of times long past.


I have tried without it.  I was unable to to see any differences  
between

using \usepackage[T1]{fontenc} and adding the \usepackage{t1enc}
line. This makes sense given the FAQ answer below.



So getting rid of the \usepackage{t1enc} in org sounds like the right
thing to do (but including it does not hurt, so there is no urgency,
iiuc.)


OK, thanks to all of you - I have removed the t1enc entry now.

- Carsten



Nick


The TeX FAQ

(http://www.tex.ac.uk/cgi-bin/texfaq2html?label=t1enc ) says:

,
| Why use fontenc rather than t1enc?
| | In the very earliest days of LaTeX2e, the only way to use the T1
| encoding was t1enc; with the summer 1994 “production” release, the
| fontenc package appeared, and provided comprehensive support for  
use of

| the encoding.
| | Nevertheless, the t1enc package remains (as part of the LaTeX
2.09
| compatibility code), but it does very little: it merely selects  
font

| encoding T1, and leaves to the user the business of generating the
| character codes required.
| | Generating such character codes could be a simple matter, if the
T1
| encoding matched any widely-supported encoding standard, since  
in that

| case, one might expect one’s keyboard to generate the character
| codes. However, the T1 encoding is a mix of several standard  
encodings,
| and includes code points in areas of the table which standard  
encodings
| specifically exclude, so no T1 keyboards have been (or ever will  
be)

| manufactured.
| | By contrast, the fontenc package generates the T1 code points
from
| ordinary LaTeX commands (e.g., it generates the é character  
codepoint
| from the command \’e). So, unless you have program-generated T1  
input,

| use \usepackage[T1]{fontenc} rather than \usepackage{t1enc}.
`

Nick


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- Carsten




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[Orgmode] Re: Archive to beginning of subtree?

2010-08-31 Thread Tom
Tom levelhalom at gmail.com writes:

 
 Is there a setting like org-reverse-note-order for archiving, so that
 the archived item goes to the beginning of the subtree instead of the
 end? org-reverse-note-order  doesn't seem to affect it.
 
 Shouldn't archiving honor the setting of org-reverse-note-order?
 

I found it:

org-archive-reversed-order


Now the only thing missing is restoring the folding state if archiving
is done in the same file, because currently org opens every tree when
archiving and leaves them in that state afterwards.


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Re: [Orgmode] a bit offtopic, fonts in exported PDF documents - oops

2010-08-31 Thread Nick Dokos
Carsten Dominik carsten.domi...@gmail.com wrote:


 On Aug 30, 2010, at 5:58 PM, Nick Dokos wrote:
 
  Erik Iverson er...@ccbr.umn.edu wrote:
 
  That would be my thought, too.  However, it appears that cm-super is
  only suggested by texlive-fonts-extra, so in general
  will not get installed with that package, unless you ask for
  suggested packages also. (This is all Debian/Ubuntu by the way).
 
 
  Right. I was wrong about texlive-fonts-extra: you need to install the
  cm-super package to get the cm-super fonts. I am investigating the
  various fonts right now and will update the org-dependencies.org =20
  file on
  Worg later on this week. We can also add a FAQ entry to point back to
  org-dependencies - that should take care of the documentation changes,
  right?

I added a question to the FAQ with a pointer to a more extended (but still
incomplete) discussion in org-dependencies. I'll try to add more information
to the table later on this week.

Nick

 
  Both this system and MikTeX
  offer cm-super as a standalone package, so perhaps just recommending
  that package (cm-super) would suffice?  I confirmed that cm-super is
  not one of the default MikTeX packages in a standard install, so
  Windows users may benefit from this advice, too.
 
  Do windows users use evince? I'd think they mostly go with Acrobat =20
  Reader,
  in which case they should have no problems with Type3 fonts.
 
  The other possible change that Erik identified is the deletion of =20=
 
  the
  t1enc package from the list of packages that org includes in =20
  exported
  LaTeX by default. I haven't tried without it, but it does indeed =20
  seem to
  be an obsolete remnant of times long past.
 
  I have tried without it.  I was unable to to see any differences =20
  between
  using \usepackage[T1]{fontenc} and adding the \usepackage{t1enc}
  line. This makes sense given the FAQ answer below.
 
 
  So getting rid of the \usepackage{t1enc} in org sounds like the right
  thing to do (but including it does not hurt, so there is no urgency,
  iiuc.)
 
 OK, thanks to all of you - I have removed the t1enc entry now.
 
 - Carsten
 
 
  Nick
 
  The TeX FAQ
  (http://www.tex.ac.uk/cgi-bin/texfaq2html?label=3Dt1enc ) says:
 
  ,
  | Why use fontenc rather than t1enc?
  | | In the very earliest days of LaTeX2e, the only way to use the T1
  | encoding was t1enc; with the summer 1994 =93production=94 release, =
 the
  | fontenc package appeared, and provided comprehensive support for =20=
 
  use of
  | the encoding.
  | | Nevertheless, the t1enc package remains (as part of the LaTeX
  2.09
  | compatibility code), but it does very little: it merely selects =20=
 
  font
  | encoding T1, and leaves to the user the business of generating the
  | character codes required.
  | | Generating such character codes could be a simple matter, if the
  T1
  | encoding matched any widely-supported encoding standard, since =20
  in that
  | case, one might expect one=92s keyboard to generate the character
  | codes. However, the T1 encoding is a mix of several standard =20
  encodings,
  | and includes code points in areas of the table which standard =20
  encodings
  | specifically exclude, so no T1 keyboards have been (or ever will =20=
 
  be)
  | manufactured.
  | | By contrast, the fontenc package generates the T1 code points
  from
  | ordinary LaTeX commands (e.g., it generates the =E9 character =20
  codepoint
  | from the command \=92e). So, unless you have program-generated T1 =20=
 
  input,
  | use \usepackage[T1]{fontenc} rather than \usepackage{t1enc}.
  `
 
  Nick
 
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Re: [Orgmode] [babel] Conditional tangling possible

2010-08-31 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 31/08/10 02:06, Eric Schulte wrote:
 Hi Rainer,
 
 The easiest way to do this should be,
 
 --8---cut here---start-8---
 ** pulling information from tags   :blue:
 
 #+begin_src R :var color=(car (org-get-tags-at (point))) :tangle example.R
   color
 #+end_src

OK - that looks good. That solves one problem.

But it is not actually conditional tangling? It is rather the transation
of a tag into a variable - or am I seeing something wrong?

I must admit I have chosen a bad example. The idea is really to have two
completely different definitions of a function, which is then tangled
depending on a tag (or property or whatever else I could use to make
this easy).

so:
- -8---cut here---start-8---

** Here is the conditional tangle   :SIM1
#+begin_src R :TANGLE_ONLY_IF__IN_TAGs SIM1 :tangle example.R
simulate - function() {
# do something
result - 15
return(result)
}
#+end_src

#+begin_src R :TANGLE_ONLY_IF__IN_TAGs SIM2 :tangle example.R
simulate - function() {
# do something else
result - -88
return(result)
}
#+end_src

- --8---cut here---end---8---

So if SIM1 is in the tags, tangle the first block, if SIM2 is in tags
then tangle the second block.

As I said, I do not have to use tags, properties would also work.

Cheers,

Rainer



 
 #+results:
 : blue
 --8---cut here---end---8---
 
 this will tangle to
 
 --8---cut here---start-8---
 color - blue
 color
 --8---cut here---end---8---
 
 Cheers -- Eric
 
 Rainer M Krug r.m.k...@gmail.com writes:
 
 Hi

 I would like to have two different versions (not in the sense of version
 control) of one program in one org file, and depending on the value if a
 tag is set or not, tangle either the one or the other. The tangled file
 has to have the same name.

 So essentially:



 ** Test Code  :VERSIONTAG
 Version 1:
 #+begin_src R :tangle result.R
   version - 1
   x - 10
 #+end_src

 Version 2:
 #+begin_src R :tangle result.R
   version - 2
   x - 13
 #+end_src

 If VERSIONTAG is Version1, result.R should contain the code as in the
 first code block, and if it is Version2, the code from the second code
 block.


 Is this possible?

 Cheers,

 Rainer


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Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
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[Orgmode] svn version number as tag or property?

2010-08-31 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi

is it possible to automatically insert the svn version number of the org
file visited by the org buffer into the text and also to pass it to a
code block as a variable?

I could use a code block with a bash script to extract that information
from svn info, but that seems to be awkward for me - there must be an
easier way.

Cheers,

Rainer

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

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:+33 - (0)9 53 10 27 44
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email:  rai...@krugs.de

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[Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Aidan Gauland
It is impossible to have closing brackets in a footnote, because they
are treated as the closing bracket for the foot note.  Example...

* A heading
This is a broken footnote.[fn:: Some book at [42-24].]

This will export to (as ASCII, for example)...
  org-fn-bug-example
  ==

Author: Aidan Gauland
Date: 2010-08-31 20:33:14 NZST


Table of Contents
=
1 A heading


1 A heading

This is a broken footnote.[1].]

This will export to (as ASCII, for example)...

[1] Some book at [42-24

This is how I am required to cite books for my academic essays, so this
is a pretty serious bug for me (and no doubt other students, as well).

Regards,
Aidan Gauland

Emacs  : GNU Emacs 24.0.50.6 (x86_64-unknown-linux-gnu, GTK+ Version 2.20.1)
 of 2010-08-29 on dimension8
Package: Org-mode version 7.01trans

current state:
==
(setq
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-agenda-files '(~/uc-files/uc-work.org)
 org-agenda-include-diary t
 org-completion-use-iswitchb t
 org-completion-use-ido t
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-export-preprocess-hook '(org-export-blocks-preprocess)
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-babel-hide-result-toggle-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-confirm-shell-link-function 'yes-or-no-p
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines

org-optimize-window-after-visibility-change)
 org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
 org-mode-hook '(#[nil \300\301\302\303\304$\207
 
[org-add-hook change-major-mode-hook org-show-block-all append local] 5]
 #[nil 
\300\301\302\303\304$\207
 
[org-add-hook change-major-mode-hook org-babel-show-result-all
append local] 5]
 
org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point 
org-babel-execute-safely-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src
org-babel-exp-inline-src-blocks))
 org-occur-hook '(org-first-headline-recenter)
 org-outline-path-complete-in-steps nil
 org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
org-beamer-auto-fragile-frames

 
org-beamer-place-default-actions-for-lists)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-export-blocks '((src org-babel-exp-src-blocks nil) (comment
org-export-blocks-format-comment t)

 (ditaa org-export-blocks-format-ditaa nil) (dot
org-export-blocks-format-dot nil))
 )



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[Orgmode] Re: org-mode + pomodoro

2010-08-31 Thread Frederic Couchet
 Sergey == Sergey Konoplev gray...@gmail.com writes:

Sergey Hi all, Are there ways to use Pomodoro technique
Sergey (http://www.pomodorotechnique.com/) with org-mode? If there
Sergey are what are the best practices?

Sergey Thank you in advice.

Hello,

I always start a clock when I work on a task. And for the Pomodoro
technique I use also the org-timer module with some configuration.

Activate the org-timer module :

(add-to-list 'org-modules 'org-timer)

Set a default value for the timer, for example :

(setq org-timer-default-timer 25)

Modify the org-clock-in so that a timer is started with the default
value except if a timer is already started :

(add-hook 'org-clock-in-hook '(lambda () 
  (if (not org-timer-current-timer) 
  (org-timer-set-timer '(16)

Fred.


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[Orgmode] synctex!! ...syncorg?

2010-08-31 Thread Kevin Brubeck Unhammer
Hi,

I just discovered synctex, which lets you shift-click a point in a pdf
in Okular and find yourself back in the tex-file at the point that
corresponds with that point in the pdf =D

But now the obvious question is: does there exist a syncorg to
transport me back into the org-mode file to the point that corresponds
to that place in the tex-file? I assume it should be possible since
org-mode outputs these \label{sec-3.3} things...

best regards,
Kevin Brubeck Unhammer

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Re: [Orgmode] synctex!! ...syncorg?

2010-08-31 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 31/08/10 12:10, Kevin Brubeck Unhammer wrote:
 Hi,
 
 I just discovered synctex, which lets you shift-click a point in a pdf
 in Okular and find yourself back in the tex-file at the point that
 corresponds with that point in the pdf =D

Now on Linux? That's great. I only knew that it worked on a mac. Could
you (possibly off list?) provide some details (where I can find it (I am
using Ubuntu), how I can use it, ...)

Rainer

 
 But now the obvious question is: does there exist a syncorg to
 transport me back into the org-mode file to the point that corresponds
 to that place in the tex-file? I assume it should be possible since
 org-mode outputs these \label{sec-3.3} things...
 
 best regards,
 Kevin Brubeck Unhammer
 
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- -- 
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Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:+33 - (0)9 53 10 27 44
Cell:   +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:  rai...@krugs.de

Skype:  RMkrug
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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Giovanni Ridolfi
Aidan Gauland aidal...@no8wireless.co.nz writes:

 Emacs  : GNU Emacs 24.0.50.6 (x86_64-unknown-linux-gnu, GTK+ Version 2.20.1)
  of 2010-08-29 on dimension8
 Package: Org-mode version 7.01trans

 It is impossible to have closing brackets in a footnote, because they
 are treated as the closing bracket for the foot note.  
 Example...

 * A heading
 This is a broken footnote.[fn:: Some book at [42-24].]

 This will export to (as ASCII, for example)...

 1 A heading
 
 This is a broken footnote.[1].]

 This will export to (as ASCII, for example)...

 [1] Some book at [42-24

 This is how I am required to cite books for my academic essays, so this
 is a pretty serious bug for me (and no doubt other students, as well).

GNU Emacs 23.2.1 (i386-mingw-nt5.1.2600) of 2010-05-08 on G41R2F1
Org-mode version
 7.01trans-commit-1d1439f91e63e71f39e93622a0af439762522c00

Also escaping the brackets does not work Example:

** A heading
This is a broken footnote.[fn:: Some book at \[42-24\].]

 Exports to:

1 A heading 

This is a broken footnote.[1].]
[1] Some book at \[42-24\

Giovanni




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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Andreas Röhler

Am 31.08.2010 12:43, schrieb Giovanni Ridolfi:

Aidan Gaulandaidal...@no8wireless.co.nz  writes:


Emacs  : GNU Emacs 24.0.50.6 (x86_64-unknown-linux-gnu, GTK+ Version 2.20.1)
  of 2010-08-29 on dimension8
Package: Org-mode version 7.01trans



It is impossible to have closing brackets in a footnote, because they
are treated as the closing bracket for the foot note.
Example...

* A heading
This is a broken footnote.[fn:: Some book at [42-24].]

This will export to (as ASCII, for example)...

1 A heading

This is a broken footnote.[1].]

This will export to (as ASCII, for example)...

[1] Some book at [42-24

This is how I am required to cite books for my academic essays, so this
is a pretty serious bug for me (and no doubt other students, as well).


GNU Emacs 23.2.1 (i386-mingw-nt5.1.2600) of 2010-05-08 on G41R2F1
Org-mode version
  7.01trans-commit-1d1439f91e63e71f39e93622a0af439762522c00

Also escaping the brackets does not work Example:

** A heading
This is a broken footnote.[fn:: Some book at \[42-24\].]

  Exports to:

1 A heading

This is a broken footnote.[1].]
[1] Some book at \[42-24\

Giovanni






Should be a way to change footnote-style, so it doesn't use brackets.



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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Carsten Dominik

Hi Aidan,

unfortunately this is difficult to fix in a good way.
I do want to go back to footnotes, because I think there are many  
things that do not yet work satisfactorily.  And then I also hope to  
address the issue you raised.  For the time being, unfortunately, I do  
not have a solution for you.


- Carsten

On Aug 31, 2010, at 10:38 AM, Aidan Gauland wrote:


It is impossible to have closing brackets in a footnote, because they
are treated as the closing bracket for the foot note.  Example...

* A heading
This is a broken footnote.[fn:: Some book at [42-24].]

This will export to (as ASCII, for example)...
 org-fn-bug-example
 ==

Author: Aidan Gauland
Date: 2010-08-31 20:33:14 NZST


Table of Contents
=
1 A heading


1 A heading

This is a broken footnote.[1].]

This will export to (as ASCII, for example)...

[1] Some book at [42-24

This is how I am required to cite books for my academic essays, so  
this

is a pretty serious bug for me (and no doubt other students, as well).

Regards,
Aidan Gauland

Emacs  : GNU Emacs 24.0.50.6 (x86_64-unknown-linux-gnu, GTK+ Version  
2.20.1)

of 2010-08-29 on dimension8
Package: Org-mode version 7.01trans

current state:
==
(setq
org-export-latex-after-initial-vars-hook '(org-beamer-after-initial- 
vars)

org-agenda-files '(~/uc-files/uc-work.org)
org-agenda-include-diary t
org-completion-use-iswitchb t
org-completion-use-ido t
org-metaup-hook '(org-babel-load-in-session-maybe)
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-export-blocks-postblock-hook '(org-exp-res/src-name-cleanup)
org-export-latex-format-toc-function 'org-export-latex-format-toc- 
default

org-export-preprocess-hook '(org-export-blocks-preprocess)
org-tab-first-hook '(org-hide-block-toggle-maybe
org-babel-hide-result-toggle-maybe)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-confirm-shell-link-function 'yes-or-no-p
org-export-first-hook '(org-beamer-initialize-open-trackers)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide- 
drawers

org-cycle-show-empty-lines

org-optimize-window-after-visibility-change)
org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
org-mode-hook '(#[nil \300\301\302\303\304$\207
	 [org-add-hook change-major-mode-hook org-show-block-all  
append local] 5]

 #[nil 
\300\301\302\303\304$\207
	 [org-add-hook change-major-mode-hook org-babel-show-result- 
all

append local] 5]
 
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute- 
safely-maybe)

org-confirm-elisp-link-function 'yes-or-no-p
org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src
org-babel-exp-inline-src-blocks))
org-occur-hook '(org-first-headline-recenter)
org-outline-path-complete-in-steps nil
org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix- 
toc

org-beamer-auto-fragile-frames

 
org-beamer-place-default-actions-for-lists)
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-export-blocks '((src org-babel-exp-src-blocks nil) (comment
org-export-blocks-format-comment t)

 (ditaa org-export-blocks-format-ditaa nil) (dot
org-export-blocks-format-dot nil))
)

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- Carsten




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[Orgmode] [babel] configuring LaTeX exports verbatim environment for exported code and results

2010-08-31 Thread Douglas Bates
I have been unable to find in the documentation whether the verbatim
environment created by LaTeX exports of source code blocks can be
configured.

Exporting to LaTeX a section like

--8---cut here---start-8---
#+LaTeX_CLASS: beamer
#+LaTeX_CLASS_OPTIONS: [presentation]
#+BEAMER_FRAME_LEVEL: 1
#+BABEL: :session :exports both :results output :tangle yes

* Fitting a simple linear regression
#+begin_src R :exports results
options(show.signif.stars=FALSE)
#+end_src
#+begin_src R
summary(fm1 - lm(optden ~ carb, Formaldehyde))
#+end_src
A final line.
--8---cut here---end---8---

produces the LaTeX section

--8---cut here---start-8---
\begin{frame}[fragile]
\frametitle{Fitting a simple linear regression}
\label{sec-1}

\begin{verbatim}
summary(fm1 - lm(optden ~ carb, Formaldehyde))
\end{verbatim}



\begin{verbatim}

Call:
lm(formula = optden ~ carb, data = Formaldehyde)

Residuals:
1 2 3 4 5 6
-0.006714  0.001029  0.002771  0.007143  0.007514 -0.011743

Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 0.005086   0.007834   0.6490.552
carb0.876286   0.013535  64.744 3.41e-07

Residual standard error: 0.008649 on 4 degrees of freedom
Multiple R-squared: 0.999,  Adjusted R-squared: 0.9988
F-statistic:  4192 on 1 and 4 DF,  p-value: 3.409e-07
\end{verbatim}

A final line.
\end{frame}
--8---cut here---end---8---

Because both the source and the results are presented in verbatim, I
don't have much control over the appearance of the code on the slide.
If I could, for example, configure the names of the exported
environment for the source code and for the results separately, I
could use LaTeX's fancyvrb.sty to adjust font sizes, colors, boxes,
etc.

Also, the blank lines before and after the verbatim environment are
problematic.  In plain text it makes sense to delimit code chunks with
blank lines but in LaTeX a blank line starts a new paragraph and you
don't always want that.

As this is my first posting please let me know if I have inadvertently
violated conventions of the list.


Also, the exports append blank lines

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[Orgmode] Possible BUG in org-wikinodes.el

2010-08-31 Thread Indraneel Majumdar

 Hi,
Is this a typo?
org-find-exact-headling-in-buffer
occurs thrice instead of
org-find-exact-headline-in-buffer

I couldn't get it to work with headling. headline works fine.
I'm new to orgmode, and lisp in general, so I may be wrong.
Please let me know if I screwed up something (please cc, I'm
not on the list)

Thanks,
Indraneel


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[Orgmode] Re: [babel] configuring LaTeX exports verbatim environment for exported code and results

2010-08-31 Thread Douglas Bates
On Tue, Aug 31, 2010 at 8:08 AM, Douglas Bates ba...@stat.wisc.edu wrote:
 I have been unable to find in the documentation whether the verbatim
 environment created by LaTeX exports of source code blocks can be
 configured.

 Exporting to LaTeX a section like

 --8---cut here---start-8---
 #+LaTeX_CLASS: beamer
 #+LaTeX_CLASS_OPTIONS: [presentation]
 #+BEAMER_FRAME_LEVEL: 1
 #+BABEL: :session :exports both :results output :tangle yes

 * Fitting a simple linear regression
 #+begin_src R :exports results
 options(show.signif.stars=FALSE)
 #+end_src
 #+begin_src R
 summary(fm1 - lm(optden ~ carb, Formaldehyde))
 #+end_src
 A final line.
 --8---cut here---end---8---

 produces the LaTeX section

 --8---cut here---start-8---
 \begin{frame}[fragile]
 \frametitle{Fitting a simple linear regression}
 \label{sec-1}

 \begin{verbatim}
 summary(fm1 - lm(optden ~ carb, Formaldehyde))
 \end{verbatim}



 \begin{verbatim}

 Call:
 lm(formula = optden ~ carb, data = Formaldehyde)

 Residuals:
        1         2         3         4         5         6
 -0.006714  0.001029  0.002771  0.007143  0.007514 -0.011743

 Coefficients:
            Estimate Std. Error t value Pr(|t|)
 (Intercept) 0.005086   0.007834   0.649    0.552
 carb        0.876286   0.013535  64.744 3.41e-07

 Residual standard error: 0.008649 on 4 degrees of freedom
 Multiple R-squared: 0.999,      Adjusted R-squared: 0.9988
 F-statistic:  4192 on 1 and 4 DF,  p-value: 3.409e-07
 \end{verbatim}

 A final line.
 \end{frame}
 --8---cut here---end---8---

 Because both the source and the results are presented in verbatim, I
 don't have much control over the appearance of the code on the slide.
 If I could, for example, configure the names of the exported
 environment for the source code and for the results separately, I
 could use LaTeX's fancyvrb.sty to adjust font sizes, colors, boxes,
 etc.

I just realized that if the code and results are wrapped in other than
the verbatim environment the org-beamer-fragile-re variable will need
to be customized.  (By the way, automatically detecting the need for
the fragile option is a great idea.)

 Also, the blank lines before and after the verbatim environment are
 problematic.  In plain text it makes sense to delimit code chunks with
 blank lines but in LaTeX a blank line starts a new paragraph and you
 don't always want that.

 As this is my first posting please let me know if I have inadvertently
 violated conventions of the list.

Well, other than my cut-and-paste glich below :-/

 Also, the exports append blank lines


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Re: [Orgmode] Possible BUG in org-wikinodes.el

2010-08-31 Thread Carsten Dominik

Hi,

the name is supposed to be headline, and this bug has been fixed  
already.


- Carsten

On Aug 30, 2010, at 11:56 PM, Indraneel Majumdar wrote:


Hi,
Is this a typo?
org-find-exact-headling-in-buffer
occurs thrice instead of
org-find-exact-headline-in-buffer

I couldn't get it to work with headling. headline works fine.
I'm new to orgmode, and lisp in general, so I may be wrong.
Please let me know if I screwed up something (please cc, I'm
not on the list)

Thanks,
Indraneel


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- Carsten




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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Christian Moe

This is a two-part problem.

1. Right square bracket in inline footnote prematurely terminates the
   footnote.

   IMO this is not a bug, it's an inherent and quite reasonable
   limitation on the inline footnote format, and is easily solved by
   falling back on the block footnote syntax.

   #+BEGIN_EXAMPLE
   ** A heading
   This is a broken footnote.[fn:somebook]

   [fn:somebook] Some book at [42-24].
   #+END_EXAMPLE

2. A number in square brackets is interpreted as a footnote marker
   (even inside another footnote).

   In ASCII export, as in Aidan's example, this doesn't matter because
   footnote markers are exported in ... square brackets. But in other
   export formats it's an occasional pain.

   Some workarounds for this problem, involving =fn:nil= or invisible
   zero-space characters, were recently posted on the list:
   http://comments.gmane.org/gmane.emacs.orgmode/28191


Cheers,
Christian


Giovanni Ridolfi wrote:

Aidan Gauland aidal...@no8wireless.co.nz writes:


Emacs  : GNU Emacs 24.0.50.6 (x86_64-unknown-linux-gnu, GTK+ Version 2.20.1)
 of 2010-08-29 on dimension8
Package: Org-mode version 7.01trans



It is impossible to have closing brackets in a footnote, because they
are treated as the closing bracket for the foot note.  
Example...


* A heading
This is a broken footnote.[fn:: Some book at [42-24].]

This will export to (as ASCII, for example)...

1 A heading

This is a broken footnote.[1].]

This will export to (as ASCII, for example)...

[1] Some book at [42-24

This is how I am required to cite books for my academic essays, so this
is a pretty serious bug for me (and no doubt other students, as well).


GNU Emacs 23.2.1 (i386-mingw-nt5.1.2600) of 2010-05-08 on G41R2F1
Org-mode version
 7.01trans-commit-1d1439f91e63e71f39e93622a0af439762522c00

Also escaping the brackets does not work Example:

** A heading
This is a broken footnote.[fn:: Some book at \[42-24\].]

 Exports to:

1 A heading 


This is a broken footnote.[1].]
[1] Some book at \[42-24\

Giovanni




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--

Christian Moe
E-mail:  m...@christianmoe.com
Website: http://christianmoe.com


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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Giovanni Ridolfi
Carsten Dominik carsten.domi...@gmail.com writes:

 unfortunately this is difficult to fix in a good way.
 I do want to go back to footnotes, because I think there are many
 things that do not yet work satisfactorily.  And then I also hope to
 address the issue you raised.  For the time being, unfortunately, I do
 not have a solution for you.

I have a workaround. 
If the author uses the a special code for [ and ], e.g.
#91; and #93; then the note is exported correctly.

** example
This is not anymore a broken footnote.[fn:: Some book at #91; 42-24 #93;.]

Exports to:
This is not anymore broken footnote.[1]
[1] Some book at #91; 42-24 #93;.
--

But then the file have to be post-processed to substitute #91; and #93;

Place these lines in .emacs, or evaluate them (goto the last )  and hit C-x 
C-e) 
for the current session :
--
(add-hook 'org-export-html-final-hook  'gio/replace-square-brackets)
(add-hook 'org-export-ascii-final-hook 'gio/replace-square-brackets)

(defun gio/replace-square-brackets ()
Replace #91; with [ and #93; with ] 
(interactive)
(setq a #91;)  ; use \[ for LaTeX export
(setq a1  [) 
(setq b #93;)  ; use \] for LaTeX export
(setq b1  ])
(ignore-errors (goto-char 1) (setq p (point)) 
(while ( p (point-max)) 
(re-search-forward a nil nil) (replace-match a1)  (setq p (point)) )  )
;;
(ignore-errors (goto-char 1) (setq p (point)) 
(while ( p (point-max)) 
(re-search-forward b nil nil) (replace-match b1)  (setq p (point)) )  )
(save-buffer) ) 
--
Tested for  HTML, ASCII.

For the LaTeX export  the line:
  This is not anymore a broken footnote.[fn:: Some book at #91;
  42-24#93;.]
exports to:

  This is not anymore a broken footnote.\footnote{Some book at \[
  42-24 \]. } 


So the LaTeX seems to convert directly the #9?; character.

Not tested for docbook.

HTH
Giovanni

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[Orgmode] org-capture and firefox/org-protocol

2010-08-31 Thread Richard Riley

My firefox key to call org-capture now causes my emacs server to
produce:

,
| Greedy org-protocol handler. Killing client.
| No server buffers remain to edit
`

It works fine from a bookmark link button.

I have no custom handlers (org-protocol-protocol-alist is nil).

I checked the code in my firefox config is the same as on the Worg.

Is there something else that needs to be configured now?

regards

r.



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Re: [Orgmode] synctex!! ...syncorg?

2010-08-31 Thread Kevin Brubeck Unhammer
2010/8/31 Rainer M Krug r.m.k...@gmail.com:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 On 31/08/10 12:10, Kevin Brubeck Unhammer wrote:
 Hi,

 I just discovered synctex, which lets you shift-click a point in a pdf
 in Okular and find yourself back in the tex-file at the point that
 corresponds with that point in the pdf =D

 Now on Linux? That's great. I only knew that it worked on a mac. Could
 you (possibly off list?) provide some details (where I can find it (I am
 using Ubuntu), how I can use it, ...)

As I got several off-list questions about where to get synctex on
GNU/Linux, I might as well reply on-list ;-)

I'm running Arch Linux with TeX Live 2009.16776, and the only thing I
had to do to get synctex working was run pdflatex like this:

pdflatex -synctex=1 foo.tex

You should also get the same effect by adding

\synctex=1

to the preamble, or something like

#+LaTeX_HEADER: \synctex=1

in your org-mode file. As for Ubuntu, if the TeX Live distribution
there is up-to-date (synctex was added in TeX Live 2008), I believe it
should work without any configuration necessary.

Note: if you were previously using the pdfsync package, you may have
to remove it from the preamble, also there was talk on the Ling-TeX
list of some programs not being able to handle file names with spaces
in them.


best regards,
Kevin Brubeck Unhammer

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[Orgmode] [babel] Why is this not tangling?

2010-08-31 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi

I want to tangle the following code into two files, specified as
properties, but no blocks are tangled - why?

I thought that the property is valid for the whole subtree below?

Thanks,

Rainer


* Simulation model HakSim
** Tool Functions
*** Layer I/O routines (spreadSim.layersIO.R)
#:PROPERTIES:
#:tangle:   spreadSim.layersIO.R
#:END:

 suitName
#+begin_src R
## Name for suitability layer
equations(ASM)$suitName - function(species)
{
return( paste(species$layer, suitability, sep=_) )
}
#+end_src
 test2
#+begin_src R
equations(ASM)$test2 - function(species)
{
return( test2 )
}
#+end_src

*** Tool functions (spreadSim.tools.R)
#:PROPERTIES:
#:tangle:   spreadSim.tools.R
#:END:

 tool1
#+begin_src R
## Name for suitability layer
equations(ASM)$tool1 - function(species)
{
return( too1 )
}
#+end_src
 tool2
#+begin_src R
## Name for suitability layer
equations(ASM)$tool2 - function(species)
{
return( too2 )
}
#+end_src


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

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:+33 - (0)9 53 10 27 44
Cell:   +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:  rai...@krugs.de

Skype:  RMkrug
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAkx9FkcACgkQoYgNqgF2egp2JwCfSEvG364tkEsuE9ZkNrXZ21EL
W0UAoIvi9uWCP8ArgmFtLanGzVfmPCSy
=5kjX
-END PGP SIGNATURE-

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Re: [Orgmode] Re: [babel] configuring LaTeX exports verbatim environment for exported code and results

2010-08-31 Thread Eric Schulte
Hi Douglas,

Douglas Bates ba...@stat.wisc.edu writes:

 On Tue, Aug 31, 2010 at 8:08 AM, Douglas Bates ba...@stat.wisc.edu wrote:
 I have been unable to find in the documentation whether the verbatim
 environment created by LaTeX exports of source code blocks can be
 configured.


It is possible to export code using the LaTeX listings package.  See
`org-export-latex-listings'
,
| org-export-latex-listings is a variable defined in `org-latex.el'.
| Its value is t
| 
| Documentation:
| Non-nil means export source code using the listings package.
| This package will fontify source code, possibly even with color.
| If you want to use this, you also need to make LaTeX use the
| listings package, and if you want to have color, the color
| package.  Just add these to `org-export-latex-packages-alist',
| for example using customize, or with something like
| 
|   (require 'org-latex)
|   (add-to-list 'org-export-latex-packages-alist '( listings))
|   (add-to-list 'org-export-latex-packages-alist '( color))
| 
| You can customize this variable.
| 
| [back]
`


 Exporting to LaTeX a section like
[...]

 Because both the source and the results are presented in verbatim, I
 don't have much control over the appearance of the code on the slide.
 If I could, for example, configure the names of the exported
 environment for the source code and for the results separately, I
 could use LaTeX's fancyvrb.sty to adjust font sizes, colors, boxes,
 etc.


Listings gives good control over the look of code on a slide, I
generally use the following as my jumping off point for listings style
in Beamer presentations
--8---cut here---start-8---
#+begin_LaTeX
  \definecolor{dkgreen}{rgb}{0,0.5,0}
  \definecolor{dkred}{rgb}{0.5,0,0}
  \definecolor{gray}{rgb}{0.5,0.5,0.5}
  \lstset{basicstyle=\ttfamily\bfseries\footnotesize,
morekeywords={virtualinvoke},
keywordstyle=\color{blue},
ndkeywordstyle=\color{red},
commentstyle=\color{dkred},
stringstyle=\color{dkgreen},
numbers=left,
numberstyle=\ttfamily\tiny\color{gray},
stepnumber=1,
numbersep=10pt,
backgroundcolor=\color{white},
tabsize=4,
showspaces=false,
showstringspaces=false,
xleftmargin=.23in
  }
#+end_LaTeX
--8---cut here---end---8---


 I just realized that if the code and results are wrapped in other than
 the verbatim environment the org-beamer-fragile-re variable will need
 to be customized.

No, I believe this works with listings blocks out of the box.

 (By the way, automatically detecting the need for the fragile option
 is a great idea.)

 Also, the blank lines before and after the verbatim environment are
 problematic.  In plain text it makes sense to delimit code chunks with
 blank lines but in LaTeX a blank line starts a new paragraph and you
 don't always want that.


You can manually place the #+results line anywhere in the org-mode file
(even immediately after the code block), however it seems the blank
lines still appear in the exported tex file.  This appears to be an
issue with the LaTeX exporter in general rather than Code blocks in
particular.


 As this is my first posting please let me know if I have
inadvertently violated conventions of the list.


Looks good to me.

Cheers -- Eric


 Well, other than my cut-and-paste glich below :-/

 Also, the exports append blank lines


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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Scot Becker
Giovanni,

Thanks for that.  I have the same problem, since I put citations in my
footnotes in the format \cite[50]{Ridolfi_2011_Autobiography}.  This is
great.  It's also a nice model for a few other petty troubles I want to
postprocess away.

Scot



On Tue, Aug 31, 2010 at 3:13 PM, Giovanni Ridolfi giovanni.rido...@yahoo.it
 wrote:

 Carsten Dominik carsten.domi...@gmail.com writes:

  unfortunately this is difficult to fix in a good way.
  I do want to go back to footnotes, because I think there are many
  things that do not yet work satisfactorily.  And then I also hope to
  address the issue you raised.  For the time being, unfortunately, I do
  not have a solution for you.

 I have a workaround.
 If the author uses the a special code for [ and ], e.g.
 #91; and #93; then the note is exported correctly.
 
 ** example
 This is not anymore a broken footnote.[fn:: Some book at #91; 42-24 #93;.]

 Exports to:
 This is not anymore broken footnote.[1]
 [1] Some book at #91; 42-24 #93;.
 --

 But then the file have to be post-processed to substitute #91; and #93;

 Place these lines in .emacs, or evaluate them (goto the last )  and hit
 C-x C-e)
 for the current session :
 --
 (add-hook 'org-export-html-final-hook  'gio/replace-square-brackets)
 (add-hook 'org-export-ascii-final-hook 'gio/replace-square-brackets)

 (defun gio/replace-square-brackets ()
 Replace #91; with [ and #93; with ] 
 (interactive)
 (setq a #91;)  ; use \[ for LaTeX export
 (setq a1  [)
 (setq b #93;)  ; use \] for LaTeX export
 (setq b1  ])
 (ignore-errors (goto-char 1) (setq p (point))
 (while ( p (point-max))
 (re-search-forward a nil nil) (replace-match a1)  (setq p (point)) )  )
 ;;
 (ignore-errors (goto-char 1) (setq p (point))
 (while ( p (point-max))
 (re-search-forward b nil nil) (replace-match b1)  (setq p (point)) )  )
 (save-buffer) )
 --
 Tested for  HTML, ASCII.

 For the LaTeX export  the line:
  This is not anymore a broken footnote.[fn:: Some book at #91;
  42-24#93;.]
 exports to:

  This is not anymore a broken footnote.\footnote{Some book at \[
  42-24 \]. }


 So the LaTeX seems to convert directly the #9?; character.

 Not tested for docbook.

 HTH
 Giovanni

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Re: [Orgmode] [BUG] some nasty bugs with PROPERTIES drawers

2010-08-31 Thread David Maus
Paul Sexton wrote:
There seems to be a fairly nasty bug caused by :PROPERTIES: drawers still
being recognised by org when they appear inside BEGIN_EXAMPLE or
BEGIN_SRC blocks. I encountered this behaviour while writing docs for
org-drill. The doc file, README.org, contains quoted examples of org
items, and also of an emacs lisp capture template containing the string
:PROPERTIES:.

The first thing I noticed was that PROPERTIES drawers inside EXAMPLE/SRC
blocks appear *folded* when the file is opened in org mode, and
'org-cycle' toggles their folded status, as if they belonged to a
real org heading.

That is cosmetic, but I also encountered a more serious problem.
README.org contains the following block of example elisp code, which
is meant to illustrate an example setup of org-capture:

 [snip]

Basically, every time I tried to export this file to HTML, Emacs would
become unresponsive (C-g did nothing) and would have to be killed with
the task manager (or xkill in Linux -- I tried on 2 systems).

I cannot reproduce this wiht Org-mode version 7.01trans (pulled
yesterday) on GNU Emacs 23.2.1 (i486-pc-linux-gnu, GTK+ Version
2.20.0) of 2010-08-14 on raven, modified by Debian

PS: I also realised that I was confused regarding how to get a syntax-
highlighted block of example source code into an org document, as
BEGIN_SRC appears to execute the code by default, which was not what
I wanted.

No, at least not for Elisp.  What is your assumption of Org mode
executing source blocks based on?

Best,
  -- David
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Re: [Orgmode] [babel] Conditional tangling possible

2010-08-31 Thread Eric Schulte
Hi Rainer,

Rainer M Krug r.m.k...@gmail.com writes:

 On 31/08/10 02:06, Eric Schulte wrote:
 Hi Rainer,
 
 The easiest way to do this should be,
 
 --8---cut here---start-8---
 ** pulling information from tags   :blue:
 
 #+begin_src R :var color=(car (org-get-tags-at (point))) :tangle example.R
   color
 #+end_src

 OK - that looks good. That solves one problem.

 But it is not actually conditional tangling? It is rather the transation
 of a tag into a variable - or am I seeing something wrong?


My fault, I misread your original message, something like the following
should work.  You can use the uppermost elisp code block to change the
value of the tangle-tag to whichever tag you wish to be tangled.

--8---cut here---start-8---
** conditional tangling
#+begin_src emacs-lisp :results silent
  (setq tangle-tag right)
#+end_src

*** first subheading   :left:
#+begin_src R :tangle (and (equal (car (org-get-tags-at (point))) tangle-tag) 
yes)
  first
#+end_src

*** second subheading :right:
#+begin_src R :tangle (and (equal (car (org-get-tags-at (point))) tangle-tag) 
yes)
  second
#+end_src
--8---cut here---end---8---

Cheers -- Eric

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Re: [Orgmode] [babel] Why is this not tangling?

2010-08-31 Thread Eric Schulte
Hi,

Rainer M Krug r.m.k...@gmail.com writes:

 Hi

 I want to tangle the following code into two files, specified as
 properties, but no blocks are tangled - why?

 I thought that the property is valid for the whole subtree below?

 Thanks,

 Rainer



It looks like you have bad properties syntax.


 * Simulation model HakSim
 ** Tool Functions
 *** Layer I/O routines (spreadSim.layersIO.R)
 #:PROPERTIES:
 #:tangle:   spreadSim.layersIO.R
 #:END:


the above should be

   :PROPERTIES:
   :tangle:   spreadSim.layersIO.R
   :END:

without the leading #s

Cheers -- Eric

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[Orgmode] Org-protocol / Chrome on Linux

2010-08-31 Thread Mattias Jämting
Hello,

Have someone managed to get org-protocol (
http://orgmode.org/worg/org-contrib/org-protocol.php) working in chrome on
linux (i use ubuntu) ?

(I have tried; it works in firefox, but not in chrome - which is my
preferred browser nowadays.)

Please let my know if it works for you, or if you have any hints on setting
it up.

/Mattias
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[Orgmode] cannot enable org-habit

2010-08-31 Thread Joseph Buchignani
Hi Org-mode,

I've read all the mailing lists and manuals and still can't get my org-habit
module working.

I presume there ought to be some sort of entry in my agenda, or the k key
should do something. I get nothing. Here is my setup:


   - org-mode 7.01h
   - emacs file included below.

The relevant portion is (add-to-list 'org-modules 'org-habit), which I have
enabled in my .emacs, to no avail.

What am I missing?

Thanks,
JB

my .emacs file:
;; Org-mode settings
(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(global-set-key \C-cl 'org-store-link)
(global-set-key \C-ca 'org-agenda)
(global-font-lock-mode 1)
 Org mode upgrade settings
(global-set-key \C-cb 'org-iswitchb)
;; (setq load-path (cons /usr/share/emacs/23.1/lisp/org/ load-path))
(require 'org-install)
;; org mode agenda enabling
(setq org-agenda-files (list
~/Desktop/Dropbox/6repos/ubu/Repository/org-mode/agenda.org))
;; making org pretty
;; (setq org-startup-indented t)

;; make logbook in drawer
(setq org-log-into-drawer LOGBOOK)

;; Enable habit tracking
;;(require 'org-habit)
(add-to-list 'org-modules 'org-habit)


;; better pasting between programs
(setq interprogram-paste-function 'x-cut-buffer-or-selection-value)

(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(x-select-enable-clipboard t)
 '(x-select-enable-primary nil))

(setq global-visual-line-mode 1)

(add-to-list 'load-path /home/dunpeel/freex/)
   (load freex-conf.el)



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[Orgmode] Re: svn version number as tag or property?

2010-08-31 Thread Achim Gratz
Rainer M Krug r.m.k...@gmail.com writes:

 I could use a code block with a bash script to extract that information
 from svn info, but that seems to be awkward for me - there must be an
 easier way.

Provided your vc setup works correctly, then (vc-working-revision FILE) will
deliver just this information.


Achim.


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[Orgmode] [babel] silent code block evaluation on export

2010-08-31 Thread Erik Iverson

Hello! I have pasted an org-mode file with my question, it's
easies to explain by copying the below file and exporting it
to HTML.

Thanks,
--Erik


* Silent code block evaluation on export.

The goal is to /run/ a code block on export for some side effect,
without any evidence in the exported file that this happened. For
example, loading some R package, reading in a dataset, or setting R
options. All this is presumably done with :session in mind, even
though I don't use it here.

In Sweave, we can specify the code block options echo = FALSE, results
= hide to faciliate this.

However, there are no command line arguments alone in org-mode that
can replicate such behavior.  Below are several examples and how they
fail.  There is also an example of a 'trick' that does work to
generate the output (or lack thereof) that we want.

/:results value/ tries to coerce its return value to a data.frame, so when
I reference 'non-conformable object' below, I mean something for which
the as.data.frame function generates an error.


* /:results value/ (the default for code blocks)

** with a simple object on the last line, a vector

This prints the return object, OK.

/:exports results :results value/
#+begin_src R :exports results :results value
2 + 2
#+end_src


** with a non-conformable object as the final value

This produces an error, as expected, and no output is produced, but
only by accident.

/:exports results :results value/
#+begin_src R :exports results :results value
summary(lm(1 ~ 1))
#+end_src

** using NULL as the last line

This does what we want, but requires a 'trick'. OK.

/:exports results :results value/
#+begin_src R :exports results :results value
summary(lm(1 ~ 1))
NULL
#+end_src


* /:results silent/

** with a simple object on the last line, a vector

This still prints the return object, it may be debateable if it
should.  The combination of /:exports results/ and
/:results silent/ does not seem inherently self-contradictory.

/:exports results :results silent/
#+begin_src R :exports results :results silent
2 + 2
#+end_src

** with a non-conformable object as the final value

However, with a non-conformable object on last line, an error is
produced when the code is evaluated in the buffer. I'm wondering if
/:results silent/ is specified, why the cast to data.frame is
occurring? It could be happening for good reason that I'm not aware
of. The lack of output here is due to an error occurring.

/:exports results :results silent/
#+begin_src R :exports results :results silent
summary(lm(1 ~ 1))
#+end_src

** using NULL as the last line

This does as we want, using the NULL trick.

/:exports results :results silent/
#+begin_src R :exports results :results silent
summary(lm(1 ~ 1))
NULL
#+end_src


* Ideas

Since the NULL trick is R-only, how could we specify command line
options to faciliate this use case?

Possible solutions:
0) There already exists a solution that I don't list here.

1) Make /:exports results :results silent/ do it, but note the results
   above with a non-conformable object!

2) Make /:exports none/ still evaluate the code block on
   export. Probably counter-intuitive.

3) Make export use the /:eval/ argument combined with /:exports/,
   maybe something like: /:exports none :eval yes/

4) Another better solution!







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[Orgmode] Re: [BUG] some nasty bugs with PROPERTIES drawers

2010-08-31 Thread Paul Sexton
David Maus dmaus at ictsoc.de writes:
 I cannot reproduce this wiht Org-mode version 7.01trans (pulled
 yesterday) on GNU Emacs 23.2.1 (i486-pc-linux-gnu, GTK+ Version
 2.20.0) of 2010-08-14 on raven, modified by Debian

There is a documentation file, README.org, that accompanies org-drill.
It can be downloaded at:
http://bitbucket.org/eeeickythump/org-drill/src/tip/README.org

The quoted emacs lisp example occurs near the end of the file. As is, it
exports to HTML (C-c C-e h) successfully for me, but if I change 
BEGIN_EXAMPLE/END_EXAMPLE to BEGIN_SRC/END_SRC for that block, it 
reproduces the bug.

 PS: I also realised that I was confused regarding how to get a syntax-
 highlighted block of example source code into an org document, as
 BEGIN_SRC appears to execute the code by default, which was not what
 I wanted.
 
 No, at least not for Elisp.  What is your assumption of Org mode
 executing source blocks based on?
 

My assumption is based on reading the manual. I couldn't find clearly stated 
anywhere exactly what BEGIN_SRC blocks do by default during export, and there 
are :eval never and eval query headline option, implying that these are not 
the default behaviours. But perhaps I read it wrong.

Paul



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[Orgmode] Re: [BUG] some nasty bugs with PROPERTIES drawers

2010-08-31 Thread Paul Sexton
Erik Iverson eriki at ccbr.umn.edu writes:
 See the :exports argument, the default is code only.
 
 http://orgmode.org/org.html#exports

That was my initial assumption, which is why I had BEGIN_SRC blocks in the file.
But then I found that it crashed during export with these blocks, and stopped
crashing once I changed them to BEGIN_EXAMPLE, which made me question my 
initial 
assumption and suspect that the BEGIN_SRC blocks were being evaluated/executed 
somehow.

Paul



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[Orgmode] Not enough arguments for format string

2010-08-31 Thread Sébastien Vauban
Hello,

Just came back of holidays, did not have time yet for reading the posts on the
ML, but git pull'ed the master branch.

When refiling, I now have this error coming up:

--8---cut here---start-8---
Debugger entered--Lisp error: (error Not enough arguments for format string)
  format(^\\(\\*+\\)[  
]+\\(?:\\(TODO\\|STARTED\\|WAIT\\|DLGT\\|DFRD\\|DONE\\|CANX\\|QTE\\|QTD\\|APP\\|EXP\\|REJ\\|OPENPO\\|CLSDPO\\))?\\(?:[
 ]*\\(\\[#.\\]\\)\\)?\\(?:[  ]*\\(?:\\[[0-9%%/]+\\]\\)\\)?[  
]*\\(%s\\)\\(?:[]*\\(?:\\[[0-9%%/]+\\]\\)\\)?\\(?:[ 
]+\\(:[[:alnum:]...@#%:]+:\\)\\)?[  ]*$ Appointments)
  (setq level (org-reduced-level (- ... ...)) txt (org-link-display-format 
(match-string 4)) re (format org-complex-heading-regexp-format (regexp-quote 
...)))
  (progn (setq level (org-reduced-level ...) txt (org-link-display-format ...) 
re (format org-complex-heading-regexp-format ...)) (when 
org-refile-use-outline-path (setq txt ...)) (push (list txt f re ...) tgs))
  (if (looking-at org-complex-heading-regexp) (progn (setq level ... txt ... re 
...) (when org-refile-use-outline-path ...) (push ... tgs)))
  (when (looking-at org-complex-heading-regexp) (setq level (org-reduced-level 
...) txt (org-link-display-format ...) re (format 
org-complex-heading-regexp-format ...)) (when org-refile-use-outline-path (setq 
txt ...)) (push (list txt f re ...) tgs))
  (catch (quote next) (when org-refile-target-verify-function (save-match-data 
...)) (when (looking-at org-complex-heading-regexp) (setq level ... txt ... re 
...) (when org-refile-use-outline-path ...) (push ... tgs)))
  (while (re-search-forward descre nil t) (goto-char (setq pos0 ...)) (catch 
(quote next) (when org-refile-target-verify-function ...) (when ... ... ... 
...)) (when (= ... pos0) (goto-char ...)))
  (save-restriction (widen) (goto-char (point-min)) (while (re-search-forward 
descre nil t) (goto-char ...) (catch ... ... ...) (when ... ...)))
  (save-excursion (save-restriction (widen) (goto-char ...) (while ... ... ... 
...)))
  (progn (if (bufferp f) (setq f ...)) (setq f (and f ...)) (if (eq 
org-refile-use-outline-path ...) (push ... tgs)) (save-excursion 
(save-restriction ... ... ...)))
  (or (setq tgs (org-refile-cache-get ... descre)) (progn (if ... ...) (setq f 
...) (if ... ...) (save-excursion ...)))
  (save-current-buffer (set-buffer (if ... f ...)) (or (setq tgs ...) (progn 
... ... ... ...)) (when org-refile-use-cache (org-refile-cache-put tgs ... 
descre)) (setq targets (append tgs targets)))
  (with-current-buffer (if (bufferp f) f (org-get-agenda-file-buffer f)) (or 
(setq tgs ...) (progn ... ... ... ...)) (when org-refile-use-cache 
(org-refile-cache-put tgs ... descre)) (setq targets (append tgs targets)))
  (while (setq f (pop files)) (with-current-buffer (if ... f ...) (or ... ...) 
(when org-refile-use-cache ...) (setq targets ...)))
  (while (setq entry (pop entries)) (setq files (car entry) desc (cdr entry)) 
(setq fast-path-p nil) (cond (... ...) (... ...) (... ...) (... ...)) (if 
(stringp files) (setq files ...)) (cond (... ...) (... ...) (... ...) (... ...) 
(... ... ...) (t ...)) (while (setq f ...) (with-current-buffer ... ... ... 
...)))
  (save-current-buffer (set-buffer (or default-buffer ...)) (while (setq entry 
...) (setq files ... desc ...) (setq fast-path-p nil) (cond ... ... ... ...) 
(if ... ...) (cond ... ... ... ... ... ...) (while ... ...)))
  (with-current-buffer (or default-buffer (current-buffer)) (while (setq entry 
...) (setq files ... desc ...) (setq fast-path-p nil) (cond ... ... ... ...) 
(if ... ...) (cond ... ... ... ... ... ...) (while ... ...)))
  (let ((case-fold-search nil) (entries ...) targets tgs txt re files f desc 
descre fast-path-p level pos0) (message Getting targets...) 
(with-current-buffer (or default-buffer ...) (while ... ... ... ... ... ... 
...)) (message Getting targets...done) (nreverse targets))
  org-get-refile-targets(nil)
  (setq org-refile-target-table (org-get-refile-targets default-buffer))
  (let ((org-refile-targets org-refile-targets) (org-refile-use-outline-path 
org-refile-use-outline-path)) (setq org-refile-target-table 
(org-get-refile-targets default-buffer)))
  org-refile-get-location(Refile to:  nil confirm)
  (save-excursion (org-refile-get-location (if goto Goto:  Refile to: ) 
default-buffer org-refile-allow-creating-parent-nodes))
  (or rfloc (save-excursion (org-refile-get-location ... default-buffer 
org-refile-allow-creating-parent-nodes)))
  (setq it (or rfloc (save-excursion ...)))
  (or (and (equal goto 2) org-clock-hd-marker (marker-buffer 
org-clock-hd-marker) (prog1 ... ...)) (setq it (or rfloc ...)))
  (if (or (and ... org-clock-hd-marker ... ...) (setq it ...)) (progn (setq 
file ... re ... pos ...) (if ... ...) (setq nbuf ...) (if goto ... ... ... ... 
... ... ...)))
  (when (or (and ... org-clock-hd-marker ... ...) (setq it ...)) (setq file 
(nth 1 it) re (nth 2 it) pos (nth 3 it)) 

Re: [Orgmode] org-capture and firefox/org-protocol

2010-08-31 Thread Sebastian Rose
Richard Riley rile...@gmail.com writes:
 My firefox key to call org-capture now causes my emacs server to
 produce:

 ,
 | Greedy org-protocol handler. Killing client.
 | No server buffers remain to edit
 `


This is in your *Messages* buffer, isn't it?
It doesn't cause any trouble, does it?

Those are just two messages to assure the author of a custom handler,
that there will be no emacsclient waiting for a  `C-x #'
(`server-edit').


   Sebastian


 It works fine from a bookmark link button.

 I have no custom handlers (org-protocol-protocol-alist is nil).

 I checked the code in my firefox config is the same as on the Worg.

 Is there something else that needs to be configured now?

 regards

 r.

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Re: [Orgmode] Org-protocol / Chrome on Linux

2010-08-31 Thread Sebastian Rose
Mattias Jämting matt...@jwd.se writes:
 Hello,

 Have someone managed to get org-protocol (
 http://orgmode.org/worg/org-contrib/org-protocol.php) working in chrome on
 linux (i use ubuntu) ?

 (I have tried; it works in firefox, but not in chrome - which is my
 preferred browser nowadays.)

 Please let my know if it works for you, or if you have any hints on setting
 it up.


Do you have Gnome libs installed?  On a current GNU/Linux you could
install protocol handlers for all programs as explained in

  http://orgmode.org/worg/org-contrib/org-protocol.php#sec-3_1


I don't know how to setup protocols with Chrome, but once you have done
that, restarting Chrome and clicking one of the test links should work:

  http://orgmode.org/worg/org-contrib/org-protocol.php#sec-3_4


Please report back if you get it to work.   Maybe you could even provide
a little description we could add to the docs.


HTH

  Sebastian


(I will not use Chrome, since I don't want sites as trusted repos in my
sources list, that uses the uninstall script in the *.deb package, to
put the site into my sources list again.)

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[Orgmode] [Patch] org-protocol default template should be nil

2010-08-31 Thread Sebastian Rose
Hi Carsten,


this little patch fixes an issue Richard brought up.

We always used the w template as the default for `org-remember' and
also used it for `org-capture' for historical reasons.

Unfortunately, this breaks, if the user has no w template defined.

The patch below simply set's the custom variable
`org-protocol-default-template-key' to nil, so the interactive template
selection is used by default.  This works for both, remember an capture.

I will adjust the docs, once the patch is applied.


diff --git a/lisp/org-protocol.el b/lisp/org-protocol.el
index 3f240fd..21f28e7 100644
--- a/lisp/org-protocol.el
+++ b/lisp/org-protocol.el
@@ -260,7 +260,7 @@ Here is an example:
   :group 'org-protocol
   :type '(alist))
 
-(defcustom org-protocol-default-template-key w
+(defcustom org-protocol-default-template-key nil
   The default org-remember-templates key to use.
   :group 'org-protocol
   :type 'string)



Thanks,

  Sebastian
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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Aidan Gauland
Thanks!  That works fine.  I suppose I should point out that I only used =
an
ASCII export for the example situation, but I ran into this problem expor=
ting
to HTML.

--Aidan Gauland



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Re: [Orgmode] Bug: Impossible to have right bracket in footnotes [7.01trans]

2010-08-31 Thread Aidan Gauland
Alan L Tyree wrote:
 Disable footnotes like [2010], but keep footnotes like [fn:2010]
 
 The reason is that I write legal texts that have references to case law
 that look like: Marreco v Richardson [1908] 2 KB 584. The dates in
 square brackets are an essential part of the reference.

Perhaps it would be best to determine for what type of writing the current way
Org handles footnotes is lacking.  Is it just academic writing in general, of
mostly only certain fields?  Both Alan and I have needed to use a workaround
for legal writing (I'm a first-year student; don't know about Alan).  What
have other people had trouble footnoting/citing in Org?

--Aidan



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Re: [Orgmode] HTML Export Problem

2010-08-31 Thread Scott Randby
On 08/30/2010 10:10 PM, Nick Dokos wrote:
 Scott Randby sran...@gmail.com wrote:
 
 Whenever I export to HTML, I get the following:

 HTML generated by org-mode TAG=7.01g in emacs 23

 I would like to get rid of the TAG= (which wasn't present in earlier
 org-mode versions) without having to edit the HTML.
 How do I do this?

 
 This was fixed on Aug. 7, so you need to get a more recent version (I
 think 7.01h had it fixed.)

Thanks, I'll upgrade sometime. I just realized I have one machine that
has 6.36c and another machine that has 7.01g. I might as well upgrade
both at the same time.

Scott

 
 See http://thread.gmane.org/gmane.emacs.orgmode/27988
 
 Nick
 

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[Orgmode] Re: [Patch] org-protocol default template should be nil

2010-08-31 Thread Richard Riley

I dont know if its related but something has broken the use of

,
| org-default-notes-file is a variable defined in `org.el'.
| Its value is refile.org
| 
| Documentation:
| Default target for storing notes.
| Used as a fall back file for org-remember.el and org-capture.el, for
| templates that do not specify a target file.
`

for me too. I tend not to specify a destination file in my templates and
instead refile at a later date (hence the variable above is set to refile.org).

Now I get a backtrace :-

,
| Debugger entered--Lisp error: (error Not enough arguments for format string)
|   format(^\\(\\*+\\)[
]+\\(?:\\(TODO\\|STARTED\\|WAITING\\|DONE\\|CANCELLED\\|REPORT\\|BUG\\|KNOWNCAUSE\\|FIXED\\))?\\(?:[
   ]*\\(\\[#.\\]\\)\\)?\\(?:[  ]*\\(?:\\[[0-9%%/]+\\]\\)\\)?[  
]*\\(%s\\)\\(?:[]*\\(?:\\[[0-9%%/]+\\]\\)\\)?\\(?:[ 
]+\\(:[[:alnum:]...@#%:]+:\\)\\)?[  ]*$ Tasks To Refile)
|   org-capture-set-target-location()
|   org-capture(nil)
|   call-interactively(org-capture nil nil)
`

As a side note it was a bit of a misnomer. Possibly the storage should
use a 'org-default-capture-file variable since notes have their own
distinct meaning.


regards

r.

(apologies if this is a double post).

Sebastian Rose sebastian_r...@gmx.de writes:

 Hi Carsten,


 this little patch fixes an issue Richard brought up.

 We always used the w template as the default for `org-remember' and
 also used it for `org-capture' for historical reasons.

 Unfortunately, this breaks, if the user has no w template defined.

 The patch below simply set's the custom variable
 `org-protocol-default-template-key' to nil, so the interactive template
 selection is used by default.  This works for both, remember an capture.

 I will adjust the docs, once the patch is applied.




 diff --git a/lisp/org-protocol.el b/lisp/org-protocol.el
 index 3f240fd..21f28e7 100644
 --- a/lisp/org-protocol.el
 +++ b/lisp/org-protocol.el
 @@ -260,7 +260,7 @@ Here is an example:
:group 'org-protocol
:type '(alist))
  
 -(defcustom org-protocol-default-template-key w
 +(defcustom org-protocol-default-template-key nil
The default org-remember-templates key to use.
:group 'org-protocol
:type 'string)





 Thanks,

   Sebastian


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Re: [Orgmode] Not enough arguments for format string

2010-08-31 Thread David Maus
Sébastien Vauban wrote:
Hello,

Just came back of holidays, did not have time yet for reading the posts on the
ML, but git pull'ed the master branch.

When refiling, I now have this error coming up:

Fixed in master.

Best,
  -- David
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Re: [Orgmode] exec code on task state progression

2010-08-31 Thread David Maus
Richard Riley wrote:

What would be the best approach, if at all possible, to having org
manage tasks which allow me set dates for a task to be scheduled and
then let me manually progress/cycle that task and have it then invoke
code/scripts?

Maybe something like this: Store the name of the function to be
executed in a property and define a function which is run in
`org-after-todo-state-change-hook' that reads this property and
executes the function if, say, the state was changed to DONE.

(defun dmj:execute-func-after-todo-change ()
  Execute function in exec_func property if entry changes to DONE.
  (when (string= state DONE)
(let ((func (intern (org-entry-get nil exec_func
  (if (fboundp func) (funcall func)

(add-hook 'org-after-todo-state-change-hook 'dmj:execute-func-after-todo-change)

For the update part you might want to look at el-get.el[1]:

,
| Short Story: el-get allows you to install and manage elisp code for
| Emacs. It supports lots of differents types of sources and is able to
| install them, update them and remove them, but more importantly it
| will init them for you.
|
| That means it will care about require ing the features you need, load
| ing the files, setting the Info paths so that C-h i shows the new
| documentation you now depend on, and finally call your own :after
| function for you to setup the extension. Or call it a package.
`

I did not try it (yet), but this looks sweet.

HTH,
  -- David

[1] http://github.com/dimitri/el-get
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