[Orgmode] Re: Proposed New Syntax For Calling Code Blocks was: Problem with Babel and sessions

[Christopher Witte]

Thanks for reply Eric.

Thanks for the reply.  The reason why I wanted this was because I have
multiple sets of data and I would like to be able to apply the same code
block to the different sets of data and have the results in different pdfs.
Is there anyway to do this with the current version of org?

Cheers,
Chris

On 10 September 2010 20:06, Eric Schulte  wrote:

> Hi Christopher,
>
> Thanks for the well documented example.
>
> The header arguments on the call line, are actually being used by the
> call line itself, not by the R block which is called.  To unpack that,
> on evaluation the call line expands to a trivial emacs-lisp code block
> which is equivalent to
>
> #+begin_src emacs-lisp :var results=chartPolAngle(pol=tableTestBabel)
> :session testBabel:file
>  results
> #+end_src
>
> So the :session header argument is used by the emacs-lisp code block in
> the call line, and never propagates to the R code block which is
> evaluated.  Notice that header arguments like :results silent, will have
> the expected results.
>
> So for now you will have to place the header argument on the actual R
> code block.
>
> That said, I think that we should provide a mechanism for passing header
> arguments through to called code blocks making the original
> functionality you described possible.  I'm not sure how best to do that,
> but currently I think we should expand the syntax used to call code
> blocks to be more similar to inline code blocks, s.t. header arguments
> can be placed inside of an optional square bracket section between the
> name of the code block and the arguments.  Using this new proposed
> syntax your example below would be written as
>
> #+call: chartPolAngle[:session testBabel :file
> testBabel.pdf](pol=tableTestBabel)
>
> I'd be interested to hear what the community thinks of this new syntax.
>
> As an unrelated note, we also need to think of a natural way to allow
> the header argument portion of a code block to span multiple lines.
>
> Best -- Eric
>
> Christopher Witte  writes:
>
> > I'm having a bit of trouble with org bable and R. When I try to execute
> the
> > code below (C-c C-c on the call line), as you can see, I get the results
> > :nil
> >
> > ---
> > #+tblname: tableTestBabel
> > |   0 | 4.40 |
> > |  30 | 4.54 |
> > |  60 | 7.09 |
> > |  90 | 9.40 |
> > | 120 | 9.22 |
> > | 150 | 6.65 |
> > | 180 | 4.22 |
> >
> > #+srcname: chartPolAngle(pol)
> > #+begin_src R
> >   angle <- pol[,1]
> >   energy <- pol[,2]
> >   plot(angle,energy)
> >   energy.model <-  nls (energy ~ a1 + a2 * (sin(pi / a3 *(angle-a4)))^2,
> > start=list(a1=3.0, a2=7.0, a3=180, a4=0.0))
> >   lines(spline(angle, fitted.values(energy.model)), lwd=2)
> >   summary(energy.model)
> > #+end_src
> >
> > #+call: chartPolAngle(pol=tableTestBabel) :session testBabel :file
> testBabel.pdf
> >
> > #+results: chartPolAngle(pol=tableTestBabel)
> > : nil
> > 
> >
> > but If I move the header arguments to the source block, as in the code
> > below, everything works fine. I also get asked "ESS [S(R): R] starting
> data
> > directory? ~/doc/org/" which I don't get with the code above.
> >
> > ---
> > #+tblname: tableTestBabel
> > |   0 | 4.40 |
> > |  30 | 4.54 |
> > |  60 | 7.09 |
> > |  90 | 9.40 |
> > | 120 | 9.22 |
> > | 150 | 6.65 |
> > | 180 | 4.22 |
> >
> > #+call: chartPolAngle(pol=tableTestBabel)
> >
> > #+results: chartPolAngle(pol=tableTestBabel)
> > : testBabel.pdf
> >
> >
> > #+srcname: chartPolAngle(pol)
> > #+begin_src R :session testBabel :file testBabel.pdf
> >   angle <- pol[,1]
> >   energy <- pol[,2]
> >   plot(angle,energy)
> >   energy.model <-  nls (energy ~ a1 + a2 * (sin(pi / a3 *(angle-a4)))^2,
> > start=list(a1=3.0, a2=7.0, a3=180, a4=0.0))
> >   lines(spline(angle, fitted.values(energy.model)), lwd=2)
> >   summary(energy.model)
> > #+end_src
> > ---
> >
> > Org doesn't appear to respect the head arguments on the call. I pulled
> from
> > git a couple days ago. Any ideas why?
> >
> > Cheers
> > Chris Witte
> > ___
> > Emacs-orgmode mailing list
> > Please use `Reply All' to send replies to the list.
> > Emacs-orgmode@gnu.org
> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>



-- 
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Molecular Imaging Group
 Leibniz-Institut für Molekulare Pharmakologie (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10
13125 Berlin, Germany
Phone: 00493094793-279
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[Orgmode] Repeating timestamps with a finish date

[Christopher Witte]

Hi,

Is there a way to get timestamps that repeat (say weekly) up to a certain
date when it stops repeating?  I have a weekly appointment that will only go
for the next 8 weeks and I don't want to have to input each appointment
separately and I don't want it cluttering up my diary beyond it's end date.

Cheers
Chris.
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[Orgmode] Re: Repeating timestamps with a finish date

[Christopher Witte]

Sorry, I didn't see the other current thread on this, please ignore.

On 19 October 2010 13:48, Christopher Witte  wrote:

> Hi,
>
> Is there a way to get timestamps that repeat (say weekly) up to a certain
> date when it stops repeating?  I have a weekly appointment that will only go
> for the next 8 weeks and I don't want to have to input each appointment
> separately and I don't want it cluttering up my diary beyond it's end date.
>
> Cheers
> Chris.
>
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[Orgmode] Org and ido mode

[Christopher Witte]

Hi,

I have org-completion-use-ido set to true but when I try and attach a file
it doesn't use ido, is there any way to change this?

Cheers,
Chris
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[Orgmode] Subtle bug with capture and refile

[Christopher Witte]

The new org capture has been working great but I have just come across a
subtle bug that has taken me a while to reliably reproduce.  I have org set
up to add TODO captures to the top of my organiser.org file.  If you try and
refile the capture TODO and the cursor is at the bottom of the capture
buffer, it will refile the next item in organiser.org and not the capture
TODO.  Hmm, that doesn't sound too clear, let me try and give an example.
My organiser.org looks like this:

-organiser.org-
* Home
** Home item 1
** Home item 2
* Work
** Work item 1


I then make a capture TODO

-capture buffer-
* TODO report capture buffer bug
!

with the cursor indicated by ! I press C-c C-w and refile to work.  Instead
of the capture note being refiled, Home get refiled so I end up with
organiser.org looking like:

-organiser.org-
*TODO report capture buffer bug
* Work
** Home
*** Home item 1
*** Home item 2
** Work item 1

if instead the cursor is on the TODO line when I refile, everything works as
expect and I end up with:

-organiser.org-
* Home
** Home item 1
** Home item 2
* Work
** TODO report capture buffer bug
** Work item 1

This has been causing me problems for a while now, but I could never work
out why this only happened some of the time.  I hope that explains the
problem with sufficient clarity, let me know if it doesn't.

Cheers
Chris Witte.
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Re: [Orgmode] Subtle bug with capture and refile

[Christopher Witte]

Work for me too, thanks for the quick fix!

Cheers
Chris.

On 21 October 2010 22:27, Carsten Dominik  wrote:

> Thanks for doing the testing.
>
> - Carsten
>
>
> On Oct 21, 2010, at 8:29 PM, John Rakestraw wrote:
>
>  Hi, Carsten --
>>
>> On Thu, 21 Oct 2010, Carsten Dominik wrote:
>>
>>> Hi Christopher,
>>>
>>> thank you for taking the time to isolate this bug.  Could
>>> you please try the following patch?
>>>
>>>
>> Your patch seems to fix the problem.
>>
>> Thanks --
>>
>> John
>>
>>  Thanks.
>>>
>>> - Carsten
>>>
>>>Modified lisp/org-capture.el
>>> diff --git a/lisp/org-capture.el b/lisp/org-capture.el
>>> index 7915f7f..537f1a4 100644
>>> --- a/lisp/org-capture.el
>>> +++ b/lisp/org-capture.el
>>> @@ -548,6 +548,7 @@ already gone."
>>>  (unless (eq (org-capture-get :type 'local) 'entry)
>>>   (error
>>>"Refiling from a capture buffer makes only sense for `entry'-
>>> type templates"))
>>> +  (if (and (bolp) (eobp)) (backward-char 1))
>>>  (let ((pos (point))
>>>(base (buffer-base-buffer (current-buffer)))
>>>(org-refile-for-capture t))
>>>
>>>
>> --
>> John Rakestraw
>>
>
>
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-- 
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 Leibniz-Institut für Molekulare Pharmakologie (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10
13125 Berlin, Germany
Phone: 00493094793-279
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Re: [Orgmode] Org and ido mode

[Christopher Witte]

Carsten,

C-c C-a a  or any of C-c C-a c/m/l don't give me an ido find file.

Cheers
Chris.

On 22 October 2010 18:03, Carsten Dominik  wrote:

>
> On Oct 19, 2010, at 5:20 PM, Christopher Witte wrote:
>
>  Hi,
>>
>> I have org-completion-use-ido set to true but when I try and attach a file
>> it doesn't use ido, is there any way to change this?
>>
>
> Do you press `C-c a a', or where exactly are you?
>
> - Carsten
>
>
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Re: [Orgmode] Org and ido mode

[Christopher Witte]

I just downloaded ido-hacks.el and added the following lines to my .emacs
(require 'ido-hacks)
(ido-hacks-mode t)
but it still does use ido for attachments.

Chris

On 23 October 2010 22:45, Samuel Wales  wrote:

> Look for ido-hacks.el.
>



-- 
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Campus Berlin-Buch
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Re: [Orgmode] [BABEL] Tangling to a hierarchy of files?

[Christopher Witte]

 On 19 January 2011 18:41, Eric Schulte  wrote:

> The reason that I push back against this, is that I often times
> accidentally use a tangle path in which the directory does not exist and
> the error notification serves as a useful warning that I either
> mis-typed the directory or need to create it.
>

Why not make the function prompt the user if they want to create the
directory? That way you get the best of both worlds.


Chris.
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Re: [Orgmode] [ANN] Org-babel integrated into Org-mode

[Christopher Witte]

I'm having trouble getting the new version of babel to work with
haskell and R under Ubuntu 10.04 using emacs-snapshot.  It works fine
for emacs-lisp.  I had to change the variable LISPF in the Makefile
to:

LISPF  =org.el  \
.
babel/ob.el \
babel/ob-table.el   \
babel/ob-lob.el \
babel/ob-ref.el \
babel/ob-exp.el \
babel/ob-tangle.el  \
babel/ob-comint.el  \
babel/ob-keys.el\
babel/langs/ob-emacs-lisp.el\
babel/langs/ob-haskell.el   \
babel/langs/ob-latex.el \
babel/langs/ob-sh.el\
babel/langs/ob-asymptote.el \
babel/langs/ob-R.el \
babel/langs/ob-gnuplot.el   

otherwise I couldn't compile my .emacs file, which contains the following:

(require 'org-install)

;;(require 'org)
;;(require 'ob)
;;(require 'ob-tangle)
;; org-babel set up
(require 'ob-haskell)
(require 'ob-latex)
(require 'ob-sh)
(require 'ob-asymptote)
(require 'ob-R)
(require 'ob-gnuplot)

The following works fine:
  #+tblname: example-table
  | 1 |
  | 2 |
  | 3 |
  | 4 |

  #+source: table-length
  #+begin_src emacs-lisp  :var table=example-table
  (length table)
  #+end_src

  #+results: table-length
  : 4

But when I try the haskell equivalent:
  #+source: table-length
  #+begin_src haskell  :var table=example-table
  length table
  #+end_src


I get:
executing haskell source code block
reference 'example-table' not found in this buffer
org-babel-ref-resolve-reference: reference 'example-table' not found
in this buffer

If I try:
  #+source: table-length
  #+begin_src haskell
  length [1,2,3]
  #+end_src


I get:
executing haskell source code block
org-babel-execute:haskell: Symbol's function definition is void: session


I also get a lot of warnings when I compile org-mode, see the attached
buiild log.


Thanks for your help,

Chris Witte.

On 23 June 2010 23:09, Eric Schulte  wrote:
> Hi,
>
> I've just merged the babel branch into the main branch of Org-mode.
> This merge culminates much integration work by Dan Davison and Tom Dye,
> as well as myself.
>
> Babel is now part of Org-mode.
>
> The biggest changes are:
>
> 1) Babel now has documentation!  It is part of Org-mode's documentation
>
>   see Chapter 14 _Working With Source Code_
>
>   also, the Babel keybindings are now listed in the refcard, and can be
>   viewed from any Org-mode buffer by pressing C-c C-v h
>
> 2) Babel will now be loaded by default along with the rest of Org-mode.
>   This means that *everyone* currently using babel will need to change
>   their Emacs config and remove the (require 'org-babel-int) and/or
>   (require 'org-babel) lines.
>
>   Support for evaluating emacs-lisp code blocks is loaded by default.
>   All other languages will need to be required explicitly.  To conform
>   to Emacs filename specifications all language require lines have been
>   shortened from e.g.
>
>   (require 'org-babel-sh)
>
>   to
>
>   (require 'ob-sh)
>
> Thanks -- Eric
>
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>
emacs -batch -q -no-site-file -eval "(setq load-path (cons (expand-file-name \"langs\" (expand-file-name \"babel\" (expand-file-name \"./lisp/\"))) (cons (expand-file-name \"babel\" (expand-file-name \"./lisp/\")) (cons (expand-file-name \"./lisp/\") (cons \"/usr/local/share/emacs/site-lisp\" load-path)" -f batch-byte-compile lisp/org.el

In org-order-calendar-date-args:
org.el:14428:31:Warning: `european-calendar-style' is an obsolete variable (as
of Emacs 23.1); use `calendar-date-style' instead.
Wrote /home/cwitte/source/elisp/org-mode/lisp/org.elc
emacs -batch -q -no-site-file -eval "(setq load-path (cons (expand-file-name \"langs\" (expand-file-name \"babel\" (expand-file-name \"./lisp/\"))) (cons (expand-file-name \"babel\" (expand-file-name \"./lisp/\")) (cons (expand-file-name \"./lisp/\") (cons \"/usr/local/share/emacs/site-lisp\" load-path)" -f batch-byte-compile lisp/org-agenda.el

In org-agenda-add-entry-to-org-agenda-diary-file:
org-agenda.el:7160:42:Warning: `european-calendar-style' is an obsolete
variable (as of Emacs 23.1); use `calendar-date-style' instead.
Wrote /home/cwitte/source/elisp/org-mode/lisp/org-agenda.elc
emacs -batch -q -no-site-file -eval "(setq load-path (cons (expand-file-name \"langs\" (expand-file-name \"babel\" (expand-file-name \"./lisp/\"))) (cons (expand-file-name \"babel\" (exp

Re: [Orgmode] [ANN] Org-babel integrated into Org-mode

[Christopher Witte]

Eric,

Thanks, it all appears to be working now.

Cheers,
Chris.

On 28 June 2010 18:59, Eric Schulte  wrote:
> Hi Christopher,
>
> Christopher Witte  writes:
>
>> I'm having trouble getting the new version of babel to work with
>> haskell and R under Ubuntu 10.04 using emacs-snapshot.  It works fine
>> for emacs-lisp.  I had to change the variable LISPF in the Makefile
>> to:
>>
>> LISPF      =  org.el                          \
>> .
>>               babel/ob.el                     \
>>               babel/ob-table.el               \
>>               babel/ob-lob.el                 \
>>               babel/ob-ref.el                 \
>>               babel/ob-exp.el                 \
>>               babel/ob-tangle.el              \
>>               babel/ob-comint.el              \
>>               babel/ob-keys.el                \
>>               babel/langs/ob-emacs-lisp.el    \
>>               babel/langs/ob-haskell.el       \
>>               babel/langs/ob-latex.el \
>>               babel/langs/ob-sh.el    \
>>               babel/langs/ob-asymptote.el     \
>>               babel/langs/ob-R.el     \
>>               babel/langs/ob-gnuplot.el
>>
>> otherwise I couldn't compile my .emacs file, which contains the following:
>>
>
> Hmm, I would think it would be possible to require files which are not
> byte-compiled.  The reason that the language files (aside from
> emacs-lisp) are not compiled by default is that they often have exotic
> requirements which will not be present on most users systems.
>
>>
>> (require 'org-install)
>>
>> ;;(require 'org)
>> ;;(require 'ob)
>> ;;(require 'ob-tangle)
>> ;; org-babel set up
>> (require 'ob-haskell)
>> (require 'ob-latex)
>> (require 'ob-sh)
>> (require 'ob-asymptote)
>> (require 'ob-R)
>> (require 'ob-gnuplot)
>>
>> The following works fine:
>>           #+tblname: example-table
>>           | 1 |
>>           | 2 |
>>           | 3 |
>>           | 4 |
>>
>>           #+source: table-length
>>           #+begin_src emacs-lisp  :var table=example-table
>>           (length table)
>>           #+end_src
>>
>>           #+results: table-length
>>         : 4
>>
>> But when I try the haskell equivalent:
>>           #+source: table-length
>>           #+begin_src haskell  :var table=example-table
>>           length table
>>           #+end_src
>>
>>
>> I get:
>> executing haskell source code block
>> reference 'example-table' not found in this buffer
>> org-babel-ref-resolve-reference: reference 'example-table' not found
>> in this buffer
>>
>> If I try:
>>           #+source: table-length
>>           #+begin_src haskell
>>           length [1,2,3]
>>           #+end_src
>>
>>
>> I get:
>> executing haskell source code block
>> org-babel-execute:haskell: Symbol's function definition is void: session
>>
>
> Thanks for bringing this up, it looks like ob-haskell has fallen victim
> to bit-rot.  I've done a fairly thorough cleanup of the file (just
> pushed up the commit).  Please give it a test run and let me know
> if/where I missed issues.
>
>>
>>
>> I also get a lot of warnings when I compile org-mode, see the attached
>> buiild log.
>>
>
> Yes, the language-specific files have not been manicured for clean
> byte-compilation.  This is certainly something that should happen, but
> probably not in the near term.
>
> Thanks -- Eric
>
>>
>>
>> Thanks for your help,
>>
>> Chris Witte.
>>
>> On 23 June 2010 23:09, Eric Schulte  wrote:
>>> Hi,
>>>
>>> I've just merged the babel branch into the main branch of Org-mode.
>>> This merge culminates much integration work by Dan Davison and Tom Dye,
>>> as well as myself.
>>>
>>> Babel is now part of Org-mode.
>>>
>>> The biggest changes are:
>>>
>>> 1) Babel now has documentation!  It is part of Org-mode's documentation
>>>
>>>   see Chapter 14 _Working With Source Code_
>>>
>>>   also, the Babel keybindings are now listed in the refcard, and can be
>>>   viewed from any Org-mode buffer by pressing C-c C-v h
>>>
>>> 2) Babel will now be loaded by default along with the rest of Org-mode.
>>>   This means that *everyone* currently using babe

Re: [Orgmode] Re: MathJax - use Tex/LaTeX/MathML in HTML pages

[Christopher Witte]

ASCIIMathML http://www1.chapman.edu/~jipsen/mathml/asciimath.html might also
be an alternative, for that you need fonts on the client (Firefox, I don't
think IE supports MathML out of the box), and it uses MathML so it is
standard compliant.

Regards
Chris.


On 4 August 2010 06:24, Bastien  wrote:

> Hi Dan,
>
> Dan Davison  writes:
>
> > It's quite convenient already (see below), so what exactly would the
> > option involve?  Can the javascript and fonts be located remotely?
>
> From what I understand, no, the javascript and fonts have to be on the
> server.
>
> I just installed an instance on orgmode.org:
>
>  http://orgmode.org/mathjax/test/
>
> > - Darlan Cavalcante has written a Worg article[1] on using jsMath with
> >   org
> > - Basically, to use jsMath all you need is
> >
> >   #+options: latex:verbatim
> >   #+style: 
>
> Great!  So to use mathjax on orgmode.org (Worg etc.) :
>
>  #+options: latex:verbatim
>  #+style:  src="/mathjax/MathJax.js">
>
> > - Mathjax was considerably slower to render the maths. (I think that
> >   under the hood it converts to mathML which jsMath does not do (?))
>
> I'm not sure.  Maybe MathJax is faster once reasonably tweaked.
>
> > As I said the other day[2], one reason I am excited about these
> > technologies is that we can produce a pdf with pretty source code
> > fontification via htmlize (rather than ugly[3] latex listings output)
> > and genuine mathematical fonts rather than ugly dvipng images. I do this
> > via CUPS print to file under linux, which allows the web browser to
> > produce a .ps or .pdf. I'd be interested to know how we can make this a
> > more "genuine" org export path.
>
> You mean org -> HTML -> ps?
>
> Is it not possible to call firefox (or Xulrunner) in batch mode to
> convert an HTML page into .ps?
>
> If so, we can have two ways of producing org->pdf, one through LaTeX,
> one through HTML...
>
> --
>  Bastien
>
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-- 
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 Leibniz-Institut für Molekulare Pharmakologie (FMP)
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13125 Berlin, Germany
Phone: 00493094793-279
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[Orgmode] Problem with Babel and sessions

[Christopher Witte]

I'm having a bit of trouble with org bable and R. When I try to execute the
code below (C-c C-c on the call line), as you can see, I get the results
:nil

---
#+tblname: tableTestBabel
|   0 | 4.40 |
|  30 | 4.54 |
|  60 | 7.09 |
|  90 | 9.40 |
| 120 | 9.22 |
| 150 | 6.65 |
| 180 | 4.22 |

#+srcname: chartPolAngle(pol)
#+begin_src R
  angle <- pol[,1]
  energy <- pol[,2]
  plot(angle,energy)
  energy.model <-  nls (energy ~ a1 + a2 * (sin(pi / a3 *(angle-a4)))^2,
start=list(a1=3.0, a2=7.0, a3=180, a4=0.0))
  lines(spline(angle, fitted.values(energy.model)), lwd=2)
  summary(energy.model)
#+end_src

#+call: chartPolAngle(pol=tableTestBabel) :session testBabel:file
testBabel.pdf

#+results: chartPolAngle(pol=tableTestBabel)
: nil


but If I move the header arguments to the source block, as in the code
below, everything works fine. I also get asked "ESS [S(R): R] starting data
directory? ~/doc/org/" which I don't get with the code above.

---
#+tblname: tableTestBabel
|   0 | 4.40 |
|  30 | 4.54 |
|  60 | 7.09 |
|  90 | 9.40 |
| 120 | 9.22 |
| 150 | 6.65 |
| 180 | 4.22 |

#+call: chartPolAngle(pol=tableTestBabel)

#+results: chartPolAngle(pol=tableTestBabel)
: testBabel.pdf


#+srcname: chartPolAngle(pol)
#+begin_src R :session testBabel :file testBabel.pdf
  angle <- pol[,1]
  energy <- pol[,2]
  plot(angle,energy)
  energy.model <-  nls (energy ~ a1 + a2 * (sin(pi / a3 *(angle-a4)))^2,
start=list(a1=3.0, a2=7.0, a3=180, a4=0.0))
  lines(spline(angle, fitted.values(energy.model)), lwd=2)
  summary(energy.model)
#+end_src
---

Org doesn't appear to respect the head arguments on the call. I pulled from
git a couple days ago. Any ideas why?

Cheers
Chris Witte
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[O] Problems with executing babel code

[Christopher Witte]

After a recent git pull, I've been having some problems executing and
editing babel code.  The following will execute:

#+srcname: Blah1
#+begin_src emacs-lisp :results value
  (concat "" "works")
#+end_src

#+results: Blah1
: works

#+call: Blah1(x=1) :results value raw

#+results: Blah1(x=1)
works



#+srcname: Blah4(x)

#+begin_src emacs-lisp
  (concat "" "works")
#+end_src

#+results:
: works

#+call: Blah4(x=1) :results value raw

#+results: Blah4(x=1)
works


but this

#+srcname: Blah2(x)
#+begin_src emacs-lisp :results value
  (concat "doesn't" "work")
#+end_src

#+call: Blah2(x=1) :results value raw

fails with the error message "setf: Wrong type argument: consp, nil", when
it had previously worked.  nb. the only difference between Blah4 and Blah2,
is the white space between the srcname and begin_src.  I get the same error
when I try and edit the code with C-'.  I'm not sure exactly when this
started, this was probably the first git pull I have done in a month or so.
Sorry I can't help track down this problem further, my lisp skills are slim
to none.


Cheers,
Chris.

Re: [O] Formal description of Org files

[Christopher Witte]

On 18 July 2011 01:14, Eric Schulte  wrote:

>
> As I mentioned earlier in this thread, I think any formal expression
> would be more useful if could be fed to existing parser-generation tools
> to automatically write Org-mode parsers, or perhaps automatically
> convert between Org-mode and other document formats.  I'm not sure
> however to what degree that is just wishful thinking..
>
>
Perhaps Pandoc (http://johnmacfarlane.net/pandoc/) would meet those
requirements.  It uses a great parsing library with a syntax that greatly
resembles a BNF grammar.  An output module is already written for org-mode,
so writing an input module would allow us to convert from org-mode to any
other of the existing Pandoc output formats (including "plain text,
markdown,
reStructuredText,
HTML , LaTeX ,
ConTeXt ,
PDF,
RTF , DocBook
XML,
OpenDocument XML ,
ODT,
GNU Texinfo , MediaWiki
markup,
textile , groff
manpages,
Emacs
org-mode , EPUB
ebooks, and
S5  and
SlidyHTML slide shows").  I've
been thinking of doing this for sometime now, as
an exercise in learning Haskell, but realistically I just don't have the
time.  does anyone else have the time?

Chris.

Re: [O] Unicode and Latex export

[Christopher Witte]

On Sun 07 Aug 2011 01:25:32 AM CEST, suvayu ali wrote:

So my question is, is there a convenient way to translate the unicode
characters into their corresponding latex commands for latex export
and keep the unicode characters as is in the org file or for html
export?


You could try using XeLaTeX, which supports unicode.  Instructions for 
setting it up with org-mode are here

http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export

Chris.

--
Dr Christopher Witte
Postdoctoral Research Fellow
Molecular Imaging Group
Leibniz-Institut für Molekulare Pharmakologie (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10
13125 Berlin, Germany
Phone: 00493094793-279

Re: [O] Unicode and Latex export

[Christopher Witte]

On 08/07/2011 02:15 PM, suvayu ali wrote:

Hello Christopher,

On Sun, Aug 7, 2011 at 12:01 PM, Christopher Witte  wrote:

You could try using XeLaTeX, which supports unicode.  Instructions for
setting it up with org-mode are here
http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export


My lisp is not very good, but what is the need for such an extensive
setup? Isn't setting org-latex-to-pdf-process to xelatex enough to
switch packends?

In any case, I tried evaluating the provided code in a scratch buffer
and processing to pdf (C-c C-e p). But it keeps failing. From the error
it seems org is still trying latex instead of xelatex and no pdf is
produced. Do you have any ideas about what could I doing wrong?

Error:

Latexmk: Run number 1 of rule 'latex'
Latexmk: Running 'latex   -interaction=batchmode
"/home/jallad/org/analysis.tex"'
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
  restricted \write18 enabled.
entering extended mode
Latexmk: References changed.
Latexmk: References changed.
Latexmk: References changed.
Collected error summary (may duplicate other messages):
   latex: Command for 'latex' gave return code 256
Latexmk: Use the -f option to force complete processing.



Chris.

Thanks a lot for your response.


Did you remember to set the variable

#+LATEX_CMD: xelatex

at the top of the org file?


Chris.

[O] Problem with org-crypt

[Christopher Witte]

Hi all,

I've been using org-crypt and find it a great little addition to 
org-mode, but I have been noticing some weird behaviour.  When I'm in a 
file that has NO encrypted entires (or :crypt: tags) and I archive a sub 
tree, I get asked the question "org-decrypt: auto-save-mode may cause 
leakage. Disable it for current buffer?".  This must mean 
org-decrypt-entry is being run but I don't understand why.  I've noticed 
that org-decrypt-entry is added to the org-reveal-start-hook, I'm not 
sure why that is.  When I don't add it to that hook, I no longer get 
asked that question and org-crypt still apears to work as expected, but 
I'm not sure if this will have broken something else.


Does anyone know why org-decrypt-entry is added to the 
org-reveal-start-hook and if it would break anything if I don't add it?


Thanks for the help
Chris.

Re: [O] Problem with org-crypt

[Christopher Witte]

On Fri 02 Sep 2011 10:43:11 AM CEST, Pieter Praet wrote:

On Wed, 31 Aug 2011 12:04:52 +0200, Christopher Witte  
wrote:

Hi all,

I've been using org-crypt and find it a great little addition to
org-mode, but I have been noticing some weird behaviour.  When I'm in a
file that has NO encrypted entires (or :crypt: tags) and I archive a sub
tree, I get asked the question "org-decrypt: auto-save-mode may cause
leakage. Disable it for current buffer?".  This must mean
org-decrypt-entry is being run but I don't understand why.  I've noticed
that org-decrypt-entry is added to the org-reveal-start-hook, I'm not
sure why that is.  When I don't add it to that hook, I no longer get
asked that question and org-crypt still apears to work as expected, but
I'm not sure if this will have broken something else.

Does anyone know why org-decrypt-entry is added to the
org-reveal-start-hook and if it would break anything if I don't add it?

Thanks for the help
Chris.



It's a known issue;  Patch available [1].

Bastien's AFK until the 5th, so won't be fixed in mainline before then.

Dropping the `add-hook' line is also a good temporary fix, won't break
anything, only prevents `org-reveal' (`C-c C-r') from decrypting entries.


Peace


Thanks, I'll look into that patch.

Chris

--
Dr Christopher Witte
Postdoctoral Research Fellow
Molecular Imaging Group
Leibniz-Institut für Molekulare Pharmakologie (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10
13125 Berlin, Germany
Phone: 00493094793-279

[O] Inline tasks and latex export

[Christopher Witte]

Hi all,

I've been trying to get inline tasks to work with the todonotes 
package.  I found some information on getting the \todo{} command to 
work but I couldn't find any info on getting the \missingfigure{} 
command to work.  Here is the solution that I came up with (mostly 
stolen from org-inlinetask.el):


Add the follow 3 lines to the start of the document:
#+LATEX_HEADER: \usepackage{todonotes}
#+TODO: TODO | DONE
#+TODO: MISSINGFIGURE | FIGUREDONE

and put this in your .emacs file
;; This should give better export of inline tasks to latex
;; #+LATEX_HEADER: \usepackage{todonotes} at the start of the org file
(setq org-inlinetask-export-templates (cons '(latex "%s %s}%s}"
'((if (equal todo "MISSINGFIGURE")
  (eval "\\missingfigure{")
(if (equal todo "") (eval 
"\\todo[inline]{\\textbf{") (format 
"\\todo[inline]{\\textbf{\\textsc\{%s}" todo))

)
heading content))
org-inlinetask-export-templates))

It works but seeing that I'm not very good with elisp, I suspect it 
could be improved on.  For instance this just adds an extra entry to 
org-inlinetask-export-templates instead of replacing the existing 
"latex" entry.  Any help on improving this would be greatly appreciated.


Cheers,
Chris Witte.

Re: [Orgmode] Status google calendar sync

[Christopher Witte]

 On 30 January 2011 02:21, Eric S Fraga  wrote:

> Torsten Wagner  writes:
>
>
> We need Emacs running on Android[1].  If Nokia can have Emacs native on
> their phones (n900), why can't Android???
>
> I can dream.
>
> vi is available, but not vim (so far as I know) so can't do org that
> way.
>

Apparently there is a native port of vim for android,
http://credentiality2.blogspot.com/2010/08/native-vim-for-android.html

So would it be possible to build a native emacs for android?

Chris.
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[Orgmode] Small bug in table editing

[Christopher Witte]

Hi,

I've been using the table editing feature of org mode, I never
realised plain text tables could be such fun to work with, and I just
came across a small bug. I had entered a table:

| Heading 1 | Heading 2 |
| 1 | 2 |
|11 |22 |


and then decided I wanted to go back and put a horizontal line after
the heading.  So I want to the start of the line after the heading and
entered "|-"

| Heading 1 | Heading 2 |
|-| 1 | 2 |
|11 |22 |

when I then pressed enter (or tab), the first line of data got eaten
up and replaced with the horizontal line like this:

| Heading 1 | Heading 2 |
|---+---|
|11 |22 |

This wasn't the behaviour I was expecting :).  While it is pretty
obvious to see what was going on in this example, if you have a long
table it isn't as obvious and I didn't notice until much later (emacs
undo in region saved the day).

Cheers,
Chris.

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Re: [Orgmode] Re: Small bug in table editing

[Christopher Witte]

I tend to disagree. I feel that anything that breaks the semantic
model of "enter = insert new line at point" is a bug.  Particularly if
it results in the loss of data.  But I can be persuaded otherwise.

Cheers
Chris


On 3 February 2011 19:27, Achim Gratz  wrote:
> Christopher Witte  writes:
>> and then decided I wanted to go back and put a horizontal line after
>> the heading.  So I want to the start of the line after the heading and
>> entered "|-"
>
> Not really a bug...anything past '|-' is considered garbage.
> Try 'C-c -' instead, or open a new line when you enter '|-'.
>
>
> Achim.
> --
> +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+
>
> Factory and User Sound Singles for Waldorf rackAttack:
> http://Synth.Stromeko.net/Downloads.html#WaldorfSounds
>
>
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Re: [Orgmode] Re: Small bug in table editing

[Christopher Witte]

As I said, I can be persuaded otherwise, but saying don't use org-mode
tables isn't very persuasive.  What is the semantic model for "enter"
when using org-mode tables? Clearly I don't understand it.

Thanks,
Chris.



On 4 February 2011 17:58, Achim Gratz  wrote:
> Christopher Witte  writes:
>> I tend to disagree. I feel that anything that breaks the semantic
>> model of "enter = insert new line at point" is a bug.
>
> Then don't use org-mode tables, because "enter" has different (and at
> least to me) more useful semantics there.
>
>
> Achim.
> --
> +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+
>
> DIY Stuff:
> http://Synth.Stromeko.net/DIY.html
>
>
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Re: [O] Emacs23 on Ubuntu recognizes 'remember', not 'capture'

[Christopher Witte]

On 17 July 2012 16:53, Rian Murphy  wrote:
> Giovanni Ridolfi  yahoo.it> writes:
> ...
>> > I'd prefer to use capture on my Ubuntu installation. I searched the gmane
>> > archives and didn't find any clues.
>>
>> Pelase, do
>> M-x emacs-version
>> and
>> M-x org-version
>>
>> in both systems; then if version is < than 6.36, you should not have
> capture, but only remember
>> [[info:org#Capture]]
>>
> ...
>>
> Giovanni,
> Thank you very much for your quick reply.
> Sure enough, I had version 6.21b of org on my Ubuntu installation.
>
> Per your advice, I tried upgrading to Emacs 24. Apparently, 24 isn't
> readily available for Ubuntu, but I got Damien Cassou's latest snapshot
> following the instrucitons
> in http://www.mikeyboldt.com/2011/11/30/install-emacs-24-in-ubuntu/.
> It upgraded Emacs to 23.1.50.1 and org to 6.30c.
> I guess I will have to live with 'remember' for a while.
>
> But thanks a lot for your help.  R.M.
>

Upgrading org is easy and there are instructions in the FAQ,
http://orgmode.org/worg/org-faq.html#updating-org

Chris.

Re: [O] Emacs23 on Ubuntu recognizes 'remember', not 'capture'

[Christopher Witte]

On 17 July 2012 18:10, Rian Murphy  wrote:
> Christopher Witte  witte.net.au> writes:
>
>>
>> On 17 July 2012 16:53, Rian Murphy  yahoo.com> wrote:
>> > Giovanni Ridolfi  yahoo.it> writes:
>> > ...
>> >> > I'd prefer to use capture on my Ubuntu installation. I searched the 
>> >> > gmane
>> >> > archives and didn't find any clues.
>> >>
> ...
>>
>> Upgrading org is easy and there are instructions in the FAQ,
>> http://orgmode.org/worg/org-faq.html#updating-org
>>
>> Chris.
>>
>>
> Chris, thanks for your help. I should have looked in the org-mode
> FAQ to start with -- I apologize.
> Oddly, however, when I do a 'git pull' and a 'make up2', then restart
> emacs, 'org-version' still tells me I have version 6.30c.
> 'emacs-version' still says 23.1.50.1.
> Maybe it's a Ubuntu thing   Thanks again, R.M.
>

I don't think it's an Ubuntu thing, I keep up to date with the git
repo under Ubuntu.  Did you run 'make install'?  You might need to run
'sudo make install'.  You should also be able to refresh org without
restarting emacs, I can't remember what the command is though.

[O] Narrow to sparse tree

[Christopher Witte]

I keep a bibliography in an org file using the excellent org-bibtex
functionality.  It has over 100 entries with a first level heading for
each item.  I tag each of the items with keywords/topics.  Using
sparse trees I can quickly find and navigate to items matching a
particular tag, but if only 4 items out of the 100 have that tag the
"signal to noise" is pretty bad.  What I would like to do is narrow
the buffer to just those entries that match the tag.  I've looked in
the manual but I couldn't find a way to do this.  Can this be done
with org?

Thanks for the help,
Chris.

ps. using M-g n or M-g M-n (next-error) with sparse trees I expected
it to wrap when you reach the end of the file but sadly this is not
the case.  Is there a reason for this?

Re: [O] Narrow to sparse tree

[Christopher Witte]

That's great, it gets me part of the way there.  I also keep notes for
each reference under their heading and I'd like to be able to see/edit
them as well.  Is there a way to do this in an agenda buffer?

On 6 September 2012 16:44, François Allisson  wrote:
> Le jeudi 06 sep 2012 à 15:46:42 (+0200), Christopher Witte a écrit :
>> I keep a bibliography in an org file using the excellent org-bibtex
>> functionality.  It has over 100 entries with a first level heading for
>> each item.  I tag each of the items with keywords/topics.  Using
>> sparse trees I can quickly find and navigate to items matching a
>> particular tag, but if only 4 items out of the 100 have that tag the
>> "signal to noise" is pretty bad.  What I would like to do is narrow
>> the buffer to just those entries that match the tag.  I've looked in
>> the manual but I couldn't find a way to do this.  Can this be done
>> with org?
>>
>> Thanks for the help,
>> Chris.
>>
>> ps. using M-g n or M-g M-n (next-error) with sparse trees I expected
>> it to wrap when you reach the end of the file but sadly this is not
>> the case.  Is there a reason for this?
>>
>
> Hi Chris,
>
> Have you think of using the agenda views? In four keystrokes, you're
> there with the best signal to noise ratio:
>
> - `C-c a' (or M-x org-agenda)
> - `<' (to restrict the agenda view to the current buffer)
> - `m' (for tags, property and todo keywords)
> - `abc'   (for tag :abc:), or (`YEAR'=2010 for PROPERTY :YEAR: equal
>to 2010, etc).
>
> HTH,
>
> François.
>
> PS: +1 for the excellent org-bibtex functionality !

[O] Visibility cycling with inline tasks

[Christopher Witte]

Hi all,

I have a document with lots of inline tasks scattered throughout it. I
want to get an overview of the document so I use S- to cycle to
CONTENTS, when I do that all of the inline tasks are displayed like
this:

* 1
** 2
*** TODO 4
*** END
*** TODO 5
*** END
*** TODO 6
*** END
*** TODO 7
*** END
*** TODO 8
*** END
** 3

this makes getting an overview of the document very difficult (it is
hard to tell that 2 and 3 are at the same level). By using a numeric
prefix that is less than the level of inline tasks but more than the
highest level used in the document (for instance M-5 S-) I can
get the result I would expect:

* 1
** 2...
** 3

Should this be the default? Is this also the behaviour that other people expect?

Cheers,
Chris Witte.

Re: [O] Visibility cycling with inline tasks

[Christopher Witte]

Thanks Carsten and Bastien!

On 22 September 2012 11:03, Carsten Dominik  wrote:
> GReat, thanks!
>
> - Carsten
>
> On 22.9.2012, at 11:02, Bastien wrote:
>
>> Hi Carsten,
>>
>> Carsten Dominik  writes:
>>
>>> I agree that this would be a good default, but not with a hard-coded 6.
>>>
>>> (add-hook 'org-cycle-hook
>>> (lambda (state) (when (eq state 'contents)
>>> (and (boundp 'org-inlinetask-min-level)
>>>  org-inlinetask-min-level
>>>  (hide-sublevels (1- org-inlinetask-min-level))
>>>
>>>
>>> And it is probably better to wrap this into a function and add that function
>>> to the default value of org-cycle-hook, after org-cucle-hide-drawers
>>
>> Done in master.  Thanks!
>>
>> --
>> Bastien
>

Re: [O] Publishing one org-file as many html files

[Christopher Witte]

o-blog should be able to do that, see:
http://renard.github.com/o-blog/tips/2012/01/07_creating-a-blog.html

On 16 October 2012 18:23, Vincent Beffara  wrote:
> Dear list,
>
> Is there a way to publish a huge org file, typically containing a single 
> date-tree, into one html file per day / per leaf of the tree ? That would be 
> a neat tool to blog using org-mode (org-capture a post into the tree, export, 
> you're done).
>
> Cheers,
>
> /vincent
>
> --
> Vincent Beffara
>
>
>

Re: [O] TeX-master: TeX-master is let-bound

[Christopher Witte]

It probably has something to do with this thread:
http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg00473.html

That thread was about auctex prompting for the master file name every
time an org file is opened.


On 26 October 2012 10:43, Christopher Schmidt
 wrote:
> Suvayu Ali  writes:
>> I believe the reason was to get rid of auctex prompting for the master
>> file name every time an org file is exported to LaTeX.
>
> The default value it t anyway.  The docstring suggests that this
> variable should be set via file variables.  I do not think org-mode
> should worry about AUCTeX.
>
> Christopher
>

Re: [O] Using Pandoc for export to EPub and Mediawiki Re: Bug: Status of the org-mediawiki.el [7.8.11]

[Christopher Witte]

For a quick work around, Pandoc can read in HTML, so perhaps you can export
org to HTML and then process it with Pandoc.
You can even use the following script so you can pipe it from the command
line.

#!/usr/bin/emacs --script
;read stdin into a temp buffer
;go into org-mode
;output the buffer as a string and pipe to stdout
(with-temp-buffer
  (progn
(condition-case nil
(let (line)
  (while (setq line (read-from-minibuffer ""))
(insert line)
(insert "\n")))
  (error nil))
(org-mode)
(princ (org-export-as-html nil nil nil 'string))
))


Chris.


On 6 January 2013 12:48, Bastien  wrote:

> Hi Bernhard,
>
> "Bernhard F.W. Gschaider"  writes:
>
> > If nobody is actively working on these export filters (Mediawiki) then
> > maybe "outsourcing" this conversion to pandoc and "only" integrating the
> > call into the "export menu" would be an interesting way to go
>
> Yes.  If you can motivate someone either from this list or from Pandoc
> community to write an Org mode reader, that'd be nice.  Even when we
> finally have a mediawiki exporter.
>
> Best,
>
> --
>  Bastien
>
>

Re: [O] C / C++ standard org file

[Christopher Witte]

Pandoc http://johnmacfarlane.net/pandoc/ should be able to handle the
conversion of html to org (but unfortunately not the reverse).

Chris.


On 9 January 2013 10:01, Jambunathan K  wrote:

> Noah Eli Abrams  writes:
>
> > Has anyone made an org-file out of the C / C++ standards? Would make
> > looking things up much more convenient.
>
> The ubiquitous format is HTML and unfortunately it is not /that/ human
> friendly.  I hope some writes a html2org puts that in GNU ELPA.  shr.el
> (part of gnus) can serve as good standing point.
>
> I hope - I mean, I hope - that it will be me.
>
> Lately, I am finding I am a bit out of juice though.
>
> >
> >
>
> --
>
>

[O] Extending attr_latex

[Christopher Witte]

I putting together a presentation using org and exporting to beamer.  I was
wondering if there is easy way to get each item in a list to display
incrementally.  Beamer supports this with the \begin{itemize}[<+->]
environment option.  Perhaps this could be achieved by extending the
#+ATTR_LaTeX: syntax.  Ideally I would like the following

** Overlays
#+ATTR_LaTeX: <+->
- one
- two
- three
- four
- five

to be exported as

\frametitle{Overlays}
\label{sec-1-10}
\begin{itemize}[<+->]
\item one
\item two
\item three
\item four
\item five
\end{itemize}
\end{frame}

Or is there already a way of achieving this? Come to think of it, prehaps
#+ATTR_beamer would be better for this?

Thanks
Chris.

[O] orgmode and auctex

[Christopher Witte]

I've had a small problem with orgmode and auctex.  Follwing the auctex
quickstart I added the following to my .emacs

(setq-default TeX-master nil)

and then from the orgmode FAQ to setup reftex in orgmode I added the
following

(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name)
   (file-exists-p (buffer-file-name))
   (reftex-parse-all))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)

With both of these, whenever I opened an org file I was asked to name the
master file.  If I comment out the setq-default I don't get the behaviour I
would like with mulitfile tex files.  My solution was to change

(setq-default TeX-master nil)

to

(add-hook 'TeX-mode-hook (lambda ()
   (setq-default TeX-master nil)))

I then appear to get the behaviour I desire.  Is this a good way to do
this?  If so I might add it to the FAQ.

Cheers
Chris.

Re: [O] orgmode and auctex

[Christopher Witte]

OK so using the setq-default inside a hook is probably not a good idea.
But I can reliably reproduce this problem, I'm surprised you couldn't.  If
I start emacs using emacs -Q and open an org file everything is fine.  If I
then evaluate this

(setq-default TeX-master nil)

(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name)
   (file-exists-p (buffer-file-name))
   (reftex-parse-all))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)

and try to open an org file I get prompted "Master file: ~/".  I'm running
Ubuntu 11.10 and the emacs-snapshot package: GNU Emacs 23.3.1
(i686-pc-linux-gnu, GTK+ Version 2.24.5), latest org pulled from git today.
Is there any more information I could provide to help diagnose this problem?

Cheers
Chris.

On 7 February 2012 19:15, Nick Dokos  wrote:

> Christopher Witte  wrote:
>
> > I've had a small problem with orgmode and auctex.  Follwing the auctex
> quickstart I added the
> > following to my .emacs
> >
> > (setq-default TeX-master nil)
> >
> > and then from the orgmode FAQ to setup reftex in orgmode I added the
> following
> >
> > (defun org-mode-reftex-setup ()
> >   (load-library "reftex")
> >   (and (buffer-file-name)
> >(file-exists-p (buffer-file-name))
> >(reftex-parse-all))
> >   (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
> > (add-hook 'org-mode-hook 'org-mode-reftex-setup)
> >
> > With both of these, whenever I opened an org file I was asked to name
> the master file.  If I comment
> > out the setq-default I don't get the behaviour I would like with
> mulitfile tex files.  My solution
> > was to change
> >
> > (setq-default TeX-master nil)
> >
> > to
> >
> > (add-hook 'TeX-mode-hook (lambda ()
> >(setq-default TeX-master nil)))
> >
> > I then appear to get the behaviour I desire.  Is this a good way to do
> this?  If so I might add it
> > to the FAQ.
> >
>
> Probably not. setq-default sets the default value of the variable
> whereas the hook is supposed to set the local value in order to override
> the default value: setting the default value from a hook seems backwards
> to me.
>
> Actually, I added the above code (*without* the TeX-mode-hook mod) to my
> minimal .emacs and opening org files does not generate any questions. Are
> you sure you have diagnosed the problem correctly?
>
> Nick
>

Re: [O] orgmode and auctex

[Christopher Witte]

Yes, I get this response when I open a .org file. I only want it when I
open a .tex file.

Cheers,
Chris

On 9 February 2012 21:08, Nick Dokos  wrote:

> Thomas Alexander Gerds  wrote:
>
> >
> > Hi Chris,
> >
> > maybe I cannot follow exactly what you are trying to do, but when I
> > start emacs -q and evaluate (setq-default TeX-master nil) and then open
> > a new file test.tex, then I get the same prompt "Master file:".
> >
>
> I think Chris means that he gets the prompt when he opens a .org file.
> I couldn't reproduce that behavior when I tried it but I have not tried
> it again yet.
>
> Nick
>
>
> > so maybe, if you do not want to get prompted, you could try setting
> > (setq-default TeX-master t).
> >
> > Cheers
> > Tomy
> >
> >
> >
> > Christopher Witte  writes:
> >
> > > OK so using the setq-default inside a hook is probably not a good
> > > idea.
> > > But I can reliably reproduce this problem, I'm surprised you couldn't.
> > > If
> > > I start emacs using emacs -Q and open an org file everything is fine.
> > > If I
> > > then evaluate this
> > >
> > > (setq-default TeX-master nil)
> > >
> > > (defun org-mode-reftex-setup ()
> > >   (load-library "reftex")
> > >   (and (buffer-file-name)
> > >(file-exists-p (buffer-file-name))
> > >(reftex-parse-all))
> > >   (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
> > > (add-hook 'org-mode-hook 'org-mode-reftex-setup)
> > >
> > > and try to open an org file I get prompted "Master file: ~/".  I'm
> > > running
> > > Ubuntu 11.10 and the emacs-snapshot package: GNU Emacs 23.3.1
> > > (i686-pc-linux-gnu, GTK+ Version 2.24.5), latest org pulled from git
> > > today.
> > > Is there any more information I could provide to help diagnose this
> > > problem?
> > >
> > > Cheers
> > > Chris.
> > >
> > > On 7 February 2012 19:15, Nick Dokos  wrote:
> > >
> > >> Christopher Witte  wrote:
> > >>
> > >> > I've had a small problem with orgmode and auctex.  Follwing the
> > > auctex
> > >> quickstart I added the
> > >> > following to my .emacs
> > >> >
> > >> > (setq-default TeX-master nil)
> > >> >
> > >> > and then from the orgmode FAQ to setup reftex in orgmode I added
> > > the
> > >> following
> > >> >
> > >> > (defun org-mode-reftex-setup ()
> > >> >   (load-library "reftex")
> > >> >   (and (buffer-file-name)
> > >> >(file-exists-p (buffer-file-name))
> > >> >(reftex-parse-all))
> > >> >   (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
> > >> > (add-hook 'org-mode-hook 'org-mode-reftex-setup)
> > >> >
> > >> > With both of these, whenever I opened an org file I was asked to
> > > name
> > >> the master file.  If I comment
> > >> > out the setq-default I don't get the behaviour I would like with
> > >> mulitfile tex files.  My solution
> > >> > was to change
> > >> >
> > >> > (setq-default TeX-master nil)
> > >> >
> > >> > to
> > >> >
> > >> > (add-hook 'TeX-mode-hook (lambda ()
> > >> >(setq-default TeX-master nil)))
> > >> >
> > >> > I then appear to get the behaviour I desire.  Is this a good way
> > > to do
> > >> this?  If so I might add it
> > >> > to the FAQ.
> > >> >
> > >>
> > >> Probably not. setq-default sets the default value of the variable
> > >> whereas the hook is supposed to set the local value in order to
> > > override
> > >> the default value: setting the default value from a hook seems
> > > backwards
> > >> to me.
> > >>
> > >> Actually, I added the above code (*without* the TeX-mode-hook mod)
> > > to my
> > >> minimal .emacs and opening org files does not generate any
> > > questions. Are
> > >> you sure you have diagnosed the problem correctly?
> > >>
> > >> Nick
> > >>
> > --
> > Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
> > University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
> > Office: CSS-15.2.07 (Gamle Kommunehospital)
> > tel: 35327914 (sec: 35327901)
> >
>

Re: [O] orgmode and auctex

[Christopher Witte]

Hi all,

(setq TeX-auto-save t)
(setq TeX-parse-self t)
(setq-default TeX-master nil)
(make-variable-buffer-local 'TeX-master) ;; I think this is need because
the variable is not buffer local until Auctex is active

(defun org-mode-reftex-setup ()
  (setq TeX-master t)
  (load-library "reftex")
  (and (buffer-file-name)
   (file-exists-p (buffer-file-name))
   (progn
 (reftex-parse-all)
 (reftex-set-cite-format "[[cite:%l][%l]]")))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
  (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)

This appears to work for me.  This should make the buffer local version of
TeX-master "t" for all org buffer and keep it the default otherwise.  Is
this a good way to work around this problem?

Cheers,
Chris.



On 11 February 2012 19:11, Nick Dokos  wrote:

> Carsten Dominik  wrote:
>
> >
> > On 9.2.2012, at 21:08, Nick Dokos wrote:
> >
> > > Thomas Alexander Gerds  wrote:
> > >
> > >>
> > >> Hi Chris,
> > >>
> > >> maybe I cannot follow exactly what you are trying to do, but when I
> > >> start emacs -q and evaluate (setq-default TeX-master nil) and then
> open
> > >> a new file test.tex, then I get the same prompt "Master file:".
> > >>
> > >
> > > I think Chris means that he gets the prompt when he opens a .org file.
> > > I couldn't reproduce that behavior when I tried it but I have not tried
> > > it again yet.
> >
> > I think this prompt comes from the function `reftex-TeX-master-file'.
> >
>
> Indeed - the backtrace is as follows:
>
>  ...
>  completing-read-default("Master file: " read-file-name-internal
> file-exists-p t "~/src/org/" file-name-history "~/src/org/foo.org" nil)
>  completing-read("Master file: " read-file-name-internal file-exists-p t
> "~/src/org/" file-name-history "~/src/org/foo.org")
>  read-file-name-default("Master file: " nil nil t nil nil)
>  read-file-name("Master file: " nil nil t nil)
>  reftex-TeX-master-file()
>  reftex-tie-multifile-symbols()
>  reftex-access-scan-info((16))
>  reftex-parse-all()
>   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> (reftex-parse-all))
>   org-mode-reftex-setup()
>  run-hooks(change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook)
>  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook))
>  run-mode-hooks(org-mode-hook)
>  org-mode()
>  set-auto-mode-0(org-mode nil)
>  set-auto-mode()
>  normal-mode(t)
>  after-find-file(nil t)
>  find-file-noselect-1(# "~/src/org/foo.org" nil nil
> "~/src/org/foo.org" (3018153 2055))
>  find-file-noselect("~/src/org/foo.org" nil nil t)
>  find-file("~/src/org/foo.org" t)
>  call-interactively(find-file nil nil)
>
>
> > The user is prompted when TeX-master is an existing variable
> > (i.e. AUCTeX is loaded), and when its value is nil or `shared'.
>
> It's actually a bit more complicated than that: it checks if
> TeX-master-file is defined as a function (i.e. AUCTEX is loaded) and if
> so calls it. It then checks if tex-main-file is defined as a function
> (i.e. Emacs LaTeX mode is loaded) and if so calls it. Then it check if
> TeX-master is t (in which case (buffer-file-name) is called to set the
> master, or 'shared (in which case it reads the file name) or non-nil (in
> which case it is used verbatim) or nil (in which case it reads the file
> name - the operative case here).
>
> I'll leave it here for now: I've been sick for a couple of days and I
> can't think straight right now (or ever...)
>
> Nick
>
>
> > Greetings
> >
> > - Carsten
> >
> > >
> > > Nick
> > >
> > >
> > >> so maybe, if you do not want to get prompted, you could try setting
> > >> (setq-default TeX-master t).
> > >>
> > >> Cheers
> > >> Tomy
> > >>
> > >>
> > >>
> > >> Christopher Witte  writes:
> > >>
> > >>> OK so using the setq-default inside a hook is probably not a good
> > >>> idea.
> > >>> But I can reliably reproduce this problem, I'm surprised you
> couldn't.
> > >>> If
> > >>> I start emacs using emacs -Q and open an org file everything is fine.
> > >>> If I
&g

Re: [O] orgmode and auctex

[Christopher Witte]

It's been working for me so far so I think I'll stick with it.
Thanks for all your help.

Chris.

On 24 February 2012 06:34, Nick Dokos  wrote:

> Christopher Witte  wrote:
>
> > Hi all,
> >
> > (setq TeX-auto-save t)
> > (setq TeX-parse-self t)
> > (setq-default TeX-master nil)
> > (make-variable-buffer-local 'TeX-master) ;; I think this is need because
> the variable is not buffer
> > local until Auctex is active
> >
> > (defun org-mode-reftex-setup ()
> >   (setq TeX-master t)
> >   (load-library "reftex")
> >   (and (buffer-file-name)
> >(file-exists-p (buffer-file-name))
> >(progn
> >  (reftex-parse-all)
> >  (reftex-set-cite-format "[[cite:%l][%l]]")))
> >   (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
> >   (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))
> > (add-hook 'org-mode-hook 'org-mode-reftex-setup)
> >
> > This appears to work for me.  This should make the buffer local version
> of TeX-master "t" for all
> > org buffer and keep it the default otherwise.  Is this a good way to
> work around this problem?
> >
>
> I think so - at least, I can't think of a better way.
>
> Nick
>

Re: [O] [babel] keep source code buffer open

[Christopher Witte]

Here is a keyboard macro I used with some success

(fset 'org-execute-from-indirect
  (lambda (&optional arg) "Keyboard macro." (interactive "p")
(kmacro-exec-ring-item (quote ("C-c ' C-c C-c C-'" 0 "%d")) arg)))

basically it just exits the source code buffer, compiles and then
reopens the source code buffer

On 11 April 2012 16:58, Torsten Wagner  wrote:
> Hi,
> yep me again.
> I find myself hitting C-' all the day long today and was wondering is
> there a way to keep the source code buffer open instead of closing it
> after pressing again C-'.
> Now I need to do
> * C-' open the source code buffer
> * do my changed
> * C-' close the buffer take over the changes
> * C-c C-e d export as PDF after evaluation of all code blocks
> * check the PDF
> * start over again
> All this comes with window splits and most of the time I hit C-s in
> the wrong buffer because I am so used to it to save my changes to
> files.
>
> I would like to make changes in the code buffer and start e.g.
> evaluation or exporting from within the source code buffer.
>
> That is
> * Press once C-'
> * make my changes
> * press C-c ?? to move all changes over into the org-mode buffer and
> evaluate the source code block
> or
> * press C-c ?? to move all changes over into the org-mode buffer and
> export the org-buffer
> repeat
>
> Is there any way to do this?
>
> That's it for today... promise
>
> Thanks
> Torsten
>

Re: [O] [OT] Generate animations (programmatic)

[Christopher Witte]

Perhaps Asymptote would meet your needs: http://asymptote.sourceforge.net/
It is even supported by babel, can output to multiple formats (mpg, gif,
SVG, 3D pdf and many others) and is fully programmable (depending on the
complexity of your models, you could directly program it in Asymptote, it
has a c++ like syntax).
Check out some of the examples here:
http://asymptote.sourceforge.net/gallery/animations/

Chris.

On 19 June 2012 05:05, Torsten Wagner  wrote:

> Hi,
>
> its a bit OT (well maybe there is a babel solution ;) )
> I am looking for a way to generate small animations for educational
> purpose. I know many here did/do/plan to do similar things, thus I
> would like to ask here.
>
> Those animations need to follow some underlying algorithms (I would
> need a correct physical, chemical, biological behavior).
> I'm not an art person (so please don't tell me to get pen and paper)
> and do not have the time (well the animations should help me but they
> are not my daytime job) to spend hours or even weeks in getting
> Blender and Co creating (superb) animations.
>
> Thus I am looking for:
>
> * Possibly a programmatic way to create animations
> * Something with a good balance of effort vs. output
> * Possibility to either inject results from other programs (scilab,
> python, matlab, etc.) or to include the necessary behavioral model
> * The output should be readable on many different platforms (Linux,
> Mac, Windows, Android, IOS, etc)
> * An open and well described output format
> * An open and well described workflow
>
> Well, the last two points are important to me, since I might use the
> animations for longer time (course material) and I would like to have
> a chance to open and modify them even in 3, 5  or even 10 years.
>
> My ideas so far
>
> * Processing language (seems interesting and fast to get results,
> however, not really an open output format, can't see the future of it
> clearly)
> * ProcessingJS (this solves the problem of having a easy to read
> output format, other problems are still the same)
> * Adobe flash (violates several of the above requirements, plugins on
> different platforms are a mess)
> * SVG + HTML5 (this looks promising as many web-browser would be
> capable to open it without plugin, but I can't find a programmatic
> easy way to start with this, any authoring tools, libs or APIs?)
> * TIKz + animation (I use Tikz already and really like it. Never used
> the animation package. However, animated PDFs are only readable with
> the Adobe Reader)
> * Python (well Python as a general language might work nice, however,
> which package could be used for animation? I used once pygames but
> this seems to be graphically disadvantaged)
> * Inkscape (there are modules to do animation, but how to get my
> behavior model into it?)
> * Blender, Gimp (steep learning curve, many many ours of work to get
> an animation)
> * Synfig, Pencil, ktoon, etc (maybe faster results compared to
> Blender, but again, how to get my behavior model into it?)
> * Powerpoint, Libreoffice Presenter (well, as soon as it comes to a
> bit more complex animations this becomes fast a nightmare)
>
> Ideally, I would love to see something like TikZ with a good way to
> add animations and to finally generate a SVG-based animation readable
> by almost all webbrowsers.
> This embedded in a language which allows me to perform the behavioral
> modeling too and I would be quite happy already.
>
> I would be glad if some of you could share there ways, ideas and
> workflows to do this kind of animations.
>
> All the best
>
> Torsten
>
>

Re: [O] Section of Org manual on images in latex export

[Christopher Witte]

On 19 June 2014 00:20, Nicolas Goaziou  wrote:

>
> Actually, it is
>
>   #+ATTR_LATEX: :float t
>
>
hmmm, I'm sure I tried that and it didn't work, but I just tested it again
and now it is working. I'm not sure what I did wrong before.

Thanks for clarifying that for me.

Cheers
Chris.

Re: [O] Requesting some help with scheduled repeated tasks

[Christopher Witte]

Hi Sagar,

I think you either want a repeating task see
http://orgmode.org/manual/Repeated-tasks.html

or to use org-clone-subtree-with-time-shift see
http://orgmode.org/manual/Structure-editing.html#Structure-editing

I think repeated tasks repeat for ever, so from your description
org-clone-subtree-with-time-shift might be better.

I hope that helps,
Chris.

On 26 January 2015 at 14:13, Sagar Shankar  wrote:

> Hi all, been using Org-Mode for just over a month now and have stumbled
> into something that I cannot still figure out how to implement.
>
> I want to set aside a fixed amount of time each day (say 2 hours) at a
> specific time(18-00-20:00 say) to work on a specific task. I want this task
> to repeat for 7 days and for state changes (from TODO to DONE) to be
> tracked for those 7 days. The latter while ideal, is also optional, as in a
> base case, I'd be happy to just get the task automatically marked TODO 7
> times in my Agenda till the 7 days are over.
>
> Right now, I've tried using the following syntax:
>
> ** TODO Work on XYZ
>SCHEDULED: <2015-01-21 Wed 20:30-21:30>-- <2015-01-28 Wed 20:30-21:30>
>
> When I mark this as complete for today, all the other occurrences are also
> marked as DONE, which I do not want. Another confusing factor is that
> instead of counting 7 occurrences of this task, Org counts it as 8 (which
> is another thing I'd love to get explained)
>
> I know tracking repeated tasks is best suited for Org-Habits but I cannot
> find anywhere in the documentation for that module, a parameter that allows
> me to track habits for only 7 times or 8 times say, and for that habit to
> be inserted into the agenda at a specific time only.
>
> Would really appreciate some advice!
>
> Thanks for your time,
> Sagar
>

[O] XeLaTeX and the new exporter

[Christopher Witte]

Hi all,

I had export working using XeLaTeX using the instructions from the
FAQ(with
some slight modifications), but after upgrading to the new export it
isn't working.  It appears the hook
org-export-latex-after-initial-vars-hook isn't defined anymore.

Any advice on what I need to change to get it to work?

Thanks
Chris.

Re: [O] Best way to make/add tech diagrams/graphics?

[Christopher Witte]

Asymptote http://asymptote.sourceforge.net/ would also be another option in
a similar vein to TikZ.


On 18 May 2013 01:14, John Hendy  wrote:

> On Fri, May 17, 2013 at 6:09 PM, Marcin Borkowski 
> wrote:
> > Dnia 2013-05-17, o godz. 11:40:17
> > John Hendy  napisał(a):
> >
> >> On Fri, May 17, 2013 at 10:13 AM, Lawrence Bottorff
> >>  wrote:
> >> > I'd like to embed images into my running org file -- for eventual
> >> > conversion to Latex or html. These would be simple diagram-style
> >> > pictures such as math or technical diagrams that cannot be done
> >> > with gnuplot or other formula-to-picture conversion software.
> >> >
> >> > Examples:
> >> >
> http://www.library.utoronto.ca/see/SEED/Vol5-1/Queiroz_Emmeche_El-Hani_files/image003.gif
> >> >
> http://math.ucr.edu/home/baez/irvine/SBGN_process_description_cropped.jpg
> >> >
> >>
> >> A few that come to mind for this sort of thing:
> >> - ditaa: http://ditaa.sourceforge.net/
> >> - graphviz/dot: http://www.graphviz.org/
> >> - my personal favorite, but quite the learning curve, it PFG/TikZ:
> >> http://www.texample.net/tikz/examples/
> >
> > Typo: it's PGF, not PFG, just in case you wanted to google it or
> > something;).
> >
>
> Oops -- typo on my part.
>
> > I'd also mention Metapost, on which I believe TikZ was modeled (at least
> > to some extent).
> >
> > Since you mentioned embedding in LaTeX, I'd also suggest TikZ; it has a
> > huge manual, but /very/ well written, with quite a few tutorials and
> > examples. One benefit is that it is tightly integrated into LaTeX,
> > but it can also export SVG (though with a few limitations compared to
> > the pdfLaTeX-produced output).  Also, you might want to check out the
> > gallery of TikZ examples here: http://www.texample.net/tikz/ .
> >
>
> The examples are great. The link I provided goes right to the examples
> vs. that sort of home page screen which only shows the most recent
> couple that have been submitted.
>
> I'll have to check out metapost, as I'd not heard of that one.
>
>
> Thanks,
> John
>
> >> Good luck!
> >> John
> >
> > Best,
> >
> > --
> > Marcin Borkowski
> > http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
> > Adam Mickiewicz University
> >
>
>

Re: [O] XeLaTeX and the new exporter

[Christopher Witte]

Thanks, that fixed it.


On 14 May 2013 12:04, Søren Mikkelsen  wrote:

> Hi Chris
>
> I asked the question a couple of weeks ago. Take a look at the hook:
>
> org-export-before-parsing-hook
>
> It worked for me.
>
> Best regards
> Søren
>
>
> On 2013-05-07 17:42, Christopher Witte wrote:
>
>> Hi all,
>>
>> I had export working using XeLaTeX using the instructions from the FAQ
>> <http://orgmode.org/worg/org-**faq.html#using-xelatex-for-**pdf-export<http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export>
>> >
>>
>> (with some slight modifications), but after upgrading to the new export
>> it isn't working.  It appears the hook
>> org-export-latex-after-**initial-vars-hook isn't defined anymore.
>>
>> Any advice on what I need to change to get it to work?
>>
>> Thanks
>> Chris.
>>
>
>
>

Re: [O] XeLaTeX and the new exporter

[Christopher Witte]

Sorry for the late reply.

I'm not entirely sure either, I pretty much just blindly followed the
instructions on the FAQ.  I don't think this is at all the minimum you need
to get xelatex working, it also sets up a few other things.  For instance
it used latexmk instead of just recompiling a few times.  Perhaps the FAQ
should be split up into a few different questions:
1. minimum setup for XeLaTeX, something similar to your setup
2. how to use latexmk

Cheers,
Chris



On 22 May 2013 19:07, Suvayu Ali  wrote:

> Hi Christopher,
>
> On Tue, May 07, 2013 at 05:42:04PM +0200, Christopher Witte wrote:
> >
> > I had export working using XeLaTeX using the instructions from the
> > FAQ<http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export
> >(with
> > some slight modifications), but after upgrading to the new export it
> > isn't working.  It appears the hook
> > org-export-latex-after-initial-vars-hook isn't defined anymore.
> >
> > Any advice on what I need to change to get it to work?
>
> I have noticed discussions on this before and I fail to understand the
> need for all the setup mentioned in the above Worg entry.  I use XeLaTeX
> almost exclusively, and all I have is something like this:
>
>   ;;; XeLaTeX customisations
>   ;; remove "inputenc" from default packages as it clashes with xelatex
>   (setf org-latex-default-packages-alist
> (remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))
>
>   (add-to-list 'org-latex-packages-alist '("" "xltxtra" t))
>   ;; choose Linux Libertine O as serif and Linux Biolinum O as sans-serif
> fonts
>   (add-to-list 'org-latex-packages-alist '("" "libertineotf" t))
>
>   ;; org to latex customisations, -shell-escape needed for minted
>   (setq org-export-dispatch-use-expert-ui t ; non-intrusive export dispatch
> org-latex-pdf-process   ; for regular export
> '("xelatex -shell-escape -interaction nonstopmode
> -output-directory %o %f"
>   "xelatex -shell-escape -interaction nonstopmode
> -output-directory %o %f"
>   "xelatex -shell-escape -interaction nonstopmode
> -output-directory %o %f"))
>
> For beamer export I add this line:
>
>   #+LaTeX_HEADER: \setsansfont{Linux Biolinum O}
>
> So far I have not encountered any problems.  Although I have to say, I
> do not use unicode in mathmode.
>
> I am curious to know why others need all this elaborate setup to use
> XeLaTeX.
>
> Cheers,
>
> --
> Suvayu
>
> Open source is the future. It sets us free.
>
>

Re: [O] XeLaTeX and the new exporter

[Christopher Witte]

Sure, I'll give it a try, but I might not get around to it for a few days.

Cheers,
Chris.


On 1 June 2013 08:43, Carsten Dominik  wrote:

> Hi Christopher,
>
> Would you like to provide a patch?
>
> - Carsten
>
> On 31.5.2013, at 09:58, Christopher Witte  wrote:
>
> Sorry for the late reply.
>
> I'm not entirely sure either, I pretty much just blindly followed the
> instructions on the FAQ.  I don't think this is at all the minimum you need
> to get xelatex working, it also sets up a few other things.  For instance
> it used latexmk instead of just recompiling a few times.  Perhaps the FAQ
> should be split up into a few different questions:
> 1. minimum setup for XeLaTeX, something similar to your setup
> 2. how to use latexmk
>
> Cheers,
> Chris
>
>
>
> On 22 May 2013 19:07, Suvayu Ali  wrote:
>
>> Hi Christopher,
>>
>> On Tue, May 07, 2013 at 05:42:04PM +0200, Christopher Witte wrote:
>> >
>> > I had export working using XeLaTeX using the instructions from the
>> > FAQ<http://orgmode.org/worg/org-faq.html#using-xelatex-for-pdf-export
>> >(with
>> > some slight modifications), but after upgrading to the new export it
>> > isn't working.  It appears the hook
>> > org-export-latex-after-initial-vars-hook isn't defined anymore.
>> >
>> > Any advice on what I need to change to get it to work?
>>
>> I have noticed discussions on this before and I fail to understand the
>> need for all the setup mentioned in the above Worg entry.  I use XeLaTeX
>> almost exclusively, and all I have is something like this:
>>
>>   ;;; XeLaTeX customisations
>>   ;; remove "inputenc" from default packages as it clashes with xelatex
>>   (setf org-latex-default-packages-alist
>> (remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))
>>
>>   (add-to-list 'org-latex-packages-alist '("" "xltxtra" t))
>>   ;; choose Linux Libertine O as serif and Linux Biolinum O as sans-serif
>> fonts
>>   (add-to-list 'org-latex-packages-alist '("" "libertineotf" t))
>>
>>   ;; org to latex customisations, -shell-escape needed for minted
>>   (setq org-export-dispatch-use-expert-ui t ; non-intrusive export
>> dispatch
>> org-latex-pdf-process   ; for regular export
>> '("xelatex -shell-escape -interaction nonstopmode
>> -output-directory %o %f"
>>   "xelatex -shell-escape -interaction nonstopmode
>> -output-directory %o %f"
>>   "xelatex -shell-escape -interaction nonstopmode
>> -output-directory %o %f"))
>>
>> For beamer export I add this line:
>>
>>   #+LaTeX_HEADER: \setsansfont{Linux Biolinum O}
>>
>> So far I have not encountered any problems.  Although I have to say, I
>> do not use unicode in mathmode.
>>
>> I am curious to know why others need all this elaborate setup to use
>> XeLaTeX.
>>
>> Cheers,
>>
>> --
>> Suvayu
>>
>> Open source is the future. It sets us free.
>>
>>
>
>

[O] Multicolumn figures with the new exporter

[Christopher Witte]

Hi all,

I can't get the multicolumn option to attr_latex to work with the new
exporter (to generate a figure* environment).  Any one know how to do this?

Thanks,
Chris.

[O] Unexpected behaviour with gnuplot source blocks

[Christopher Witte]

Hi all,

I had some wierd behaviour with gnuplot source blocks and I'm not sure of
the best way to fix it.

I have gnuplot source blocks that write output files that I insert into the
document using links, as such:

#+begin_src gnuplot :file transInc.eps
reset
set encoding utf8
set output "./fig/transInc.eps"
.
#+end_src
[[fig/transInc.eps]]

and I have two documents in different directories, say 'a' and 'b' that do
this.
If I go to the first document in folder 'a' and export it to latex and then
go to the second document in folder 'b' and also export it to latex, all
the generated plots end up in 'a'.  It took me a while to work it out, but
this is because only one gnuplot session is started and 'reset' doesn't
reset output.  Killing the gnuplot buffer fixes this, but that is annoying
if I frequently switch back and forth between the documents.

I could use full paths, but that seams like a pain, any other suggestions?

Thanks for the help,
Chris.

Re: [O] Unexpected behaviour with gnuplot source blocks

[Christopher Witte]

On 20 June 2013 18:12, Eric Schulte  wrote:

> Why not do the following instead which would be equivalent and simpler.
> The output will be automatically set from the value of your :file header
> argument.
>
> #+begin_src gnuplot :file fig/transInc.eps
>   reset
>   set encoding utf8
>   .
> #+end_src
>
>
That kinda works, but I think you still need to set the terminal type
within the source block.  Using the above the command "set terminal eps"
gets sent to gnuplot, but you actually need "set terminal postscript eps".

The following works

#+BEGIN_SRC gnuplot :file test.eps
  reset
  set terminal postscript eps
  .
#+END_SRC

Thanks for the help!
Chris.

Re: [O] Problems with org-bibtex

[Christopher Witte]

I have found that opening a (any) bibtex file fixes this for the session. I
have no idea why though.

Chris.


On 21 November 2013 09:25, Sean O'Halpin  wrote:

> Hi,
>
> I was just trying the same thing (prompted by the recent discussion).
> It turned out I had to
>
> #+begin_src emacs-lisp
>   (bibtex-set-dialect)
> #+end_src
>
> first.
>
> Regards,
> Sean
>
>
> On Thu, Nov 21, 2013 at 3:55 AM, Marvin Doyley 
> wrote:
> > Hi there,
> >
> > I have decided to give org-bibtex a try. I have loaded it in my .emacs
> file,
> > but whenever I copy a bibtex entry and try to use org-bibtex-yank I get
> the
> > following error
> >
> > Symbol's function definition is void: bibtex-beginning-of-entry
> >
> > Could someone tell me what this mean and how to fix it.
> >
> > Thanks
> > M
>
>

Re: [O] How to end a :session?

[Christopher Witte]

perhaps what you want is a named session, see
http://orgmode.org/manual/session.html

On 28 May 2015 at 10:44, Rainer M Krug  wrote:

> Hi
>
> I can start a session as follow:
>
> --8<---cut here---start->8---
> #+begin_src R :session Test
> cat("Session Test\n")
> #+end_src
> --8<---cut here---end--->8---
>
> Now I hava an R session named *Test*. But how can I closes this session?
> I thought about just quitting R
>
> --8<---cut here---start->8---
> #+begin_src R :session Test
> q(save = "no)
> #+end_src
> --8<---cut here---end--->8---
>
> but this does not return as ESS is waiting for the prompt (">").
>
> Is there a way of closing the session *Test* and close the buffer?
>
> My reasoning is that I want to do different longer analysis in one org
> file and start each in its own session, i.e. clean R. But as they
> involve several steps, I don't want to put them into one code block.
>
> So I have several code blocks which I want to execute in a "throw away
> session" which I would like to discard afterwards.
>
> So I am looking for something like
>
> #+CLOSE_SESSION Test
>
> which would then close the session *Test*
>
> Is something like this possible at the moment?
>
> Rainer
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
> Tel :   +33 - (0)9 53 10 27 44
> Cell:   +33 - (0)6 85 62 59 98
> Fax :   +33 - (0)9 58 10 27 44
>
> Fax (D):+49 - (0)3 21 21 25 22 44
>
> email:  rai...@krugs.de
>
> Skype:  RMkrug
>
> PGP: 0x0F52F982
>

[O] Link to using calc in embedded mode with org-mode broken

[Christopher Witte]

Hi,

In the orgmode manual section *15.10.1 Packages that Org cooperates with*
http://orgmode.org/manual/Cooperation.html
the link to using calc's embedded mode with org-mode is broken
http://orgmode.org/calc/Embedded-Mode.html#Embedded-Mode

Does anyone know what happened to that page?

Cheers,
Chris.

[O] Emacs freezes

[Christopher Witte]

Hi all,

I'm getting a weird problem with orgmode and flyspell mode. Using the
latest version of org from git, open the attached file test.org and run M-x
flyspell-mode, emacs will lock up. It has something to do with tables.

Alternatively, make a new (empty) org file, run flyspell-mode, and start
making a new table by writing |sdf|sdf|, and it will lock up emacs.

Using an older version of org (7.9.3) this problem doesn't occur.

I'm using Emacs 24.3.1 on Ubuntu 12.04.

Any ideas what could be causing this?

Thanks for your help.

Chris.


test.org
Description: Binary data

Re: [O] Emacs freezes

[Christopher Witte]

Fantastic! All working now.

Cheers,
Chris


On 22 March 2014 09:19, Nicolas Goaziou  wrote:

> Hello,
>
> Christopher Witte  writes:
>
> > I'm getting a weird problem with orgmode and flyspell mode. Using the
> > latest version of org from git, open the attached file test.org and run
> M-x
> > flyspell-mode, emacs will lock up. It has something to do with tables.
> >
> > Alternatively, make a new (empty) org file, run flyspell-mode, and start
> > making a new table by writing |sdf|sdf|, and it will lock up emacs.
> >
> > Using an older version of org (7.9.3) this problem doesn't occur.
> >
> > I'm using Emacs 24.3.1 on Ubuntu 12.04.
> >
> > Any ideas what could be causing this?
>
> Yes, two entries with the same key in cache. Anyway it should be fixed
> now.
>
> Thank you for the detailed report, and sorry for the delay.
>
>
> Regards,
>
> --
> Nicolas Goaziou
>

Re: [O] Using Emacs, Org-mode and R for Research Writing in Social Sciencess

[Christopher Witte]

The latest version of Pandoc can now also read in org mode files
http://johnmacfarlane.net/pandoc/releases.html#pandoc-1.12.4-07-may-2014
So perhaps the conversion of Org->Latex is no longer needed.

Chris.


On 14 May 2014 09:00, Vikas Rawal  wrote:

> >
> > pandoc -f latex -t docx test.tex -o test.docx
> >
> > I see Org has exported my "W m^{-2}" as "W m$^{\text{-2}}$", which is
> > not what I would expect in LaTeX. In OS X Pages.app viewing the docx
> > this appears as "W m". In Word it shows up either as just "-2" or "W
> > m-2". In Word, the Math shows up with each character as a box (the math
> > is just missing in Pages). In Word the figures are missing (they appear
> > in Pages).
> >
>
>
> First, you should differentiate between whether the problem is in
> Org->LaTeX conversion, or in LaTeX->Docx conversion.
>
> From what you describe above, the problem seems to be in Org->LaTeX
> conversion.
>
> For me, $W m^{-2}$ in Org produces correct LaTeX markup, and I get a good
> docx using Pandoc.
>
> Vikas
>

[O] Section of Org manual on images in latex export

[Christopher Witte]

Hi all,

After quite a bit of mucking around and finally resorting to checking the
source code, I worked out how to wrap an image in a figure environment
without a caption.  The final solution

#+ATTR_LATEX: :float figure

was trivial, but the manual wasn't too helpful on this particular subject.

So others don't have to go through the same troubles I think the manual
could be slightly reworded. In the section "Images in Latex export"
http://orgmode.org/manual/LaTeX-specific-attributes.html#LaTeX-specific-attributes
I think the following sentence:

"You can also ask Org to export an image as a float without specifying
caption by setting the :float attribute."

should be change to:

"You can also ask Org to export an image as a float without specifying a
caption by setting the :float attribute *to figure*."

Also a summary of the the attributes and their valid values, as is done for
Latex tables would be useful.


Cheers,
Chris.

ps. I tried to find out if I could make those changes myself, but after
much clicking and searching, I could only find:
http://orgmode.org/worg/org-contribute.html but that doesn't say anything
about contributing to the documentation.