Re: [O] Feature request: lists with letters

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Titus von der Malsburg <malsb...@posteo.de> writes:
>
>> One issue with org-list-allow-alphabetical is that we get numbers
>> instead of letters when we export to HTML and LaTeX.  I saw the earlier
>> thread [0] that gives the reasoning for this but I find it
>> unsatisfying.  If Org allows us to distinguish between -, +, 1., 1), a.,
>> A., a), A), this should also be honored by the exporter.
>
> This is also why I dislike the feature.
>
>> Otherwise it’s rather pointless to allow that distinction in the first
>> place.
>
> Exactly.
>
>> IMHO, a clean solution would be to either drop everything but - and
>> 1. or to keep all these and make the exporters honor them.  The former
>> would breaks existing documents and is therefore out of the
>> question.  This leaves us with the second solution.
>
> I wouldn't rule that out. Breaking changes happen. We can provide tools
> to fix existing documents.
>
> Actually, I like the idea of keeping only "-" and "1.". We could
> implement other bullet types as overlays.
>
>> Any chance you are willing to reconsider the decision to ignore
>> allow-alphabetical during export?
>
> I still agree with Carsten in the thread you pointed out. Org document
> is about structure. The bullet in about typesetting.

I must admit, I haven't read the thread mentioned, and I am sure
Carsten's point was correct, but orgmode is more and more used for
non-structure tasks. As an example I see the whole field of reproductive
research and scientific paper writing, which, in my opinion, has many
more elements than structure. Another example are html emails (like them
or not - I also dislike them) which people compose in org, or org as a
LaTeX frontend.

Exporting, i.e. typesetting and sharing, becomes much more important
these days and possibly as important as the structure.

In a nutshell: I agree with Titus' point and also would love to have
alphabetical bullets.

But it is for me not that important if they are alphabetical or numeric
in org - a simple command / which I could put in front of the list, and
*which could be interpreted by the exporter* to do the right thing for
this list would be fine, simmilar to bold, verbtin, ...
The implementation would then be in the exporter.

Cheers,

Rainer

>
>> I think it would be very useful to have that. I know there are other
>> ways to get alphabetical bullets in exported documents but they are
>> all specific to certain export targets and the beauty of Org mode is
>> precisely that we can export to many different targets.
>
> The beauty of Org is also to allow to control different export targets
> in the same document.
>
> I think this is a non-issue.
>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] What would you like to see in the next MobileOrg iOS?

[Rainer M Krug]

Sean Escriva <sean.escr...@gmail.com> writes:

> Hi fellow Org users,
>
> I'm the current maintainer of MobileOrg for iOS[1]. We've recently been 
> working on a refreshed release of the current version of MobileOrg and it 
> will be released soon as v1.7. After
> this release v1 will be in maintenance mode while we focus efforts on the 
> next version.
>
> We've started plans on the future version of MobileOrg, dubbed just v2 
> currently. It will be a major rewrite and we need your input. We hope to not 
> just improve the codebase but also
> add more features that would be useful specifically to mobile users and 
> provide a great Org mode experience on an iOS device.
>
> We've started a specification document[2] which is slowly evolving and we'd 
> like to track issues for discussion[3] with the community of users before 
> making decisions.
>
> If you have any additional requirements feel free to add them as an issue or 
> by pull request[4]. Your input is much appreciated!

Thanks - this looks like I might use MobileOrg again when version 2 is
out! Great.

One more idea (of which I don't know if it is possible) - sync of org /
emacs calender tasks to the iOS calender. This would be brilliant.

I filed an Issue https://github.com/MobileOrg/mobileorg.next/issues/2
but I think you have to set the tag?

Looking forward to version 2,

Cheers,

Rainer

>
> Sean 
>
> [1] https://github.com/MobileOrg/mobileorg
> [2] 
> https://github.com/MobileOrg/mobileorg.next/blob/specification/docs/MobileOrgv2.org
>  
> [3] https://github.com/MobileOrg/mobileorg.next/labels/discussion 
> [4] https://github.com/MobileOrg/mobileorg.next/issues 
>

-- 
Rainer M. Krug
email: Rainerkrugsde
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Re: [O] Using an org based init file slows down emacs startup by 50x..help needed :(

[Rainer M Krug]

Xebar Saram <zelt...@gmail.com> writes:

> Ok so i think the reason really is that i have way to many lisp code blocks 
> as suggested. i found out a very interesting post that maybe of interest to 
> alot of
> org users

Well - it took on my MacBook Pro Retina about 30 seconds -

,
| Wrote /Users/rainerkrug/tmp/settings.el [745 times]
| Tangled 745 code blocks from settings.org
`

so I guess something else is fishy in your setup

Rainer


>
> http://www.holgerschurig.de/en/emacs-efficiently-untangling-elisp/
>
> this creates a new function that very efficiently tangles my org file and the 
> time goes from 6 minutes to 25 seconds!!
>
> this is a link to an example init file
>
> https://bitbucket.org/holgerschurig/emacsconf/src/416b2bba2d1d334b9c6ddbd56f8c7f8bd8bc4aab?at=master
>
> i really think this should go somewhere in the org documentation 
>
> best to all
>
> Z
>
> On Sat, Dec 10, 2016 at 2:53 PM, Xebar Saram <zelt...@gmail.com> wrote:
>
>  Ok some more exploring made me realize that also using `M-x 
> org-babel-load-file` on the setting.org file and tangling it takes a LONG 
> time (like 6-7
>  minutes) so its not a problem of the init its the actual tangling of the 
> file. 6-7 minutes cant be normal right? 
>
>  im attaching my settings.org file
>
>  would appreciate any help
>
>  Z
>
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] tangling and COMMENT entries

[Rainer M Krug]

Alan Schmitt <alan.schm...@polytechnique.org> writes:

> Hello,
>
> When using org-babel-load-file, are entries with a COMMENT keyword
> supposed to be tangled? I thought they were not, but I'm seeing them in
> the generated .el file.

I am using COMMETNS all the time to exclude blocks from tangling in my
emacs.org - and it works.


,
| Org mode version 9.0 (release_9.0-60-g047451 @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
`

Cheers,

Rainer

>
> Thanks,
>
> Alan

-- 
Rainer M. Krug
email: Rainerkrugsde
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Re: [O] Add preamble support to ob-plantuml.el

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Thibault Marin <thibault.ma...@gmx.com> writes:
>
>> I use it to define common skin options (http://plantuml.com/skinparam)
>> for all the plantuml blocks in an org file.  I don't know if there is a
>> better way to that.
>
> What about using noweb syntax then?

Or prologue?

,
| 14.8.2.28 ‘:prologue’
| .
| 
| The value of the ‘prologue’ header argument will be prepended to the
| code block body before execution.  For example, ‘:prologue "reset"’ may
| be used to reset a gnuplot session before execution of a particular code
| block, or the following configuration may be used to do this for all
| gnuplot code blocks.  Also see *note epilogue::.
`

But apart from this: I think it would be in general a good idea to add
version infos of emacs and org to source code blocks - possibly even of
the executable? This would be one more step towards easy
reproducability.

Cheers,

Rainer

>
> Regards,
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Capture templates - using result from %^g twice?

[Rainer M Krug]

Aaron Ecay <aarone...@gmail.com> writes:

> Hi Rainer,
>
> 2016ko azaroak 18an, Rainer M Krug-ek idatzi zuen:
>> 
>
>>> :SHEET: %(mapconcat #'identity (org-get-tags-at nil t) ":")
>> 
>> Thanks - this looks good to me, but the ="= causes problems and ends the
>> template early. I tried to replace =":"= with =':'= but this did =not
>> work either (invalid-read-syntax).
>> 
>> How can I get this to work?
>
> You need to escape the quotes with a single backslash.

I did it like this:

:SHEET:  %(mapconcat #'identity (org-get-tags-at nil t) \":\")

But it still does not work as, my guess, nothing is returned - the
"field" is empty

Rainer

-- 
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Re: [O] Capture templates - using result from %^g twice?

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> Hm - I seem to ask strange questions here. Any ideas?
>
> %\2 is not working because it is used to repeat %^{prompt} placeholders,
> not %^g or %^G, per documentation.

Ok - thanks for the clarification.

>
> You could try (untested)
>
>   :SHEET: %(mapconcat #'identity (org-get-tags-at nil t) ":")

Thanks - this looks good to me, but the ="= causes problems and ends the
template early. I tried to replace =":"= with =':'= but this did =not
work either (invalid-read-syntax).

How can I get this to work?

Rainer.

>
>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Capture templates - using result from %^g twice?

[Rainer M Krug]

Hm - I seem to ask strange questions here. Any ideas?

Rainer

Rainer M Krug <rai...@krugs.de> writes:

> Hi
> I have the following capture template and would like to re-use the tag
> entered by %^g . I try to use %\2 but this is not working.
>
> Is there a way that I can re-use the tag entered by %^g and add it as a 
> property?
>
> Thanks,
>
> Rainer
>
> ,
> | ("s"  "Change logged in buffer - for spreadsheet changes"
> |  entry   (file+headline (lambda() (buffer-file-name)) "CHANGES")  
> |  "* %^{Header of CHANGES item} :%^g:
> | :PROPERTIES:
> | :SHEET: %\2
> | :AUTHOR:  Rainer M Krug, rai...@krugs.de
> | :DATE: %T
> | :END:
> | %?")
> `

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] Capture templates - using result from %^g twice?

[Rainer M Krug]

Hi
I have the following capture template and would like to re-use the tag
entered by %^g . I try to use %\2 but this is not working.

Is there a way that I can re-use the tag entered by %^g and add it as a 
property?

Thanks,

Rainer

,
| ("s"  "Change logged in buffer - for spreadsheet changes"
|  entry   (file+headline (lambda() (buffer-file-name)) "CHANGES")  
|  "* %^{Header of CHANGES item} :%^g:
| :PROPERTIES:
| :SHEET: %\2
| :AUTHOR:  Rainer M Krug, rai...@krugs.de
| :DATE: %T
| :END:
| %?")
`


-- 
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

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Re: [O] Capture template to capture in current buffer

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Hi
>>
>> I am trying to get an in-buffer logging to work. I want to log some
>> changes in the file and I am using the following template, which was
>> working some (longer?) time ago:
>>
>> (setq org-capture-templates
>>   `(
>> ;; ::
>> ;; In File Logging ::
>> ;; ::
>> ("c"   "Changes to be logged in buffer"
>>  entry   (file+headline (buffer-file-name) "CHANGES Log")   
>>  "* %^{Header of CHANGES item}\nLOGGED: %T \n- link :: %a \n- 
>> author   :: Rainer M Krug, email: rai...@krugs.de\n %?")
>> ))
>>
>> But now I get the following error message when using the capture
>> template:
>>
>> ,
>> | if: Target buffer ".notes" for file+headline should be in Org mode
>> `
>>
>> Any suggestions on how I can get this to work?
>
> It should work again in latest Org ELPA.
>
> In Org 9.1, you will need to change it to 
>
>   (file+headline (lambda () (buffer-file-name) ...))

Thanks - upgraded to newest master from git and used the syntax you
gave - works perfectly.

Thanks,

Rainer

>
>
> Regards,

-- 
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email: Rainerkrugsde
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Re: [O] Capture template to capture in current buffer

[Rainer M Krug]

Eric S Fraga <e.fr...@ucl.ac.uk> writes:

> On Monday, 14 Nov 2016 at 08:05, Rainer M Krug wrote:
>> Is it only me who want's to do this, or is this working for everybody else?
>
> I would like to do this but it doesn't work for me either.  What appears
> to be happening is that org captures the note to the default notes file,
> org-default-notes-file.  This defaults to ~/.notes.  It doesn't capture
> to the buffer-file-name.

Exactly the same here - thanks for confirming.

>
> This looks like a bug to me.

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Capture template to capture in current buffer

[Rainer M Krug]

Is it only me who want's to do this, or is this working for everybody else?

Rainer

Rainer M Krug <rai...@krugs.de> writes:

> Hi
>
> I am trying to get an in-buffer logging to work. I want to log some
> changes in the file and I am using the following template, which was
> working some (longer?) time ago:
>
> (setq org-capture-templates
>   `(
> ;; ::
> ;; In File Logging ::
> ;; ::
> ("c"   "Changes to be logged in buffer"
>  entry   (file+headline (buffer-file-name) "CHANGES Log")   
>  "* %^{Header of CHANGES item}\nLOGGED: %T \n- link :: %a \n- 
> author   :: Rainer M Krug, email: rai...@krugs.de\n %?")
> ))
>
> But now I get the following error message when using the capture
> template:
>
> ,
> | if: Target buffer ".notes" for file+headline should be in Org mode
> `
>
> Any suggestions on how I can get this to work?
>
> Thanks,
>
> 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
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] Capture template to capture in current buffer

[Rainer M Krug]

Hi

I am trying to get an in-buffer logging to work. I want to log some
changes in the file and I am using the following template, which was
working some (longer?) time ago:

--8<---cut here---start->8---
(setq org-capture-templates
  `(
;; ::
;; In File Logging ::
;; ::
("c"   "Changes to be logged in buffer"
 entry   (file+headline (buffer-file-name) "CHANGES Log")   
 "* %^{Header of CHANGES item}\nLOGGED: %T \n- link :: %a \n- 
author   :: Rainer M Krug, email: rai...@krugs.de\n %?")
))
--8<---cut here---end--->8---

But now I get the following error message when using the capture
template:

,
| if: Target buffer ".notes" for file+headline should be in Org mode
`

Any suggestions on how I can get this to work?

Thanks,

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

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[O] Defining directory tree structure from org-attach to reflect headers

[Rainer M Krug]

Hi

I have effectively the same question as Adm here:
[http://emacs.stackexchange.com/questions/26412/human-readable-directory-tree-with-org-attach]

I would like to have the directory tree of the attachments managed by
org-attach to reflect the document structure as defined by the
headlines.

To quote from his question:

,
| * This headline
|   ** This sub-headline 1
|   ** This sub-headline 2
| * This second headline
| 
| matches to the directory structure:
| 
| - This headline
|   - This sub-headline 1
|   - This sub-headline 2
| - This second headline
`

I started using to set the directories, but for this I need the
additional step of defining it per subtree. Is there a way to configure
org-attach to automatically use the header name instead of the uuid?

Thanks,

Rainer


-- 
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email: Rainerkrugsde
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Re: [O] [RFC] Change visibility for bracket links

[Rainer M Krug]

Le mercredi 5 octobre 2016, Nicolas Goaziou <m...@nicolasgoaziou.fr> a
écrit :

> Hello,
>
> I'd like to make the following change to bracket links display (i.e.,
> when `org-highlight-links' contains `bracket', which is the default).
>
> Basically, I want to leave a visible pair of brackets around the link,
> i.e.,
>
>   [[uri][description]]
>
> is displayed as
>
>   [description]
>
> instead of
>
>   description
>
> and
>
>   [[uri]]
>
> is displayed as
>
>   [uri]
>
> instead of
>
>   uri
>
>
+1

Very good suggestion.

Rainer

The rationale behind this suggestion is that editing a mostly invisible
> link is unintuitive when point is at the boundaries of its visible part.
>
> More precisely, in the following visible part of a link
>
>   description
>
> if point hits "d" from the right, changes happen in the description of
> the link, but if point comes from the left, changes happen before the
> link.
>
> I guess I could get used to it, but sometimes, the link happens to be at
> column 0. In this case, the only way to "come from the left" is to move
> to the previous line and go past the newline character. This is, IMO,
> very annoying, notwithstanding the fact that it is impossible to realize
> at the beginning of the buffer.
>
> Leaving a pair of brackets, OTOH, disambiguates the situation. Editing
> before the opening bracket makes changes before the link. Conversely,
> editing after the former makes changes to the uri or the description,
> whichever is displayed.
>
> The cost a little more visual clutter, but it seems very acceptable to
> me. I attach a quick patch for testing.
>
> Feedback welcome.
>
> Regards,
>
> --
> Nicolas Goaziou0x80A93738
>


-- 
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 (F):   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug

Re: [O] Best diagram, image software?

[Rainer M Krug]

Lawrence Bottorff <borg...@gmail.com> writes:

> I know lots of you use Emacs and org mode to prepare scholarly books
> and papers, either doing the HTML or, more probably, the Latex
> export. Question: Let's say I want to produce a math text with
> Emacs/org-mode/Latex. What is the best way to make diagrams and
> images? I've seen things like Inkscape and LibreOffice Draw. But then
> there is Gnuplot and Tikz. Yes, what Tikz does seems optimal, but the
> learning curve is a year's sabbatical. Just wondering what you people
> are using to do your images.

Depends, what kind of images you are talking about. If they are data
based (graphs, ...) I use R or GRASS (spatial data, GIS). For non-data
driven images, I use tikz (conceptual models) or PlantUML
[[http://plantuml.com/]] for different kinds of diagrams (uml, ...).

Thank there is obviously Inkscape and Scribus and GIMP as well.

Cheers,

Rainer


>
> LB
>

-- 
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Re: [O] attach file C-c C-a m - problem with file completion

[Rainer M Krug]

Rainer M Krug <rai...@krugs.de> writes:

> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>
>> Hello,
>>
>> Rainer M Krug <rai...@krugs.de> writes:
>>
>>>> I started using attachments and really like them. But I have a problem
>>>> with the completion of file names. I use ido usually and it works fine -
>>>> but not here. How can I register ido completion for org-attach?
>>>
>>> Forgot to mention - it always points to the .org file in which I want to
>>> attach the file and I can't change the directory.
>>
>> I'm not sure to understand. What doesn't work? If a use "C-c C-a m" on
>> a headline, I get a completion window where I can change directory.
>
> OK - I'll try to explain.
>
> I am in a file called attach.org.
> I press C-c C-a m in a headline and I get the completion window in the
> mini buffer - so far so good.
> But I can't change the directory.
>
> I disabled ido, and it is working now. So this is a problem in IDO. I
> will see if I can figure out what it is.

OK - the culprit is the following code from
https://www.emacswiki.org/emacs/InteractivelyDoThings#toc15 :

,
| (defvar ido-enable-replace-completing-read t
|   "If t, use ido-completing-read instead of completing-read if possible.
| 
| Set it to nil using let in around-advice for functions where the
| original completing-read is required.  For example, if a function
| foo absolutely must use the original completing-read, define some
| advice like this:
| 
| (defadvice foo (around original-completing-read-only activate)
|   (let (ido-enable-replace-completing-read) ad-do-it))")
| 
| ;; Replace completing-read wherever possible, unless directed otherwise
| (defadvice completing-read
|   (around use-ido-when-possible activate)
|   (if (or (not ido-enable-replace-completing-read) ; Manual override 
disable ido
|   (and (boundp 'ido-cur-list)
|ido-cur-list)) ; Avoid infinite loop from ido calling this
|   ad-do-it
| (let ((allcomp (all-completions "" collection predicate)))
|   (if allcomp
|   (setq ad-return-value
| (ido-completing-read prompt
|allcomp
|nil require-match initial-input hist def))
| ad-do-it
`

Any suggestion why this is happening? For the moment, I just disabled
this code completely.

Cheers,

Rainer

>
> Thanks,
>
> Rainer
>
>
>
>
>> I do not use Ido, tho.
>>
>> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] attach file C-c C-a m - problem with file completion

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>>> I started using attachments and really like them. But I have a problem
>>> with the completion of file names. I use ido usually and it works fine -
>>> but not here. How can I register ido completion for org-attach?
>>
>> Forgot to mention - it always points to the .org file in which I want to
>> attach the file and I can't change the directory.
>
> I'm not sure to understand. What doesn't work? If a use "C-c C-a m" on
> a headline, I get a completion window where I can change directory.

OK - I'll try to explain.

I am in a file called attach.org.
I press C-c C-a m in a headline and I get the completion window in the
mini buffer - so far so good.
But I can't change the directory.

I disabled ido, and it is working now. So this is a problem in IDO. I
will see if I can figure out what it is.

Thanks,

Rainer




> I do not use Ido, tho.
>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] attach file C-c C-a m - problem with file completion

[Rainer M Krug]

Rainer M Krug <rai...@krugs.de> writes:

> Hi
>
> I started using attachments and really like them. But I have a problem
> with the completion of file names. I use ido usually and it works fine -
> but not here. How can I register ido completion for org-attach?

Forgot to mention - it always points to the .org file in which I want to
attach the file and I can't change the directory.

>
> Thanks,
>
> Rainer

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] attach file C-c C-a m - problem with file completion

[Rainer M Krug]

Hi

I started using attachments and really like them. But I have a problem
with the completion of file names. I use ido usually and it works fine -
but not here. How can I register ido completion for org-attach?

Thanks,

Rainer


-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] inlinetask with :noexport: seems to be exported?

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> OK - your example works, but the following doesn't:
>>
>> * Foo
>>
>> Foo
>>
>> *** TODO :noexport: Bar *** END
>>
>> Effectively, it is exported if the inline task has ho header text.
>
> This is because your syntax is invalid. You cannot have a headline
> without text but with tags. :noexport: is treated as the headline (or
> inlinetask) text.
>
> You can add a space entity, e.g., \nbsp{}, to work around the problem.

OK - makes sense.

Thanks

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] inlinetask with :noexport: seems to be exported?

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> I wanted to define some inlinetask (works - love it) but want to keep
>> most of them in the org file and not export them. Adding :noexport: does
>> not work.
>
> FWIW, I cannot reproduce it. I tested with the following document, after
> evaluating (require 'org-inlinetask).
>
> * Foo
>
> Foo
>
> *** Begin :noexport:
> Bar
> *** END

OK - your example works, but the following doesn't:

--8<---cut here---start->8---
* Foo

Foo

*** TODO :noexport:
Bar
*** END
--8<---cut here---end--->8---

Effectively, it is exported if the inline task has ho header text.

Cheers,

Rainer

>
>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] inlinetask with :noexport: seems to be exported?

[Rainer M Krug]

Hi

I wanted to define some inlinetask (works - love it) but want to keep
most of them in the org file and not export them. Adding :noexport: does
not work.

Is there a way of not exporting selected inlinetasks?

Thanks

Rainer


-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Capture with org-directory not working?

[Rainer M Krug]

Adam Porter <a...@alphapapa.net> writes:

> Rainer Krug <r.m.k...@gmail.com> writes:
>
>> But It seems to abusing the basic idea of custom-set-variables as this
>> sounds as if it is used by the customise interface.
>
> What I mean is, you can use the customize interface to store your
> org-capture-templates.  It's already set up for that.  You can either
> edit it through the customize interface, or you can edit it directly in
> the init file and then evaluate the ~(custom-set-variables~ sexp manually.
>

OK - but I prefer to keep my configurations in my .emacs.el file to make
it reproducible.


Thanks,

Rainer

>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Capture with org-directory not working?

[Rainer M Krug]

Nick Dokos <ndo...@gmail.com> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Hi
>>
>> I have the following capture template:
>>
>> ,
>> |   ("T"   "TODO to be logged in notes.org"
>> |entry   (file+headline (concat org-directory "/notes.org") "Tasks") 
>>
>> |;; entry   (file+headline "~/org/notes.org" "Tasks")
>> |"* TODO [#D] \n%i \n:PROPERTIES: \n:END: \n%? \n%a")
>> `
>>
>> As it is now, it is not working, but when I use the secont=d entry line,
>> it is working.
>>
>
> Try (!!note the backquote at the beginning  and the comma before the concat 
> form!!):
>
> (setq org-capture-templates
>  `(
>...
>("T"   "TODO to be logged in notes.org"
> entry   (file+headline ,(concat org-directory "/notes.org") "Tasks")  
>   
> "* TODO [#D] \n%i \n:PROPERTIES: \n:END: \n%? \n%a")
>...))
>

Thanks! the problem was the missing comma, as I had the backquote
already there. This must have changed some time ago, as I used these
templates before. This is working now.

But now I realized that my other in-file capture templates are giving
the same message. Here is one of my in-file capture templates:

,
| (setq org-capture-templates
|   `(
| ;; ::
| ;; In File Logging ::
| ;; ::
| ("p"   "Problem to be logged in buffer"
|  entry   (file+headline (buffer-file-name) "QUESTIONS")  
| ...
| ))
`

I assume it also has to do with the evaluation, but putting a comma in
front of (buffer-file-name) does not change anything. 

Thanks,

Rainer


>
> See
>
>   (info "(elisp) Backquote")

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] Capture with org-directory not working?

[Rainer M Krug]

ame orig-buf) 
(file-name-nondirectory (buffer-file-name orig-buf))) :annotation annotation 
:initial initial :return-to-wconf (current-window-configuration) :default-time 
(or org-overriding-default-time (org-current-time))) 
(org-capture-set-target-location) (condition-case error (org-capture-put 
:template (org-capture-fill-template)) ((error quit) (if (get-buffer 
"*Capture*") (kill-buffer "*Capture*")) (error "Capture abort: %s" error))) 
(setq org-capture-clock-keep (org-capture-get :clock-keep)) (if (equal goto 0) 
(org-capture-insert-template-here) (condition-case error 
(org-capture-place-template (equal (car ...) (quote function))) ((error quit) 
(if (and ... ...) (kill-buffer ...)) (set-window-configuration (org-capture-get 
:return-to-wconf)) (error "Capture template `%s': %s" (org-capture-get :key) 
(nth 1 error (if (and (derived-mode-p (quote org-mode)) (org-capture-get 
:clock-in)) (condition-case nil (progn (if ... ...) (org-clock-in) (set ... t)) 
(error "Could not start the clock in this capture buffer"))) (if 
(org-capture-get :immediate-finish) (org-capture-finalize))
  (cond ((equal goto (quote (4))) (org-capture-goto-target)) ((equal goto 
(quote (16))) (org-capture-goto-last-stored)) (t (let* ((orig-buf 
(current-buffer)) (annotation (if (and (boundp ...) 
org-capture-link-is-already-stored) (plist-get org-store-link-plist 
:annotation) (condition-case nil (progn ...) (error nil (entry (or 
org-capture-entry (org-capture-select-template keys))) initial) (setq initial 
(or org-capture-initial (and (org-region-active-p) (buffer-substring (point) 
(mark) (if (stringp initial) (progn (remove-text-properties 0 (length 
initial) (quote (read-only t)) initial))) (if (stringp annotation) (progn 
(remove-text-properties 0 (length annotation) (quote (read-only t)) 
annotation))) (cond ((equal entry "C") (customize-variable (quote 
org-capture-templates))) ((equal entry "q") (user-error "Abort")) (t 
(org-capture-set-plist entry) (org-capture-get-template) (org-capture-put 
:original-buffer orig-buf :original-file (or (buffer-file-name orig-buf) (and 
... ...)) :original-file-nondirectory (and (buffer-file-name orig-buf) 
(file-name-nondirectory ...)) :annotation annotation :initial initial 
:return-to-wconf (current-window-configuration) :default-time (or 
org-overriding-default-time (org-current-time))) 
(org-capture-set-target-location) (condition-case error (org-capture-put 
:template (org-capture-fill-template)) ((error quit) (if ... ...) (error 
"Capture abort: %s" error))) (setq org-capture-clock-keep (org-capture-get 
:clock-keep)) (if (equal goto 0) (org-capture-insert-template-here) 
(condition-case error (org-capture-place-template ...) (... ... ... ...)) (if 
(and ... ...) (condition-case nil ... ...)) (if (org-capture-get 
:immediate-finish) (org-capture-finalize
  org-capture(nil)
  funcall-interactively(org-capture nil)
  call-interactively(org-capture nil nil)
  command-execute(org-capture)
--8<---cut here---end--->8---

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

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Re: [O] Suggestion: Export templates: use drawers to group

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> If I have many headers in a document, it is easy to loose the overview
>> for me.
>>
>> So I started to use drawers:
>>
>> :OPTIONS:
>> ...
>> :END:
>>
>> :LATEX:
>> 
>> :END:
>>
>> :BABEL:
>> ...
>> :END:
>>
>> and have only the "standard" content type options open (DESCRIPTION,
>> KEYWORDS, SUBTITLE, DATE, AUTHOR, ...)
>>
>> Would this be something to include into the templates which can be
>> inserted (C-e C-L #)? This would make it much easier to work with these
>> options.
>
> Do you suggest that `org-export-insert-default-template' should group
> options within drawers by default?

Yes - that was my idea.

>
> If so, I'm not too keen of the idea of imposing drawers to the user.

My reasoning is that it makes organizing options easier and that users
get introduced into the idea of using dawers.

> Besides, templates are already separated by back-end so you can insert
> them within pre-created drawers already. 

True - it is not difficult, but might be more intuitive and lead to
easier readable options.

>
> There is no "babel" or "options" category, though. I guess we could
> create them, if needed.

No - I don't think they are needed, as there are many different use
cases for babel - but thinking about it, it might be an idea to insert
the most widely used options for babel and set them at their default
values - so documents become more robust and the options become
introduced to the user.

Cheers,

Rainer


>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] Suggestion: Export templates: use drawers to group

[Rainer M Krug]

Hi

If I have many headers in a document, it is easy to loose the overview
for me.

So I started to use drawers:

:OPTIONS:
...
:END:

:LATEX:

:END:

:BABEL:
...
:END:

and have only the "standard" content type options open (DESCRIPTION,
KEYWORDS, SUBTITLE, DATE, AUTHOR, ...)

Would this be something to include into the templates which can be
inserted (C-e C-L #)? This would make it much easier to work with these
options.

Cheers,

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


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Re: [O] convert MS power point to org mode?

[Rainer M Krug]

Le dimanche 11 septembre 2016, Xebar Saram <zelt...@gmail.com> a écrit :

> hi all
>
> anyone have any experience with converting M$ power point to org mode?
>
>
If I remember correctly, you can export to word, which should give you the
text and possibly pictures (?). Haven't tried it,  though.

Cheers,

Rainer


> i have a bunch of courses i teach with presentations in ppt from a few
> years ago and since i now use org-reveal would love to have a quick(ish)
> way to convert them to org
>
> best
>
> Z
>


-- 
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 (F):   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug

Re: [O] crash when editing R blocks in org

[Rainer M Krug]

Xebar Saram <zelt...@gmail.com> writes:

> Hi all
>
> i have emacs crashing on me when i edit R code blocks in org
>
> here is the terminal output:
>
> https://paste.xinu.at/xg6/
>
> does that give any clues? should i file a bug in org or emacs?
>
> how do proceed with trying to figure out whats causing this?

What version of emacs, org, possibly R, minimal reproducible example,
when does it occur, what are the steps to reproduce it?

Without this information, nothing can be done. But I never experienced
this in my workflow.

GNU Emacs 25.1.1 (x86_64-apple-darwin15.5.0, Carbon Version 157 AppKit1404.47) 
of 2016-07-28
Org-mode version 8.3.5 (release_8.3.5-1028-gfb517f @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"

Rainer

>
> best
>
> Z

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>
>> Hello,
>>
>> Rainer M Krug <rai...@krugs.de> writes:
>>
>>> \section[Level 1]{Level 1\hfill{}\textsc{andHereIsTheTag}}
>>
>> IIUC, according to this line, tags should be removed from the toc.
>>
>> This issue may be related to Beamer.
>
> From the Beamer manual, 10.2 (latest TL version): 
>
>  \section<⟨mode specification⟩>[⟨short section name⟩]{⟨section name⟩}
>
>  Starts a section. No heading is created. The ⟨section name⟩ is shown in
>  the table of contents and in the navigation bars, except if ⟨short 
> section
>  name⟩ is specified. In this case, ⟨short section name⟩ is used in the
>  navigation bars instead. If a ⟨mode specification⟩ is given, the command
>  only has an effect for the specified modes.
>
> I guess the most sane solution is to not support tags:not-in-toc in
> ox-beamer (or in general).

I agree - that might be the easiest solution.

Rainer


>
> A latex hack might be something like this (untested):
>
> \section{title}
> \section*{title \hfill :tags:} % to not mess up if someone uses 
> article mode
>
>
> Here’s another hack that can be applied in a org latex document class.
>
> http://tex.stackexchange.com/questions/203105/short-section-name-in-toc
>
> Rasmus

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

John Hendy <jw.he...@gmail.com> writes:

> On Fri, May 27, 2016 at 11:15 AM, Rainer M Krug <rai...@krugs.de> wrote:
>> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>>
>>> Hello,
>>>
>>> Rainer M Krug <rai...@krugs.de> writes:
>>>
>>>> When I generate a pdf, the tags are in the TOC - but tags:not-in-toc
>>>> means that the tags are *not* in the toc - possibly only in the headers
>>>> itself? I don't know.
>>>>
>>>> Just checked, the tags are also in the toc in html export.
>>>>
>>>> According to the documentation:
>>>>
>>>> ,
>>>> | If this is the symbol ‘not-in-toc’, tags will be removed from
>>>> | table of contents entries, but still be shown in the headlines of
>>>> | the document.
>>>> `
>>>>
>>>> This is not working anymore.
>>>
>>> I cannot reproduce it, at least on HTML, LaTeX, and ASCII export. Could
>>> you show an ECM ?
>>
>> OK. Here it is:
>>
>> --8<---cut here---start->8---
>> #+TITLE: An Example
>> #+EMAIL: rai...@krugs.de
>>
>> #+OPTIONS:   tags:not-in-toc
>>
>> #+LATEX_CLASS: beamer
>> #+OPTIONS:   H:2 toc:t
>>
>> * Level 1   :andHereIsTheTag:
>> ** A Frame
>> #+begin_example
>> Org-mode version 8.3.4 (release_8.3.4-850-g9dbeaa @ 
>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>> GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
>> 1404.46) of 2016-05-24
>> #+end_example
>> --8<---cut here---end--->8---
>>
>>
>> The problem is beamer - with the other exports it works. With beamer,
>> I get the pdf at [[https://www.dropbox.com/s/fc6z9wszxl5vv9i/text.pdf?dl=0]]
>>
>
> As is, I get the tag in beamer, article, and html. You're saying you
> *don't* get the tag in article/html, but you *do* in beamer? If so, I
> can't reproduce. Behavior is consistent with what I'd expect, namely
> that tags export, but setting tags:nil turns that off.

The tags *do* export to the *headers*, which is expected, but *should not* be
in the toc.

Cheers,

Rainer

>
>
> John
>
>> Cheers,
>>
>> Rainer
>>
>>>
>>> Regards,
>>
>> --
>> Rainer M. Krug
>> email: Rainerkrugsde
>> PGP: 0x0F52F982

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> OK. Here it is:
>>
>> #+TITLE: An Example
>> #+EMAIL: rai...@krugs.de
>>
>> #+OPTIONS:   tags:not-in-toc
>>
>> #+LATEX_CLASS: beamer
>> #+OPTIONS:   H:2 toc:t
>>
>> * Level 1   :andHereIsTheTag:
>> ** A Frame
>> #+begin_example
>> Org-mode version 8.3.4 (release_8.3.4-850-g9dbeaa @ 
>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>> GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
>> 1404.46) of 2016-05-24
>> #+end_example
>>
>>
>> The problem is beamer - with the other exports it works. With beamer,
>> I get the pdf at [[https://www.dropbox.com/s/fc6z9wszxl5vv9i/text.pdf?dl=0]]
>
> I cannot reproduce it. Could you show the LaTeX code generated?

Here it is

Rainer

--8<---cut here---start->8---
% Created 2016-06-01 Wed 10:04
% Intended LaTeX compiler: pdflatex
\documentclass[presentation]{beamer}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage{color}
\usepackage{listings}
\usetheme{default}
\author{Rainer M. Krug}
\date{\today}
\title{An Example}
\hypersetup{
 pdfauthor={Rainer M. Krug},
 pdftitle={An Example},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 25.0.94.1 (Org mode 8.3.4)}, 
 pdflang={English}}
\begin{document}

\maketitle
\begin{frame}{Outline}
\tableofcontents
\end{frame}


\section[Level 1]{Level 1\hfill{}\textsc{andHereIsTheTag}}
\label{sec:orgf7a1edf}
\begin{frame}[fragile,label={sec:org61ac01b}]{A Frame}
 \begin{verbatim}
Org-mode version 8.3.4 (release_8.3.4-850-g9dbeaa @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
1404.46) of 2016-05-24
\end{verbatim}
\end{frame}
\end{document}
--8<---cut here---end--->8---

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Some LaTeX Beamer / org-mode questions

[Rainer M Krug]

Florian Lindner <mailingli...@xgm.de> writes:

> Hello,
>
> I'm working on my first presentation using org mode together with latex
> beamer (until now, I produce the slide using beamer only).

Same as me - beamer in org is really niche when you get the hang of it
(still not completely there).

>
> The top of my org file looks like that:
>
> #+startup: beamer
> #+LATEX_CLASS: beamer
>
> #+LATEX_CLASS_OPTIONS: [presentation]
> #+BEAMER_THEME: Boadilla
> #+LATEX_HEADER: \author[me]{\underline{me}, co1, co2}
> #+LATEX_HEADER: \title[short title]{multi line long title}
> #+LATEX_HEADER: \subtitle{subtitle}
> #+LATEX_HEADER: \institute[short institute]{multi line long institute}

You could use
#+BEAMER_HEADER: instead of #+LATEX_HEADER: - makes it clearer and is
only inserted when exporting to beamer.

>
> This works so far, except the title. Since I do not set a title using
> #+TITLE, org-mode sets a default \title{presentation}. How can I omit that?
>
> Is there a more elegant way to achieve the settings like above? Especially
>
> - The short and version of title, author and institute.
> - The multi line (\\) formatting
> - The subtitle

Don't know - but wopuld really like to know as well.

Rainer

>
> Thanks!
>
> Florian
>
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> When I generate a pdf, the tags are in the TOC - but tags:not-in-toc
>> means that the tags are *not* in the toc - possibly only in the headers
>> itself? I don't know.
>>
>> Just checked, the tags are also in the toc in html export.
>>
>> According to the documentation:
>>
>> ,
>> | If this is the symbol ‘not-in-toc’, tags will be removed from
>> | table of contents entries, but still be shown in the headlines of
>> | the document.
>> `
>>
>> This is not working anymore.
>
> I cannot reproduce it, at least on HTML, LaTeX, and ASCII export. Could
> you show an ECM ?

OK. Here it is:

--8<---cut here---start->8---
#+TITLE: An Example
#+EMAIL: rai...@krugs.de

#+OPTIONS:   tags:not-in-toc

#+LATEX_CLASS: beamer
#+OPTIONS:   H:2 toc:t

* Level 1   :andHereIsTheTag:
** A Frame
#+begin_example
Org-mode version 8.3.4 (release_8.3.4-850-g9dbeaa @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
1404.46) of 2016-05-24
#+end_example
--8<---cut here---end--->8---


The problem is beamer - with the other exports it works. With beamer,
I get the pdf at [[https://www.dropbox.com/s/fc6z9wszxl5vv9i/text.pdf?dl=0]]

Cheers,

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> Makes sense - I just wasn't aware of the tags:nil property. Probably it
>> should be added to the beamer template headers (C-ce#)?
>
> It belongs to the default template, since this is a generic option.
> I don't think it's a good idea to add duplicates in templates.
>
>> I had
>>
>> #+OPTIONS: tags:not-in-toc
>>
>> in my org file, but the tags were still in the toc of the beamer
>> export.
>
> From your document, adding tags:not-in-toc, I get
>
>   \begin{document}
>
>   \begin{frame}{Outline}
>   \tableofcontents
>   \end{frame}
>
>
>   \section[Level 1]{Level 1\hfill{}\textsc{presentation}}
>   \label{sec:org057dfd7}
>   \begin{frame}[label={sec:org1551704}]{Frame 1}
>   Some Text
>   \end{frame}
>   \end{document}
>
> Do you know what should be generated instead?

When I generate a pdf, the tags are in the TOC - but tags:not-in-toc
means that the tags are *not* in the toc - possibly only in the headers
itself? I don't know.

Just checked, the tags are also in the toc in html export.

According to the documentation:

,
| If this is the symbol ‘not-in-toc’, tags will be removed from
| table of contents entries, but still be shown in the headlines of
| the document.
`

This is not working anymore.

Cheers,


Rainer


>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] B_column does not insert :BEAMER_COL:

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Right - that works. But Why do the others have B_ names, while this
>> environment has BMCOL?
>
> "BMCOL" is a terrible name. However, it is not an environment per se
> since it controls both "columns" and "column" environments.


To quote from the Beamer Manual (emphasis added):

12.7 Splitting a Frame into Multiple Columns:

,
| The *main environment for creating columns* is called columns. Inside
| this environment, you can either place several *column environments*,
| each of which creates a new column, or use the \column command to
| create new columns.
`

But I think you are referring to BMCOL. This adds the :BEAMER_col:
property, which is converted on export to the column environment with
the given width, i.e. the same as B_column plus the width in
PROPERTIES. As far as I see, it does nothing with the columns
(B_columns) environment - or am I missing something here?

>
> There is a use-case for handling "columns" independently on "BMCOL"
> (i.e., add specific options to the environment). I'm not so sure about
> "column". There might be the same reason.

I don't think one can use B_columns without specifying the width
in :PROPERTIES: and nothing stops me to add additional PROPERTIES in the
BMCOL property. 

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] B_column does not insert :BEAMER_COL:

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> When I set the B_column environment, the property :BEAMER_env: is as
>> expected, automatically set to =column=, but exporting to beamer results
>> in an error as the environment is is not actually used in the resulting
>> latex file. The environment is only correctly created, if the
>> property :BEAMER_COL: is added.
>>
>> This is counter-intuitive and not obvious. Would it be possible to
>> add :BEAMER_COL: automatically as well?
>
> I think the column environment is a left-over for previous
> implementation and should be removed. 
>
> Couldn't you use BMCOL instead ("|")?

Right - that works. But Why do the others have B_ names, while this
environment has BMCOL?

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] B_column does not insert :BEAMER_COL:

[Rainer M Krug]

Hi

When I set the B_column environment, the property :BEAMER_env: is as
expected, automatically set to =column=, but exporting to beamer results
in an error as the environment is is not actually used in the resulting
latex file. The environment is only correctly created, if the
property :BEAMER_COL: is added.

This is counter-intuitive and not obvious. Would it be possible to
add :BEAMER_COL: automatically as well?

Thanks,

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

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Re: [O] BUG: org-beamer-select-environment select multiple environments not working?

[Rainer M Krug]

John Hendy <jw.he...@gmail.com> writes:

> Just to comment on the original attempt, block and column (which is |,
> not c which is columnS) are not mutually exclusive. I just did a
> presentation and used both together. I'm not sure on the use-case for
> columnS, but my structure was two side by side columns in a slide:
>
> #+begin_src org
> * slide
> ** col1  :B_block:BMCOL:
>:PROPERTIES:
>:BEAMER_env: block
>:BEAMER_col: 0.5
>:END:
>
> - list
> - of
> - items
>
> ** col2  :B_block:BMCOL:
>:PROPERTIES:
>:BEAMER_env: block
>:BEAMER_col: 0.5
>:END:
>
> [[pic]]
> #+end_src
>
> Probably not that helpful, just wanted to clarify that some
> environments are still compatible (in case someone finds this and
> thinks that *all* multiple combos are not possible anymore).

Is it possible that *only B_* environments are mutually exclusive?

Rainer

>
>
> John
>
>
> On Wed, May 25, 2016 at 3:31 PM, Nicolas Goaziou <m...@nicolasgoaziou.fr> 
> wrote:
>> Hello,
>>
>> Rasmus <ras...@gmx.us> writes:
>>
>>> Not necessarily.  On the top of my head, you could have a column group
>>> with columns inside.  This example used to be possible.  I haven't checked
>>> now.
>>
>> This one is not possible anymore. A column environment implies columns.
>> You can also provide a columns environment explicitly, at a higher
>> level, e.g., to provide specific options.
>>
>> Regards,
>>
>> --
>> Nicolas Goaziou
>>
>

-- 
Rainer M. Krug
email: Rainerkrugsde
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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>
>> Hello,
>>
>> Rainer M Krug <rai...@krugs.de> writes:
>>
>>> But in my document, I have
>>>
>>> #+SELECT_TAGS: export presentation
>>>
>>> in which case, I would have expected, that the tags defined here are not
>>> exported?
>>
>> It's arguably better. 
>>
>> OTOH, it is easier to remove them with a filter (or globally with
>> tags:nil) than to add them back if we automatically delete them. So,
>> I tend to think we shouldn't remove them automatically.
>>
>> WDYT?
>
> FWIW I agree with not being clever here.  It becomes a too convoluted
> definition of tags.  Aside, I can’t think of single case where I would
> *export* tags (but that’s another story).

Different usage scenarios I guess. But most certainly not in my usage
pattern of org (literate programming, data analysis, R, paper,
presentations, ...)

Cheers,

Rainer
-- 
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email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> But in my document, I have
>>
>> #+SELECT_TAGS: export presentation
>>
>> in which case, I would have expected, that the tags defined here are not
>> exported?
>
> It's arguably better. 
>
> OTOH, it is easier to remove them with a filter (or globally with
> tags:nil) than to add them back if we automatically delete them. So,
> I tend to think we shouldn't remove them automatically.
>
> WDYT?

Makes sense - I just wasn't aware of the tags:nil property. Probably it
should be added to the beamer template headers (C-ce#)?

>
>> But I already have =tags:not-in-toc= but they were in the TOC?
>
> I don't understand that question.

I had

#+OPTIONS: tags:not-in-toc

in my org file, but the tags were still in the toc of the beamer export.

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] BUG: org-beamer-select-environment select multiple environments not working?

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>
>> Hello,
>>
>> Rainer M Krug <rai...@krugs.de> writes:
>>
>>> It seems that I can not longer select multiple environments at the same
>>> time by using org-beamer-select-environment.
>>>
>>> - I am on a header
>>> - I press C-c C-b
>>> - then C-c to enable multiple selections
>>> - press (b)lock and (c)olumn and both are selected
>>> - press [RET] to accept
>>> - only one gets applied (in my case column)
>>
>> Aren't environments mutually exclusive?

An environment per level - you might be right.
But one environment *in* another makes sense.

>
> Not necessarily.  On the top of my head, you could have a column group
> with columns inside.  This example used to be possible.  I haven't checked
> now.

So the proper way to do it, would than to have one block environment
encapsulated in a column environment:

** A column :B_column:
*** A Block in a column :B_block:

Makes actually sense, as a column in a block would be something different.

So there is actually no reason to be able to assign multiple
environments to an org header.

Couldn't this than be removed from the dialog?

Also: what does the ! (Groups) mean in the dialog?

Thanks,

Rainer

-- 
Rainer M. Krug
email: Rainerkrugsde
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[O] BUG: org-beamer-select-environment select multiple environments not working?

[Rainer M Krug]

Hi

It seems that I can not longer select multiple environments at the same
time by using org-beamer-select-environment.

- I am on a header
- I press C-c C-b
- then C-c to enable multiple selections
- press (b)lock and (c)olumn and both are selected
- press [RET] to accept
- only one gets applied (in my case column)

# GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
1404.46) of 2016-05-24
# Org-mode version 8.3.4 (release_8.3.4-842-g58f5def @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)

Cheers,

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

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Re: [O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Hi Rainer,
>
> Thanks for the bug report.
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> Please not that the tag :presentation: becomes exported as part of the
>> header.
>
> Isn't this expected behavior?

OK - you are obviously right.

But in my document, I have

--8<---cut here---start->8---
#+SELECT_TAGS: export presentation
--8<---cut here---end--->8---

in which case, I would have expected, that the tags defined here are not
exported?

But it all might be because I misunderstood tags as something which is
not exported but used similarly to properties.

>
>> I would like to use the tags to filter for export, so they should not
>> become part otf the headers.
>
> It seems to work when I specify this option in your document.
>
> #+OPTIONS:  tags:nil

Thanks - works as expected.

But I already have =tags:not-in-toc= but they were in the TOC?

Rainer


>
> Rasmus

-- 
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[O] BUG: in beamer export non-beamer tags exported as part of header

[Rainer M Krug]

Hi

the following document

--8<---cut here---start->8---
#+startup: beamer
#+STARTUP: oddeven
#+LATEX_CLASS: beamer
#+LATEX_CLASS_OPTIONS: [bigger] 
#+BEAMER_THEME: Madrid
#+BEAMER_COLOR_THEME: spruce
#+OPTIONS:   H:2 toc:t
#+SELECT_TAGS: export
#+EXCLUDE_TAGS: noexport

* Level 1 :presentation:
** Frame 1
Some Text
--8<---cut here---end--->8---

becomes exported as

,
| % Created 2016-05-24 Tue 12:45
| % Intended LaTeX compiler: pdflatex
| \documentclass[bigger]{beamer}
| \usepackage[utf8]{inputenc}
| \usepackage[T1]{fontenc}
| \usepackage{graphicx}
| \usepackage{grffile}
| \usepackage{longtable}
| \usepackage{wrapfig}
| \usepackage{rotating}
| \usepackage[normalem]{ulem}
| \usepackage{amsmath}
| \usepackage{textcomp}
| \usepackage{amssymb}
| \usepackage{capt-of}
| \usepackage{hyperref}
| \usepackage{color}
| \usepackage{listings}
| \usetheme{Madrid}
| \usecolortheme{spruce}
| \author{Rainer M. Krug}
| \date{\today}
| \title{}
| \hypersetup{
|  pdfauthor={Rainer M. Krug},
|  pdftitle={},
|  pdfkeywords={},
|  pdfsubject={},
|  pdfcreator={Emacs 25.0.94.1 (Org mode 8.3.4)}, 
|  pdflang={English}}
| \begin{document}
| 
| \begin{frame}{Outline}
| \tableofcontents
| \end{frame}
| 
| 
| \section{Level 1\hfill{}\textsc{presentation}}
| \label{sec:org46cc55c}
| \begin{frame}[label={sec:org8dc9e52}]{Frame 1}
| Some Text
| \end{frame}
| \end{document}
`

Please not that the tag :presentation: becomes exported as part of the
header.

I would like to use the tags to filter for export, so they should not
become part otf the headers.

GNU Emacs 25.0.94.1 (x86_64-apple-darwin15.4.0, Carbon Version 157 AppKit 
1404.46) of 2016-05-24
Org-mode version 8.3.4 (release_8.3.4-842-g58f5def @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)

Cheers,

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

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[O] Export of subtree via narrowing to subtree - setting name of exported document?

[Rainer M Krug]

Hi

I have a document which consists of several subtrees (presentation, paper, and
other data). I would now like to export each of the two subtrees
(presentation and paper) into different PDF files. I know of the
EXPORT_FILE_NAME property, but somehow I do not manage to export the
subtree via this mechanism, but I narrow the document to the subtree and
than export it t(he top-header has the tag :ignoreheader:) and it
works - but it obviously does not use the EXPORT_FILE_NAME property.

Is there a a way that I can set the name of the exported file using
this approach (narrowing to subtree, than export "whole" document) in
the subtree?

Cheers,

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

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[O] Best way of including tikz into latex (pdf and beamer) export with preview?

[Rainer M Krug]

Hi

What is the best way of including tikz into org for latex export (beamer
and pdf), and to have preview as well?

Thanks,

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

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Re: [O] Annotating org exporters

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Sebastian Fischmeister <sfisc...@uwaterloo.ca> writes:
>
>> Is there a simple way to build regex-based extensions to the exporters?
>
> Yeah, filters.  But I don’t think this is the best way to go about it.
>
>> For example, I would like to convert this string "=>" to $\rightarrow$
>> when converting the document to latex.
>>
>> There are lots of other uses, where I could create my shortcuts and
>> insert them in orgmode files without creating a lot of clutter in the
>> file.
>
> This sounds a bit like org-entities.  I use this together with cdlatex for
> quickly inserting such things.

Great - learned something. Never knew about org-entities.

Would it be possible to generate *easily* a pdf with all the org-entities?
Possibly include it in org as a kind of a cheat-sheet for org-entities?

Reading the help in this case is possible but not easy...

Rainer


>
> Try to type \Rightarrow and type C-c C-x \
> Also try to export to text (non-unicode).  You will get the desired symbol.
>
> Alternatively, you can use one of the many input methods such as TeX or
> rfc1345 in which case you can get the ‘⇒’ by typing ‘\Rightarrow’ or
> ‘&=>’, respectively.  In latex, you can setup unicode-math.
>
> Hope it helps,
> Rasmus

-- 
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email: Rainerkrugsde
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Re: [O] Annotating org exporters

[Rainer M Krug]

Sebastian Fischmeister <sfisc...@uwaterloo.ca> writes:

> Hi,
>
> Is there a simple way to build regex-based extensions to the exporters?
> For example, I would like to convert this string "=>" to $\rightarrow$
> when converting the document to latex.
>
> There are lots of other uses, where I could create my shortcuts and
> insert them in orgmode files without creating a lot of clutter in the
> file.

I like this idea. It would be ideal if one could define these in the
header of the org document - easy to maintain and to edit.

Cheers,

Rainer

>
>   Sebastian
>

-- 
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Re: [O] PATCH: Add new output formats to plantuml

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> attached please find a patch which adds additional output file types for
>> plantuml.
>
> Applied. Thank you.
>
> Could you provide an entry for ORG-NEWS?

Here it is - hopefully in the right format. The link to the RESULT of
the example needs to be adjusted, image attached.

Cheers,

Rainer

--8<---cut here---start->8---
*** Support for additional plantuml output formats 
The support for output formats of [[http://plantuml.com/][plantuml]] has been 
extended to now include:

All Diagrams:
- png ::
- svg ::
- eps ::
- pdf ::
- vdx ::
- txt :: ASCII art
- utxt :: ASCII art using unicode characters

Class Diagrams:
- xmi ::
- html ::

State Diagrams:
- scxml ::

The output formats are determined by the file extension specified using the 
:file property:

#+begin_src plantuml :file diagram.png
@startuml
Alice -> Bob: Authentication Request
Bob --> Alice: Authentication Response

Alice -> Bob: Another authentication Request
Alice <-- Bob: another authentication Response
@enduml
#+end_src

#+RESULTS:
[[file:/Users/rainerkrug/diagram.png]]

Please note that *pdf* *does not work out of the box* and needss
additional setup in addition to plantuml. See
[[http://plantuml.com/pdf.html]] for details and setup information.
--8<---cut here---end--->8---



>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] PATCH: Add new output formats to plantuml

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> attached please find a patch which adds additional output file types for
>> plantuml.
>
> Applied. Thank you.

Thanks

>
> Could you provide an entry for ORG-NEWS?

Will do.

Rainer

>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Result from evaluation of code in Title or footer (fancyhdr)?

[Rainer M Krug]

Sharon Kimble <boudic...@skimble.plus.com> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Hi
>>
>> I have a DESCRIPTION file, in which I store the version of the document,
>> which I extract with the following code:
>>
>> src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}
>>
>
> Have you looked at the latex package 'mversion'? I use it and have it
> working on my document, with it in the date place of my title it shows
> "Build - \version", and the "version.dat" shows '2.0;' meaning
> version 2.0 and it being increased in the '' field with every build.
> You can put it in your header or footer, whichever you want.

Brilliant - mVersion works nicely. Exactly what I was looking for.

I only had to adjust latexmk as it ran into an endless loop by adding

--8<---cut here---start->8---
$hash_calc_ignore_pattern{'dat'} = '^[0-9]';
--8<---cut here---end--->8---

to my latexmk config file.


Thanks,

Rainer

>
> Thanks
> Sharon.
>
>>
>> At the moment, I have one Header, which contains the version.
>>
>> * Version src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}:paper:
>> :PROPERTIES:
>> :header-args: :exports results
>> :header-args+: :tangle no
>> :END:
>> Version src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}
>>
>> Is there a way, that I can have this dynamically in the Title of the
>> document, or in a footer after LaTeX export (using fancyhdr)?
>>
>> Thanks,
>>
>> Rainer

-- 
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email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Result from evaluation of code in Title or footer (fancyhdr)?

[Rainer M Krug]

Eric S Fraga <e.fr...@ucl.ac.uk> writes:

> On Monday,  2 May 2016 at 13:41, Rainer M Krug wrote:
>
> [...]
>
>> Is there a way, that I can have this dynamically in the Title of the
>> document, or in a footer after LaTeX export (using fancyhdr)?
>
> Maybe something along these lines:
>
>   @@latex:\rfoot{@@ Version src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION} 
> @@latex:}@@
>
> immediately after the first headline?  Assumes fancyhdr.

Thanks - I am combining this with Sharon's suggestion.

Very nice,

Rainer

-- 
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email: Rainerkrugsde
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[O] Result from evaluation of code in Title or footer (fancyhdr)?

[Rainer M Krug]

Hi

I have a DESCRIPTION file, in which I store the version of the document,
which I extract with the following code:

--8<---cut here---start->8---
src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}
--8<---cut here---end--->8---

At the moment, I have one Header, which contains the version.

--8<---cut here---start->8---
* Version src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}:paper:
:PROPERTIES:
:header-args: :exports results
:header-args+: :tangle no
:END:
Version src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION}
--8<---cut here---end--->8---

Is there a way, that I can have this dynamically in the Title of the
document, or in a footer after LaTeX export (using fancyhdr)?

Thanks,

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
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[O] Beamer \usebackgroundtemplate - better solution?

[Rainer M Krug]

Hi

I am using the following structure for \usebackgroundtemplate in Beamer:

--8<---cut here---start->8---
*** Overview of The Case Study
:PROPERTIES:
:header-args: :eval never-export 
:header-args+: :file-ext pdf
:END:
#+LATEX: {
#+LATEX: \usebackgroundtemplate{

#+ATTR_LATEX: :width 1\paperwidth :height 1\paperheight :options keepaspectratio
 [[./bramble2.jpg]]
#+LATEX: }

 Some slide
  - one
  - two
  - three

*** 
#+LATEX: }
--8<---cut here---end--->8---

which works, but I don't like it that much because of the disconnected
nature of the beginning (in the header Overview...) and the closing
bracket (in the header without text). Also, this header without text is
rather fragile, as using tab on it, indents the header and does not fold
(cursor has to be on the stars to fold).

I assume that I can use org-beamer-environments-extra, but I don't
really see how (I would like to have the image as an argument).

I saw http://orgmode.org/worg/exporters/beamer/ox-beamer.html but this
does not help me with using the image as an argument.

Any suggestions?

Thanks,

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

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Re: [O] :kkepaspectratio in included imad=ge in LaTeX export

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> I would like to have the keepaspectratio attribute in the
>> \includegraphice.
>>
>> I tried:
>>
>> #+ATTR_LATEX: :width 1\paperwidth :height 1\paperheight :keepaspectratio
>>  [[./bramble2.jpg]]
>>
>> but this results obviously in
>>
>> \includegraphics[width=1\paperwidth,height=1\paperheight]{./bramble2.jpg}
>>
>> as the option keepaspectratio does not exist in org.
>>
>> Is there a way that I can add arbitrary LaTeX option like
>> keepaspectratio?
>
> You can use :options. See (info "(org) LaTeX specific attributes").

How could I miss that?  No idea.

Thanks a lot,works perfectly,

Rainer

>
> Regards,

-- 
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email: Rainerkrugsde
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[O] PATCH: Add new output formats to plantuml

[Rainer M Krug]

Hi

attached please find a patch which adds additional output file types for
plantuml.


Cheers,

Rainer

From 839cb3194e6a40e577c5cab3b0a69961238924c9 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <r.m.k...@gmail.com>
Date: Mon, 2 May 2016 11:00:23 +0200
Subject: [PATCH] lisp/op-plantuml.el: Add new output formats

* lisp/ob-paltuml (org-babel-execute:plantuml): add new output formats
  of plantuml:
  - pdf : this needs extra java mudules to run which are mentioned on the
plantml website (http://fr.plantuml.com/pdf.html)
  - vdx
  - xmi
  - scxml
  - html
  - txt (ascii art)
  - utxt (ascii art using unicode)

  The output format is based on the extension of the output file.
---
 lisp/ob-plantuml.el | 16 
 1 file changed, 16 insertions(+)

diff --git a/lisp/ob-plantuml.el b/lisp/ob-plantuml.el
index 0e07f2d..6cc55a2 100644
--- a/lisp/ob-plantuml.el
+++ b/lisp/ob-plantuml.el
@@ -59,10 +59,26 @@ This function is called by `org-babel-execute-src-block'."
 		(concat "java " java " -jar "
 			(shell-quote-argument
 			 (expand-file-name org-plantuml-jar-path))
+			(if (string= (file-name-extension out-file) "png")
+			" -tpng" "")
 			(if (string= (file-name-extension out-file) "svg")
 			" -tsvg" "")
 			(if (string= (file-name-extension out-file) "eps")
 			" -teps" "")
+			(if (string= (file-name-extension out-file) "pdf")
+			" -tpdf" "")
+			(if (string= (file-name-extension out-file) "vdx")
+			" -tvdx" "")
+			(if (string= (file-name-extension out-file) "xmi")
+			" -txmi" "")
+			(if (string= (file-name-extension out-file) "scxml")
+			" -tscxml" "")
+			(if (string= (file-name-extension out-file) "html")
+			    " -thtml" "")
+			(if (string= (file-name-extension out-file) "txt")
+			" -ttxt" "")
+			(if (string= (file-name-extension out-file) "utxt")
+			" -utxt" "")
 			" -p " cmdline " < "
 			(org-babel-process-file-name in-file)
 			" > "
-- 
2.8.2


-- 
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
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[O] :kkepaspectratio in included imad=ge in LaTeX export

[Rainer M Krug]

Hi

I would like to have the keepaspectratio attribute in the
\includegraphice.

I tried:

--8<---cut here---start->8---
#+ATTR_LATEX: :width 1\paperwidth :height 1\paperheight :keepaspectratio
 [[./bramble2.jpg]]
--8<---cut here---end--->8---

but this results obviously in

--8<---cut here---start->8---
\includegraphics[width=1\paperwidth,height=1\paperheight]{./bramble2.jpg}
--8<---cut here---end--->8---

as the option keepaspectratio does not exist in org.

Is there a way that I can add arbitrary LaTeX option like
keepaspectratio?

Thanks,

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


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Re: [O] Beamer presantation, Abstract and Article in same document - how to structure and how to export?

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Hi,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> I would like to have one document containing
>>
>> 1) abstract for
>> 2) a presentation and 
>> 3) a resulting paper
>>
>> My question is: how can I structure this an how can I handle the export?
>>
>> Obviously under different top level headers:
>>
>> * Abstract
>> #+begin_abstract
>> Needs top be written
>> #+end_abstract
>>
>> * Presentation
>> ** Title
>> *** first slide
>> ...
>> * Paper
>> ** Abstract
>> How can I refer to the abstract above?
>> ** ...
>
> While you may not necessarily *need* beamerarticle, you might still find
> it enlightening.  See section 21.2 in the beamer manual.
>
> Example:
>
> #+title: beamer example with text not shown
> #+options: h:2
>
> #+latex_class_options: [ignorenonframetext]
> * h1
> text that is not part of any slide 
> ** my first slide
> - a
> - b
>
> Another companion is #+include which you can use to extract named element
> from one file to the other, e.g. to share tables.

Thanks - both good ideas. I will look into them. I have already put the
[ignorenonframetext] option in.

>
>> But what about the specific settings? Can I set them per subtree?
>>
>> #+LaTeX_CLASS: beamer
>> #+LaTeX_CLASS_OPTIONS: [bigger]
>
> Isn't the latex class guess correctly?

I only copied from the work examples - but it is true - I don't need
this - and to leave it out, actually makes life much easier.

>
>> I could than export each subtree separate?
>
> Should be easy to do with a bit of lisp.

I use emacs, org, ess and gnus , but I never managed to get a real grasp
of elisp.

>
>> Can I define the name for the exported document per subtree?
>
>   
> http://orgmode.org/org.html#index-property_002c-EXPORT_005fFILE_005fNAME-1651

OK - thanks - found it.

>
>> How can I switch easily between different settings?
>
> For #+LaTeX_CLASS_OPTIONS I'd maybe use a macro.
> I'd also use this for setting export tags, e.g. 
>
> #+MACRO: exclude-tags (eval (mapconcat 'identity (list "#+EXCLUDE_TAGS:" 
> "noexport" (concat "no" (symbol-name org-export-current-backend))) " "))
>
> You might also find the if clause in this macro interesting:
>
> #+MACRO: abbr (eval (if (org-export-derived-backend-p 
> org-export-current-backend 'html) "@@html: title=\"$2\">@@$1@@html:@@" "$1"))

Thanks - I will look into this. I used macros already - but this looke=s
very interesting.

Cheers,

Rainer

>
> Hope it helps,
> Rasmus

-- 
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email: Rainerkrugsde
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[O] Beamer presantation, Abstract and Article in same document - how to structure and how to export?

[Rainer M Krug]

Hi

I would like to have one document containing

1) abstract for
2) a presentation and 
3) a resulting paper

My question is: how can I structure this an how can I handle the export?

Obviously under different top level headers:

--8<---cut here---start->8---
* Abstract
#+begin_abstract
Needs top be written
#+end_abstract

* Presentation
** Title
*** first slide
...
* Paper
** Abstract
How can I refer to the abstract above?
** ...
--8<---cut here---end--->8---

But what about the specific settings? Can I set them per subtree?

--8<---cut here---start->8---
#+LaTeX_CLASS: beamer
#+LaTeX_CLASS_OPTIONS: [bigger]
--8<---cut here---end--->8---

I could than export each subtree separate?

Can I define the name for the exported document per subtree?

How can I switch easily between different settings?

Any suggestions or examples?

Or should I use publishing (I am always reluctant, as it seems so complicated)?

Thanks,

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

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Re: [O] State of things: Email with orgmode?

[Rainer M Krug]

Eric S Fraga <e.fr...@ucl.ac.uk> writes:

> On Monday, 25 Apr 2016 at 19:33, Rainer M Krug wrote:
>> Eric S Fraga <e.fr...@ucl.ac.uk> writes:
>>
>>> Table of Contents
>>>
>>> * 1. An example 
>>>
>>> One of the links between org and email is using org-mime-htmlize which
>>
>> Very nice - but I have two question:
>>
>> 1) do I have to load something to have this function? I don't seem to
>> have it
>
> org-mime.el is in org contrib package.  I am not sure how you might be
> able to get this as it will depend on how you get org in the first
> place.  Are you using org from git or melpa or from the web site
> directly?

git - found it. Thanks.

>
>>
>> 2) What is the easiest way of writing a mail in gnus in org format? I
>> would like to have all features of org if possible?
>
> I simply change to org mode (e.g. M-x org-mode RET) to compose and then
> back to message mode (M-x message-mode RET) when ready to htmlize the
> buffer and send the email.

I thought there might be an easier way, but this one definitely gives the
most complete feature set.

Thanks,

Rainer
-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] State of things: Email with orgmode?

[Rainer M Krug]

Eric S Fraga <e.fr...@ucl.ac.uk> writes:

> Table of Contents
>
> * 1. An example 
>
> One of the links between org and email is using org-mime-htmlize which

Very nice - but I have two question:

1) do I have to load something to have this function? I don't seem to
have it

2) What is the easiest way of writing a mail in gnus in org format? I
would like to have all features of org if possible?

Rainer

> will take your email buffer (using gnus in my case but a message
> buffer) and create a text+html mime encoded email in which the plain
> text is parsed as an org file and exported to HTML.
>
>
> I don't use this often but I do use it now and again, for instance when a 
> table is a necessary element of the email or if I want to have some LaTeX 
> equations
> in the email.
>
>
> 1 An example
>
> For instance, the following equation may appear in the email, depending on 
> what you are using to view your emails:
>
>
> \begin{equation}
> y = \sqrt{x}
> \end{equation}
>
>
> eric
>
>
> –
>
>
>
> Eric S Fraga (0xFFFCF67D), Emacs 25.0.92.1, Org release_8.3.4-739-g789412
>

-- 
Rainer M. Krug
email: Rainerkrugsde
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Re: [O] Recent bug? in R source blocks generating images

[Rainer M Krug]

William Denton <w...@pobox.com> writes:

> Sorry about that; hit send too soon.
>
> There's something odd happening to me tonight with R source blocks and 
> :session.
>
> This works, and generates an image:
>
> #+BEGIN_SRC R :results graphics :file example.png
> plot(1)
> #+END_SRC
>
>
> But if I start an R session (M-x R) and then run this, with :session, I get 
> an 
> error.
>
> #+BEGIN_SRC R :session :results graphics :file example.png
> plot(1)
> #+END_SRC
>
> The error is
>
> + + Error: unexpected symbol in:
> "plot(1)
> },error=function(e){plot(x=-1:1, y=-1:1, type='n"
>
> That error= bit at the end looks related to my plot() example, but I don't 
> think 
> it is: the same error appears if I use ggplot2 (which is how I noticed it).
>
> This is with Emacs and Org compiled from current source trees.  It was 
> working 
> earlier this week, but I've updated since then.  I refreshed everything 
> (including R packages) and still get the error.  I looked at the recent Org 
> commits but don't see what might have done it, but I also don't think I'm 
> doing 
> anything wrong.

Working for me on

OS X El Capitan
GNU Emacs 25.0.92.1 (x86_64-apple-darwin15.3.0, NS appkit-1404.34 Version 
10.11.3 (Build 15D21)) of 2016-03-07
Org-mode version 8.3.4 (release_8.3.4-702-gcd47ab @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)

but not working anymore on

Org-mode version 8.3.4 (release_8.3.4-709-g519f78 
@/Users/rainerkrug/.emacs.d/org-mode/lisp/)

than I went back to

Org-mode version 8.3.4 (release_8.3.4-702-gcd47ab 
@/Users/rainerkrug/.emacs.d/org-mode/lisp/)

and it was not working either. But there was an update of ESS at the
same time which should have caused this.

OK - commit 9be858b of ESS is still fine.


Could you please submit this to the ESS list?


Cheers,

Rainer

>
> Bill

-- 
Rainer M. Krug
email: Rainerkrugsde
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[O] set :eval to eval on export for one subtree

[Rainer M Krug]

Hi

I have

,
| #+PROPERTY: header-args :eval no-export
| ... 
`

and other header arguments set at the beginning of my document.

But now I have one subtree, which I want to eval on export. Is there a
way of un-setting the :eval header argument for one subtree or is there
a special (default) value I could sewt it to?

Thanks,

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

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Re: [O] set default width for figure floats?

[Rainer M Krug]

John Kitchin <jkitc...@andrew.cmu.edu> writes:

> Rainer M Krug writes:
>
>> John Kitchin <jkitc...@andrew.cmu.edu> writes:
>>
>>> Maybe you want org-image-actual-width
>>>
>>> This sets teh width in org, if you have a working imagemagick.
>>
>> No - I don't want any scaling. They are graphs I have created in R and I
>> want to conserve the font sizes in the paper.
> This is only scaling in the org buffer. I find high resolution (high
> dpi) are often too large in my emacs, so I set this to be something like
> 300 to 600 to keep the figures reasonably sized in the buffer. It has no
> effect on the LaTeX export.

OK - I'll keep it in ind when I view the images in org.

Thanks,

Rainer
>
>>
>>>
>>> org-latex-image-default-width contains the default latex scaling.
>>> Probably you can set this to nil to avoid scaling.
>>
>> Setting it to "" works perfectly. I have now set:
>>
>> --8<---cut here---start->8---
>> #+BIND: org-latex-image-default-width ""
>> --8<---cut here---end--->8---
>>
>> as well as
>>
>> --8<---cut here---start->8---
>> # Local Variables:
>> # eval: (visual-line-mode 1)
>> # org-latex-image-default-width: ""
>> # End:
>> --8<---cut here---end--->8---
>>
>> I don't know if one is sufficient - I just leave them in and might try
>> later.
>>
>> Thanks a lot,
>>
>> Rainer
>>
>>>
>>>
>>> Rainer M Krug writes:
>>>
>>>> I think this has been asked before, but I can't find it:
>>>>
>>>> Is there a way of setting the default width for images included as
>>>>
>>>> [[file:map-All.png]]
>>>>
>>>> in org documents? It seems that the default is
>>>>
>>>> \includegraphics[width=.9\linewidth]{map-All.png}
>>>>
>>>> and I don't want the images to be scaled, but to let them keep their own
>>>> size.
>>>>
>>>> Is this possible (I'd like to avoid having to use #+ATTR_LATEX :width
>>>> before each - and even then I would have no idea to unset the value)
>>>>
>>>> Thanks,
>>>>
>>>> Rainer
>>>
>>>
>>> --
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] set default width for figure floats?

[Rainer M Krug]

John Kitchin <jkitc...@andrew.cmu.edu> writes:

> Maybe you want org-image-actual-width
>
> This sets teh width in org, if you have a working imagemagick.

No - I don't want any scaling. They are graphs I have created in R and I
want to conserve the font sizes in the paper.

>
> org-latex-image-default-width contains the default latex scaling.
> Probably you can set this to nil to avoid scaling.

Setting it to "" works perfectly. I have now set:

--8<---cut here---start->8---
#+BIND: org-latex-image-default-width ""
--8<---cut here---end--->8---

as well as

--8<---cut here---start->8---
# Local Variables:
# eval: (visual-line-mode 1)
# org-latex-image-default-width: ""
# End:
--8<---cut here---end--->8---

I don't know if one is sufficient - I just leave them in and might try
later.

Thanks a lot,

Rainer

>
>
> Rainer M Krug writes:
>
>> I think this has been asked before, but I can't find it:
>>
>> Is there a way of setting the default width for images included as
>>
>> [[file:map-All.png]]
>>
>> in org documents? It seems that the default is
>>
>> \includegraphics[width=.9\linewidth]{map-All.png}
>>
>> and I don't want the images to be scaled, but to let them keep their own
>> size.
>>
>> Is this possible (I'd like to avoid having to use #+ATTR_LATEX :width
>> before each - and even then I would have no idea to unset the value)
>>
>> Thanks,
>>
>> Rainer
>
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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[O] set default width for figure floats?

[Rainer M Krug]

I think this has been asked before, but I can't find it:

Is there a way of setting the default width for images included as

[[file:map-All.png]]

in org documents? It seems that the default is

\includegraphics[width=.9\linewidth]{map-All.png}

and I don't want the images to be scaled, but to let them keep their own
size.

Is this possible (I'd like to avoid having to use #+ATTR_LATEX :width
before each - and even then I would have no idea to unset the value)

Thanks,

Rainer
-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


signature.asc
Description: PGP signature

Re: [O] Bug: can not evaluate any code blocks after enabling additional languages [8.3.4 (release_8.3.4-639-gd5a603 @ /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)]

[Rainer M Krug]

Kyle Meyer <k...@kyleam.com> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:
>>
>>> Hello,
>>>
>>> Rainer M Krug <rai...@krugs.de> writes:
>>>
>>>> Debugger entered--Lisp error: (void-function org-babel-get-header)
>>>
>>> This looks like a mixed installation. This function was removed in
>>> development version and code base doesn't use it anymore.
>>
>> I don't think so - I use org from git uncompiled and, as you can see int
>> the init.el, initialize it (require 'org) before calling 
>> (package-initialize).
>>
>> For some unknown reasons, the function
>> org-babel-execute-src-block(nil) (in the org-git directory) calls
>> org-babel-execute:sh in the installation directory of emacs.
>>
>> So wy is this the case? I see that the file ob.sh.el seems to be renamed
>> in ob-shell.el - is this the case? Do I have to change the language sh
>> to shell?
>
> This has been reported on the list a few times.  See
> http://thread.gmane.org/gmane.emacs.orgmode/102877/focus=102882.

OK - thanks. This is solved now. But now I am stuck with the following,
where again, org-element-cache-reset is in the emacs packed org-mode,
while orgmode() is in the git version, and the changed org-set-local()
causes an error. Any suggestions?

,
| Debugger entered--Lisp error: (void-function org-set-local)
|   org-set-local(org-element--cache [cl-struct-avl-tree- [nil nil nil 0] 
org-element--cache-compare])
|   org-element-cache-reset()
|   (let ((delay-mode-hooks t)) (outline-mode) (setq major-mode (quote 
org-mode)) (setq mode-name "Org") (progn (if (get (quote outline-mode) (quote 
mode-class)) (put (quote org-mode) (quote mode-class) (get (quote outline-mode) 
(quote mode-class (if (keymap-parent org-mode-map) nil (set-keymap-parent 
org-mode-map (current-local-map))) (let ((parent (char-table-parent 
org-mode-syntax-table))) (if (and parent (not (eq parent 
(standard-syntax-table nil (set-char-table-parent org-mode-syntax-table 
(syntax-table (if (or (abbrev-table-get org-mode-abbrev-table :parents) (eq 
org-mode-abbrev-table local-abbrev-table)) nil (abbrev-table-put 
org-mode-abbrev-table :parents (list local-abbrev-table (use-local-map 
org-mode-map) (set-syntax-table org-mode-syntax-table) (setq local-abbrev-table 
org-mode-abbrev-table) (if (featurep (quote xemacs)) (if (boundp (quote 
outline-mode-menu-heading)) (progn (easy-menu-remove outline-mode-menu-heading) 
(easy-menu-remove outline-mode-menu-show) (easy-menu-remove 
outline-mode-menu-hide))) (define-key org-mode-map [menu-bar headings] (quote 
undefined)) (define-key org-mode-map [menu-bar hide] (quote undefined)) 
(define-key org-mode-map [menu-bar show] (quote undefined))) 
(org-load-modules-maybe) (if (featurep (quote xemacs)) (progn (easy-menu-add 
org-org-menu) (easy-menu-add org-tbl-menu))) (org-install-agenda-files-menu) 
(if org-descriptive-links (progn (add-to-invisibility-spec (quote 
(org-link) (add-to-invisibility-spec (quote (org-cwidth))) 
(add-to-invisibility-spec (quote (org-hide-block . t))) (if (featurep (quote 
xemacs)) (progn (set (make-local-variable (quote line-move-ignore-invisible)) 
t))) (set (make-local-variable (quote outline-regexp)) org-outline-regexp) (set 
(make-local-variable (quote outline-level)) (quote org-outline-level)) (setq 
bidi-paragraph-direction (quote left-to-right)) (if (and org-ellipsis (fboundp 
(quote set-display-table-slot)) (boundp (quote buffer-display-table)) (fboundp 
(quote make-glyph-code))) (progn (if org-display-table nil (setq 
org-display-table (make-display-table))) (set-display-table-slot 
org-display-table 4 (vconcat (mapcar (function (lambda ... ...)) (if (stringp 
org-ellipsis) org-ellipsis "..." (setq buffer-display-table 
org-display-table))) (org-set-regexps-and-options) (org-set-font-lock-defaults) 
(if (and org-tag-faces (not org-tags-special-faces-re)) (progn 
(org-set-tag-faces (quote org-tag-faces) org-tag-faces))) (set 
(make-local-variable (quote calc-embedded-open-mode)) "# ") 
(modify-syntax-entry 64 "w") (modify-syntax-entry 34 "\"") (modify-syntax-entry 
92 "_") (modify-syntax-entry 126 "_") (set (make-local-variable (quote 
font-lock-unfontify-region-function)) (quote org-unfontify-region)) (set 
(make-local-variable (quote org-table-may-need-update)) t) (org-add-hook (quote 
before-change-functions) (quote org-before-change-function) nil (quote local)) 
(org-add-hook (quote kill-buffer-hook) (quote org-check-running-clock) nil 
(quote local)) (org-macro-initialize-templates) 
(org-update-radio-target-regexp) (set (make-local-variable (quote 
indent-line-function)) (quote org-indent-line)) (set (make-local-variable 
(quote inden

Re: [O] Bug: can not evaluate any code blocks after enabling additional languages [8.3.4 (release_8.3.4-639-gd5a603 @ /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)]

[Rainer M Krug]

Nicolas Goaziou <m...@nicolasgoaziou.fr> writes:

> Hello,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> Debugger entered--Lisp error: (void-function org-babel-get-header)
>
> This looks like a mixed installation. This function was removed in
> development version and code base doesn't use it anymore.

I don't think so - I use org from git uncompiled and, as you can see int
the init.el, initialize it (require 'org) before calling (package-initialize).

For some unknown reasons, the function
org-babel-execute-src-block(nil) (in the org-git directory) calls
org-babel-execute:sh in the installation directory of emacs.

So wy is this the case? I see that the file ob.sh.el seems to be renamed
in ob-shell.el - is this the case? Do I have to change the language sh
to shell?


>
> It was still called in a few Babel libraries within contrib/, but I just
> fixed them.
>
>
> Regards,

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] Bug: can not evaluate any code blocks after enabling additional languages [8.3.4 (release_8.3.4-639-gd5a603 @ /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)]

[Rainer M Krug]

Sorry for tp:

Additional info:

Works under Org-mode version 8.3.4 (8.3.4-dist @ 
/Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)

Rainer M Krug <rai...@krugs.de> writes:

> * Configuration
> Org-mode version 8.3.4 (release_8.3.4-639-gd5a603 @ 
> /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)
> GNU Emacs 25.0.92.1 (x86_64-apple-darwin15.3.0, NS appkit-1404.34 Version 
> 10.11.3 (Build 15D21)) of 2016-03-07
>
> init.el:
>
> ,
> | (setq package-user-dir (concat "~/.emacs.d/elpa/"
> |;; if we use emacs-version we get a
> |;; LOT of pre-release directories.
> |(int-to-string emacs-major-version)
> |"."
> |(int-to-string emacs-minor-version)))
> | (add-to-list 'Info-default-directory-list "~/.emacs.d/ess/doc")
> | (add-to-list 'Info-default-directory-list "~/.emacs.d/org-mode/doc")
> | (defadvice desktop-restore-file-buffer
> | (around my-desktop-restore-file-buffer-advice)
> |   "Be non-interactive while starting a daemon."
> |   (if (and (daemonp)
> |(not server-process))
> |   (let ((noninteractive t))
> | ad-do-it)
> | ad-do-it))
> | (ad-activate 'desktop-restore-file-buffer)
> | 
> | 
> | (add-to-list 'load-path "~/.emacs.d/org-mode/lisp")
> | (add-to-list 'load-path "~/.emacs.d/org-mode/contrib/lisp")
> | (require 'org)
> | 
> | (setq package-archives '(
> |  ("ELPA" . "http://tromey.com/elpa/;)
> |  ("Melpa" . "http://melpa.org/packages/;)
> |  ("org" . "http://orgmode.org/elpa/;)
> |  ("gnu" . "http://elpa.gnu.org/packages/;)))
> | 
> | (require 'package)
> | (package-initialize)
> | 
> | (unless (package-installed-p 'use-package)
> |   (package-refresh-contents)
> |   (package-install 'use-package))
> | (setq use-package-verbose t)
> | (require 'use-package)
> | (setq use-package-verbose t)
> `
>
> * The problem
> This works:
>
> #+begin_src emacs-lisp 
> (message "4") 
> #+end_src
>
> #+RESULTS:
> : 4
>
> Let's enable some more languages:
>
> #+begin_src emacs-lisp 
> (org-babel-do-load-languages
>   'org-babel-load-languages
>   '((emacs-lisp . nil)
> (R . t)
> (sh . t)))
> #+end_src
>
> #+RESULTS:
>
> And try again:
>
> #+begin_src emacs-lisp 
> (message "4") 
> #+end_src
>
> Debugger message:
>
> Debugger entered--Lisp error: (void-function org-babel-get-header)
>   org-babel-get-header(((:colname-names) (:rowname-names) (:result-params 
> "replace" "replace") (:result-type . value) (:comments . "") (:shebang . "") 
> (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . "no") (:exports . 
> "code") (:results . "replace") (:session . "none") (:hlines . "no")) :var)
>   org-babel-variable-assignments:sh(((:colname-names) (:rowname-names) 
> (:result-params "replace" "replace") (:result-type . value) (:comments . "") 
> (:shebang . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . 
> "no") (:exports . "code") (:results . "replace") (:session . "none") (:hlines 
> . "no")))
>   org-babel-execute:sh("echo 4" ((:colname-names) (:rowname-names) 
> (:result-params "replace" "replace") (:result-type . value) (:comments . "") 
> (:shebang . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . 
> "no") (:exports . "code") (:results . "replace") (:session . "none") (:hlines 
> . "no")))
>   funcall(org-babel-execute:sh "echo 4" ((:colname-names) (:rowname-names) 
> (:result-params "replace" "replace") (:result-type . value) (:comments . "") 
> (:shebang . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle . 
> "no") (:exports . "code") (:results . "replace") (:session . "none") (:hlines 
> . "no")))
>   (let ((result (funcall cmd body params))) (if (and (eq (cdr (assoc 
> :result-type params)) (quote value)) (or (member "vector" result-params) 
> (member "table" result-params)) (

[O] Bug: can not evaluate any code blocks after enabling additional languages [8.3.4 (release_8.3.4-639-gd5a603 @ /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)]

[Rainer M Krug]

 C-c can do nothing useful at 
this location")) (let* ((context (org-element-context)) (type (org-element-type 
context))) (cond ((eql type (quote link)) (setq context (org-element-property 
:parent context)) (setq type (org-element-type context))) ((memql type (quote 
...)) (setq context (org-element-lineage context ... (if (eq type (quote 
paragraph)) (progn (let (...) (if ... ... (cond ((eql type (quote clock)) 
(org-clock-update-time-maybe)) ((eql type (quote dynamic-block)) 
(save-excursion (goto-char ...) (org-update-dblock))) ((eql type (quote 
footnote-definition)) (goto-char (org-element-property :post-affiliated 
context)) (call-interactively (quote org-footnote-action))) ((eql type (quote 
footnote-reference)) (call-interactively (quote org-footnote-action))) ((memql 
type (quote ...)) (save-excursion (goto-char ...) (call-interactively ...))) 
((eql type (quote item)) (let* (... ... ... ... ... ...) (org-list-set-checkbox 
... struct ...) (org-list-struct-fix-ind struct parents 2) 
(org-list-struct-fix-item-end struct) (org-list-struct-fix-bul struct prevs) 
(org-list-struct-fix-ind struct parents) (let ... ... ...))) ((eql type (quote 
keyword)) (let (... ...) (if ... ...) (let ... ... --rtn)) (message "Local 
setup has been refreshed")) ((eql type (quote plain-list)) (let* (... ... ... 
... ... ...) (cond ... ...) (org-list-write-struct struct ... old-struct) 
(org-update-checkbox-count-maybe) (save-excursion ... ...))) ((memql type 
(quote ...)) (call-interactively (quote org-property-action))) ((memql type 
(quote ...)) (call-interactively (quote org-update-radio-target-regexp))) ((eql 
type (quote statistics-cookie)) (call-interactively (quote 
org-update-statistics-cookies))) ((memql type (quote ...)) (if (eq ... ...) 
(message "%s" ...) (let ... ...))) ((eql type (quote timestamp)) 
(org-timestamp-change 0 (quote day))) (t (or (run-hook-with-args-until-success 
...) (user-error "C-c C-c can do nothing useful at this location"
  org-ctrl-c-ctrl-c(nil)
  funcall-interactively(org-ctrl-c-ctrl-c nil)
  call-interactively(org-ctrl-c-ctrl-c nil nil)
  command-execute(org-ctrl-c-ctrl-c)


Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

 http://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org-mode mailing list.



Emacs  : GNU Emacs 25.0.92.1 (x86_64-apple-darwin15.3.0, NS appkit-1404.34 
Version 10.11.3 (Build 15D21))
 of 2016-03-07
Package: Org-mode version 8.3.4 (release_8.3.4-639-gd5a603 @ 
/Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)




-- 
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


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Re: [O] org-file using tramp + babel?

[Rainer M Krug]

"Charles C. Berry" <ccbe...@ucsd.edu> writes:

> On Thu, 14 Jan 2016, John Kitchin wrote:
>
>> Hi, I opened an org file using tramp on a remote server. It opened fine,
>> and I had no trouble writing text and saving it. For fun I tried running
>> a src block (a shell block that just returned the hostname), and got
>> this error:
>>
>>> %s'...failed
>> tramp-file-name-handler: Couldn't write region to
>> `/scp:jkitc...@gilgamesh.cheme.cmu.edu:/var/folders/5q/lllv2yf95hg_n6h6kjttbmdwgn/T/ob-input-30024dza',
>> decode using `base64 -d -i >%s' failed
>>
>> Should this have worked? It looks like it tried to write a local path
>> from my Mac to the server, and that path doesn't exist there.
>
> This works for me from my mac on a remote Centos system.
>
> I think this tripped me up in the past, but my notes do not reveal the fix 
> I used.
>
> I think this is a temporary-file-directory issue, but nothing in my init 
> pertains to that variable or tramp.
>
> In my emacs-init.org, I do have
>
> #+BEGIN_SRC emacs-lisp
> (setq default-directory "/Users/cberry/")
> #+END_SRC

I tried this as I have the same error messages as the John and opened a
flie in tramp afterwards. (I did set the variable in a running emacs
session and did not restart).

>
> and I see a lot of references to this in tramp-compat.el. So, maybe 
> setting it is enough to get emacs and/or tramp to use my local client for 
> temp files.
>
> In *Messages* I see this after running the src block:
>
> Evaluate this shell code block on your system? (y or n) y
> executing Shell code block...
> Tramp: Encoding local file 
> `/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/tramp.560h4h' using 
> `base64-encode-region'...done
> Tramp: Decoding remote file `/scp::/tmp/ob-input-560Uub' 
> using `base64 -d -i >%s'...done
> Tramp: Encoding local file 
> `/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/tramp.5607Mu' using 
> `base64-encode-region'...done
> Tramp: Decoding remote file `/scp::/tmp/ob-error-560uCo' 
> using `base64 -d -i >%s'...done
> ...

I get:

,
| Tramp: Encoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.81150IIU' using 
`base64-encode-region'...done
| Tramp: Decoding remote file `/scp:pogoplug:/tmp/sh-script-8115079N' using 
`base64 -d -i >%s'...done
| Tramp: Encoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.81150VSa' using 
`base64-encode-region'...done
| Tramp: Decoding remote file `/scp:pogoplug:/tmp/sh-script-8115079N' using 
`base64 -d -i >%s'...done
| Tramp: Encoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.81150vmm' using 
`base64-encode-region'...done
| Tramp: Decoding remote file `/scp:pogoplug:/tmp/ob-input-81150icg' using 
`base64 -d -i >%s'...done
| Tramp: Encoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.81150J7y' using 
`base64-encode-region'...done
| Tramp: Decoding remote file `/scp:pogoplug:/tmp/ob-error-811508ws' using 
`base64 -d -i >%s'...done
| Tramp: Encoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.811507EC' using 
`base64-encode-region'...done
| Tramp: Decoding remote file `/scp:pogoplug:/tmp/ob-input-81150icg' using 
`base64 -d -i >%s'...done
| Wrote /scp:pogoplug:/tmp/ob-input-81150icg
| Tramp: Inserting `/scp:pogoplug:/tmp/ob-error-811508ws'...
| Tramp: Encoding remote file `/scp:pogoplug:/tmp/ob-error-811508ws' with 
`base64 <%s'...done
| Tramp: Decoding local file 
`/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/tramp.81150IPI' with 
`base64-decode-region'...done
| Tramp: Inserting `/scp:pogoplug:/tmp/ob-error-811508ws'...done
| Babel evaluation exited with code 1
| Code block produced no output.
`

So there is still a reference to an remote directory.

and I still get the error:

,
| /bin/sh: 1: /scp:pogoplug:/tmp/sh-script-81150VZO: not found
`


>
>
> and when I issue `C-h v temporary-file-directory RET' in the buffer of the 
> remote file,
> I get the same `/var/folders/...' which is what `echo $TMPDIR' shows locally.

Here I have:

,
| Its value is "/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/"
`

Also on Mac, remote is Debian.

Cheers,

Rainer

>
> HTH,
>
> Chuck
>
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] org-file using tramp + babel?

[Rainer M Krug]

Martin Yrjölä <martin.yrj...@gmail.com> writes:

> Hi John,
>
> John Kitchin <jkitc...@andrew.cmu.edu> writes:
>
>> Hi, I opened an org file using tramp on a remote server. It opened fine,
>> and I had no trouble writing text and saving it. For fun I tried running
>> a src block (a shell block that just returned the hostname), and got
>> this error:
>>
>>>%s'...failed
>> tramp-file-name-handler: Couldn't write region to
>> `/scp:jkitc...@gilgamesh.cheme.cmu.edu:/var/folders/5q/lllv2yf95hg_n6h6kjttbmdwgn/T/ob-input-30024dza',
>> decode using `base64 -d -i >%s' failed
>>
>> Should this have worked? It looks like it tried to write a local path
>> from my Mac to the server, and that path doesn't exist there.
>>
>> Some details (not sure they are relevant):
>> I am running Emacs on a Mac, and opened a file on a remote Centos5
>> server.
>
> Howard Abrams has written an extensive answer to this problem in his
> blog [1]. The problem is that the Mac uses a different folder for
> temporary files. Howard also proposes a fix and refers to a mailing list
> message regarding the bug [2].

I think it would be nice if one could find a fix for this in org.

>
> Hope this helps,
> Martin
>
> [1] http://www.howardism.org/Technical/Emacs/literate-devops.html#fn.2
> [2] http://lists.gnu.org/archive/html/emacs-orgmode/2013-09/msg00992.html
>
>

-- 
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982


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Re: [O] For Org, numbered backups or version control? Which settings?

[Rainer M Krug]

Envoyé de mon iPhone

> Le 28 déc. 2015 à 13:47, Jorge  a écrit :
> 
> Hi.  My ~/org folder, with its sub directories, has a total of 13 .org
> files.  Five of them are agenda files.  I set up numbered backup, with
> the backups going to a separate directory: ~/auto-backups.  For the
> most important org files, I raised the number of numbered backups
> kept.  For example, my biggest org file has the following local
> variables:
>  - Local variables:
>  - auto-save-interval: 150
>  - version-control: t
>  - kept-new-versions: 80
>  - End:
> 
> I sincronize both ~/org and ~/auto-backups to a cloud syncing service.
> ~/auto-backups now is 97MiB, about 2% of my 5.5GiB cloud quota.
> 
> Do you recommend keeping my current setup?  Or should I adopt some
> version control system to have better history (right now I save only
> the latest 80 versions, and Emacs saves a new backup only on the Emacs
> session's first save)?
> 

I would look into hit for version control. This would give you more control and 
no limit for the number of versions. 

Re: [O] blog refurbised: how is it in 2015 ?

[Rainer M Krug]

Xavier Maillard <xav...@maillard.im> writes:

> Hey,
>
> in the same vein I am refurbishing my Gnus (and love it), I'd like, as a 2k16
> resolution (right word in english ?), to restart my long abandoned blog. As
> usual, this is something I can't imagine doing outside GNU emacs and thus
> orgmode.

agreed - blogging from org is very nice.

I should do the same!

>
> My question is simply: what are the tools/technics in 2015 to blog ? Can you
> share some good recipes with me ?

It depends where your blog is managed. If you are using wordpress, I can
suggest org2blog - very nice to manage your posts there.

Cheers,

Rainer



>
> Thank you
>
> -- Xavier.

-- 
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email: Rainerkrugsde
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Re: [O] README for bitbucket - export to which format?

[Rainer M Krug]

Grant Rettke <g...@wisdomandwonder.com> writes:

> On Fri, Dec 4, 2015 at 6:38 AM, Rainer M Krug <rai...@krugs.de> wrote:
>
> Most Git sites using the Github Flavored Markdown, and there is a
> package for that in contrib: =ox-gfm=
>
> http://orgmode.org/cgit.cgi/org-mode.git/plain/contrib/lisp/ox-gfm.el

Thanks - good to know, but I decided to move to gitlab.

Cheers,

Rainer
-- 
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email: Rainerkrugsde
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[O] README for bitbucket - export to which format?

[Rainer M Krug]

Hi

There are many formats available for READMEs on bitbucket, but
unfortunately not org mode (I am staying on bitbucket for private repos
and move them to github as soon as they can be made public - matter of
finances).

So what is the best export format from org for bitbucket READMEs? At the
moment I am using text (UTF8) Which works, but I would like to have
syntax highlighting and clickable links?

Thanks,

Rainer

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

Centre of Excellence for Invasion Biology
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Re: [O] README for bitbucket - export to which format?

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> There are many formats available for READMEs on bitbucket, but
>> unfortunately not org mode (I am staying on bitbucket for private repos
>> and move them to github as soon as they can be made public - matter of
>> finances).
>
> You could try Gitlab.  It supports Org.

Interesting - looks like a alternative. Are there any other advantages
over BitBucket?

>
>> So what is the best export format from org for bitbucket READMEs? At the
>> moment I am using text (UTF8) Which works, but I would like to have
>> syntax highlighting and clickable links?
>
> Probably Rst or markdown...

I am using markdown - works, although I have to disable the toc.

Thanks,

Rainer
>
> Rasmus

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

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Re: [O] README for bitbucket - export to which format?

[Rainer M Krug]

Jeroen Tiebout <jer...@tinktenk.be> writes:

> As far as I know markdown is the de facto standard for readme files on
> both GitHub and BitBucket.
> Org exporter does a fine job of translating your org file to .md

Thanks - I tried it before and it did not work, =but I realized that the
toc was the problem. disabled toc export and it works fine.

Thanks,

Rainer

>
> Hope that helps.
>
> Jeroen
>
> On Friday 2015-12-04 13:38:47 CET, Rainer M Krug <rai...@krugs.de> wrote:
>
>> Hi
>>
>> There are many formats available for READMEs on bitbucket, but
>> unfortunately not org mode (I am staying on bitbucket for private repos
>> and move them to github as soon as they can be made public - matter of
>> finances).
>>
>> So what is the best export format from org for bitbucket READMEs? At the
>> moment I am using text (UTF8) Which works, but I would like to have
>> syntax highlighting and clickable links?
>>
>> Thanks,
>>
>> Rainer
>

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

Centre of Excellence for Invasion Biology
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Re: [O] Jumping between source blocks in a file

[Rainer M Krug]

Rainer M Krug <rai...@krugs.de> writes:

> Andreas Leha <andreas.l...@med.uni-goettingen.de> writes:
>
>> Hi Andrew,
>>
>> Martin Yrjölä <martin.yrj...@gmail.com> writes:
>>> Hi Andrew!
>>>
>>> Andrew Kirkpatrick writes:
>>>
>>>> If this is deemed useful, I'm happy to make changes suitable for
>>>> inclusion in the project.
>>>
>>> Thanks for sharing! I would certainly want these functions included in
>>> org-mode by default. They streamline at least my literate programming
>>> workflow substantially.
>>>
>>
>> Sorry for joining late.  I too find these useful.
>
> Absolutely - very useful. Please include!
>>
>> (Also useful would be the possibility to jump to noweb references
>> directly from the src buffer...)
>
> Very nice idea indeed - or possibly even expand them when executing? But
> I think this would be a job for the mode in the source buffer...

Actually, expand them when opening the Source Buffer (C-c ') and
possibly update them when closing?

>
> At the moment, these noweb references are very nice, but not so nice when
> debugging a source block where they are used.
>
> Cheers,
>
> Rainer
>
>>
>> Regards,
>> Andreas
>>
>>
>>

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

Centre of Excellence for Invasion Biology
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Re: [O] Jumping between source blocks in a file

[Rainer M Krug]

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

> Rainer M Krug <rai...@krugs.de> writes:
>> Rainer M Krug <rai...@krugs.de> writes:
>>
>>> Andreas Leha <andreas.l...@med.uni-goettingen.de> writes:
>>>
>>>> Hi Andrew,
>>>>
>>>> Martin Yrjölä <martin.yrj...@gmail.com> writes:
>>>>> Hi Andrew!
>>>>>
>>>>> Andrew Kirkpatrick writes:
>>>>>
>>>>>> If this is deemed useful, I'm happy to make changes suitable for
>>>>>> inclusion in the project.
>>>>>
>>>>> Thanks for sharing! I would certainly want these functions included in
>>>>> org-mode by default. They streamline at least my literate programming
>>>>> workflow substantially.
>>>>>
>>>>
>>>> Sorry for joining late.  I too find these useful.
>>>
>>> Absolutely - very useful. Please include!
>>>>
>>>> (Also useful would be the possibility to jump to noweb references
>>>> directly from the src buffer...)
>>>
>>> Very nice idea indeed - or possibly even expand them when executing? But
>>> I think this would be a job for the mode in the source buffer...
>>
>> Actually, expand them when opening the Source Buffer (C-c ') and
>> possibly update them when closing?
>>
>
> This might conflict with open Source Buffers for the referenced code
> block.

True - than simply deliminate them with something like

## <> BEGIN
...
## <> END

and *don't* update them at the end?

Probably better: language specific - for R one could write the block to
a temporary file and then insert a =source()= to execute it:


## DO NOT EDIT - AUTO INSERTED - BEGIN
source("<>.R")
## DO NOT EDIT - AUTO INSERTED - END

Would make debugging much easier, if they would be in the source block
where they are used.

And if no language specific behavior is supplied, use the present
behavior.

>
>>>
>>> At the moment, these noweb references are very nice, but not so nice when
>>> debugging a source block where they are used.
>
> Exactly.

Let's do some brainstorming how this could be solved.

Cheers,

Rainer

>
> Regards,
> Andreas
>
>

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

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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Re: [O] Jumping between source blocks in a file

[Rainer M Krug]

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

> Hi Andrew,
>
> Martin Yrjölä <martin.yrj...@gmail.com> writes:
>> Hi Andrew!
>>
>> Andrew Kirkpatrick writes:
>>
>>> If this is deemed useful, I'm happy to make changes suitable for
>>> inclusion in the project.
>>
>> Thanks for sharing! I would certainly want these functions included in
>> org-mode by default. They streamline at least my literate programming
>> workflow substantially.
>>
>
> Sorry for joining late.  I too find these useful.

Absolutely - very useful. Please include!
>
> (Also useful would be the possibility to jump to noweb references
> directly from the src buffer...)

Very nice idea indeed - or possibly even expand them when executing? But
I think this would be a job for the mode in the source buffer...

At the moment, these noweb references are very nice, but not so nice when
debugging a source block where they are used.

Cheers,

Rainer

>
> Regards,
> Andreas
>
>
>

-- 
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
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Re: [O] Latex export: How to handle multiple authors, emails, institutes

[Rainer M Krug]

Envoyé de mon iPhone

> Le 26 nov. 2015 à 16:26, Fatma Başak Aydemir  a écrit :
> 
> Hi all,
> 
> I'm trying to write a conference paper which has multiple authors from 
> multiple institues. I tried to insert author infor by adding the following 
> block
> 
> #+BEGIN_LaTeX
> \author{First Author\inst{1}, Second Author\inst{1}, Third Author\inst{2}}
> \authorrunning{Author et al.}
> \institute{University of X, Country\\
> \email{\{f.author, s.author\}@uX.edu}
> \and
> University of Y, CountryY\\
> \email{\{t.author\}@uY.edu}}
> #+END_LATEX
> 
> I failed (the title says no institute given, does not show emails) since the 
> latex block is inserted after \maketitle command. How can insert author & 
> institue information in the header?
> 

Check the

#+Latx_header:

Directive - it is added line by line to the preamble. 

Cheers, 

Rainer 

> If related, I'm using Springer LNCS style, org v 20151123.
> 
> Best,
> 
> -- 
> 
> Fatma Başak Aydemir
> PhD Student at ICT International Doctoral School
> Department of Information Engineering and Computer Science
> University of Trento
> Skype: fatmabasak.aydemir
> E-mail: ayde...@disi.unitn.it
> 
> 

Re: [O] LATEX text in figure environment

[Rainer M Krug]

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

> Rainer M Krug <rai...@krugs.de> writes:
>> Rasmus <ras...@gmx.us> writes:
>>
>>> Rainer M Krug <rai...@krugs.de> writes:
>>>
>>>> Hi
>>>>
>>>> I want to add a todo note (from the todonotes package) in a figure
>>>> environment. What I want should look as follow, so that the to note sits
>>>> in the environment (based on [http://tex.stackexchange.com/a/256802/6941]
>>>> ):
>>>>
>>>> ,
>>>> | \begin{figure}[htb]
>>>> | \centering
>>>> | \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
>>>> | \caption{from \cite{Roura-Pascual2009_rmkc}}
>>>> | \todo[inline]{This figure needs to be redone and further info added}
>>>> | \end{figure}
>>>> `
>>>
>>> This works up to the order of caption and the todo macro.
>>>
>>> #+caption: from \cite{Roura-Pascual2009_rmkc}
>>> #+begin_figure
>>> [[file:fig-strategies.pdf]]
>>> #+latex: \todo[inline]{This figure needs to be redone and further info 
>>> added}
>>> #+end_figure
>>
>> Thanks,
>>
>> Rainer
>
> Hi Rainer,
>
> And if you do not mind the todonote in the caption (should work, I
> guess) this might work as well:
>
> #+CAPTION: from cite:Roura-Pascual2009_rmkc @@latex:\todo[inline]{This figure 
> needs to be redone and further info added}@@
> [[file:fig-strategies.pdf]]

True - I could use the @@...@@.


Thanks,

Rainer

>
> Best,
> Andreas
>
>
>

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

Centre of Excellence for Invasion Biology
Stellenbosch University
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[O] LATEX text in figure environment

[Rainer M Krug]

Hi

I want to add a todo note (from the todonotes package) in a figure
environment. What I want should look as follow, so that the to note sits
in the environment (based on [http://tex.stackexchange.com/a/256802/6941]
):

,
| \begin{figure}[htb]
| \centering
| \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
| \caption{from \cite{Roura-Pascual2009_rmkc}}
| \todo[inline]{This figure needs to be redone and further info added}
| \end{figure}
`

I tried

--8<---cut here---start->8---
#+LATEX: \todo[inline]{This figure needs to be redone and further info added}
#+CAPTION: from cite:Roura-Pascual2009_rmkc
[[file:fig-strategies.pdf]]
--8<---cut here---end--->8---

but this results in the todo being outside the environment:

,
| \todo[inline]{This figure needs to be redone and further info added}
| \begin{figure}[htb]
| \centering
| \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
| \caption{from \cite{Roura-Pascual2009_rmkc}}
| \end{figure}
`

--8<---cut here---start->8---
#+CAPTION: from cite:Roura-Pascual2009_rmkc
[[file:fig-strategies.pdf]]
#+LATEX: \todo[inline]{This figure needs to be redone and further info added}
--8<---cut here---end--->8---

resulting in the todo being behind the environment and

--8<---cut here---start->8---
#+CAPTION: from cite:Roura-Pascual2009_rmkc
#+LATEX: \todo[inline]{This figure needs to be redone and further info added}
[[file:fig-strategies.pdf]]
--8<---cut here---end--->8---

resulting in no environment at all (as #+CAPTION is not before the
figure).

At the moment I am using


--8<---cut here---start->8---
#+begin_figure
{{{if-latex-else([[file:fig-strategies.pdf]], [[file:fig-strategies.png]])}}}
#+LATEX: \caption{from \cite{Roura-Pascual2009_rmkc}}
#+LATEX: \todo[inline]{This figure needs to be redone and further info added}
#+end_figure
--8<---cut here---end--->8---

which gives me what I want:


,
| \begin{figure}
| \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
| \caption{from \cite{Roura-Pascual2009_rmkc}}
| \todo[inline]{This figure needs to be redone and further info added}
| \end{figure}
`

But it is really not org-ish (caption specified as LaTeX, citation as
latex, environment specified).

Is there a way to achieve this more org like? Am I missing some #+?

Thanks,

Rainer

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

Centre of Excellence for Invasion Biology
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[O] @@latex:...@@ syntax - where can I find info on it?

[Rainer M Krug]

Hi

I read at tha moment a lot of mails here regarding the @@latex:...@@ (or
@@html:...@@) syntax. I understand d=that these fragments are only
inserted when the corresponding backend is used - correct?

Where can I find further information on this? i in the org-info file
does not give anything (except C-@ which is something completely
different) and googling also nothing?

Thanks,

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

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Re: [O] @@latex:...@@ syntax - where can I find info on it?

[Rainer M Krug]

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

> Hi Rainer,
>
> Rainer M Krug <rai...@krugs.de> writes:
>> Hi
>>
>> I read at tha moment a lot of mails here regarding the @@latex:...@@ (or
>> @@html:...@@) syntax. I understand d=that these fragments are only
>> inserted when the corresponding backend is used - correct?
>>
>> Where can I find further information on this? i in the org-info file
>> does not give anything (except C-@ which is something completely
>> different) and googling also nothing?
>>
>
> I am not aware of a central place for this.  But it is mentioned in
> the backend specific manual pages of section 12.  For instance
> [[http://orgmode.org/manual/Quoting-LaTeX-code.html#Quoting-LaTeX-code][Section
> 12.7.4 Quoting LaTeX code]] for the latex case.

Thanks - They should be somewhere listed, as they seem to be a very
useful construct. 

I assume, replacing "latex" with any export backend name (e.g. html or odt), 
will do the
same for the other backend?

Thanks a lot,

Rainer

>
> Best,
> Andreas
>
>

-- 
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

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Re: [O] LATEX text in figure environment

[Rainer M Krug]

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

> Hi Rainer,
>
> Rainer M Krug <rai...@krugs.de> writes:
>> Hi
>>
>> I want to add a todo note (from the todonotes package) in a figure
>> environment. What I want should look as follow, so that the to note sits
>> in the environment (based on [http://tex.stackexchange.com/a/256802/6941]
>> ):
>>
>> ,
>> | \begin{figure}[htb]
>> | \centering
>> | \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
>> | \caption{from \cite{Roura-Pascual2009_rmkc}}
>> | \todo[inline]{This figure needs to be redone and further info added}
>> | \end{figure}
>> `
>>
>> I tried
>>
>> #+LATEX: \todo[inline]{This figure needs to be redone and further info added}
>> #+CAPTION: from cite:Roura-Pascual2009_rmkc
>> [[file:fig-strategies.pdf]]
>>
>>
>> but this results in the todo being outside the environment:
>>
>> ,
>> | \todo[inline]{This figure needs to be redone and further info added}
>> | \begin{figure}[htb]
>> | \centering
>> | \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
>> | \caption{from \cite{Roura-Pascual2009_rmkc}}
>> | \end{figure}
>> `
>>
>> #+CAPTION: from cite:Roura-Pascual2009_rmkc
>> [[file:fig-strategies.pdf]]
>> #+LATEX: \todo[inline]{This figure needs to be redone and further info added}
>>
>>
>> resulting in the todo being behind the environment and
>>
>> #+CAPTION: from cite:Roura-Pascual2009_rmkc
>> #+LATEX: \todo[inline]{This figure needs to be redone and further info added}
>> [[file:fig-strategies.pdf]]
>>
>>
>> resulting in no environment at all (as #+CAPTION is not before the
>> figure).
>>
>> At the moment I am using
>>
>> #+begin_figure
>> {{{if-latex-else([[file:fig-strategies.pdf]], [[file:fig-strategies.png]])}}}
>> #+LATEX: \caption{from \cite{Roura-Pascual2009_rmkc}}
>> #+LATEX: \todo[inline]{This figure needs to be redone and further info added}
>> #+end_figure
>>
>> which gives me what I want:
>>
>>
>> ,
>> | \begin{figure}
>> | \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
>> | \caption{from \cite{Roura-Pascual2009_rmkc}}
>> | \todo[inline]{This figure needs to be redone and further info added}
>> | \end{figure}
>> `
>>
>> But it is really not org-ish (caption specified as LaTeX, citation as
>> latex, environment specified).
>>
>> Is there a way to achieve this more org like? Am I missing some #+?
>>
>
> Does this do what you want?
>
> #+ATTR_LATEX: :caption \caption{from
> cite:Roura-Pascual2009_rmkc}\todo[inline]{This figure needs to be
> redone and further info added}
> [[file:fig-strategies.pdf]]


Yup - partly after removing the line breaks:

,
| \begin{figure}[htb]
| \centering
| \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
| \caption{from cite:Roura-Pascual2009_rmkc} \todo[inline]{This figure needs to 
be redone and further info added}
| \end{figure}
`

The problem is, if I use the org-ref syntax in a latex fragment, it does
not get expanded properly, and the underscore is interpreted as a math symbol.

I now use

--8<---cut here---start->8---
From \protect\cite{Roura-Pascual2009_rmkc
--8<---cut here---end--->8---

as my caption. This works, but is still really LaTeXish (the reference)

Thanks,

Rainer

>
> Best,
> Andreas
>
>

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

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Re: [O] LATEX text in figure environment

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> Hi
>>
>> I want to add a todo note (from the todonotes package) in a figure
>> environment. What I want should look as follow, so that the to note sits
>> in the environment (based on [http://tex.stackexchange.com/a/256802/6941]
>> ):
>>
>> ,
>> | \begin{figure}[htb]
>> | \centering
>> | \includegraphics[width=.9\linewidth]{fig-strategies.pdf}
>> | \caption{from \cite{Roura-Pascual2009_rmkc}}
>> | \todo[inline]{This figure needs to be redone and further info added}
>> | \end{figure}
>> `
>
> This works up to the order of caption and the todo macro.
>
> #+caption: from \cite{Roura-Pascual2009_rmkc}
> #+begin_figure
> [[file:fig-strategies.pdf]]
> #+latex: \todo[inline]{This figure needs to be redone and further info added}
> #+end_figure

Thanks,

Rainer

[...]


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Re: [O] [BUG] in export to odt -

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> I tried in LibreOffice, and indeed it does not seem to be possible. I
>> don't know what the convention is, but I don't like that an invald .odt
>> file is produced. Maybe give a warning about "incompatible features" or
>> just drop the footnote in the footnote?
>
> Dropping it is a possibility, though not a very nice one.

Agreed - for me it doesn't matter anymore, as the footnote in the
footnote was only a TODO reminder.

>
> You can insert a cross-reference to a footnote within a footnote.  But I
> don’t know how to insert a footnote without also adding a reference in the
> text.  If the latter is possible, that way should work.

This sounds like the way to go, but I would suggest that until there is
a solution (for this apparently not supported feature in LibreOffice?)
to either drop the footnote and give a warning in emacs, or insert the
footnote text in the footnote as verbatim text.

Cheers,

Rainer

>
> Rasmus

-- 
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[O] [odt-export] Setting Text Colour for odt export

[Rainer M Krug]

Hi

I am using 

--8<---cut here---start->8---
\color{red} some red text \color{black} and we continue with black
--8<---cut here---end--->8---

to set the text colour for sections in my document for LaTeX export, but
this does obviously does not org for odt export.

What can I use to achieve the same for odt export?

Thanks

Rainer
-- 
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UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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Re: [O] [odt-export] Setting Text Colour for odt export

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Hi,
>
> Rainer M Krug <rai...@krugs.de> writes:
>
>> I am using 
>>
>> \color{red} some red text \color{black} and we continue with black
>>
>> to set the text colour for sections in my document for LaTeX export, but
>> this does obviously does not org for odt export.
>>
>> What can I use to achieve the same for odt export?
>
> You can use a macro.  {{{color(text, red)}}}.  You then specify a macro
> that inserts
>
>  @@latex:{\color{red} text}odt: text:style-name="red">text@@,
OK - that looks nice. Where can I read more about the @@...@@ syntax in
org? For conditional backend specific syntax I was only using

--8<---cut here---start->8---
#+MACRO: clearpage (eval (if (org-export-derived-backend-p 
org-export-current-backend 'latex) "\\clearpage"""   ))
--8<---cut here---end--->8---

but the @@...@@ looks clearer to me.

>
> Unfortunately, it doesn’t seem like odt provides inline styles, so you may
> have to add new styles for each color; see:
>
> 
> https://www.gnu.org/software/emacs/manual/html_node/org/Creating-one_002doff-styles.html

Hm. This sounds problematic, as I have to convert these to docx and send
them finally to the co-authors.

At the moment odt export just inserts "\color{red}" so I'll leave it
for this at the moment.

Thanks,

Rainer

>
> Hope it helps,
> Rasmus

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

Centre of Excellence for Invasion Biology
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Re: [O] [BUG] in export to odt -

[Rainer M Krug]

Rasmus <ras...@gmx.us> writes:

> Rainer M Krug <rai...@krugs.de> writes:
>
>> The odt is attached for reference.
>
> Please also provide an odt document with the expected, working result.
> (I could not produce such a document in LO within 20s, but perhaps it’s
> possible).

I am not a LibreOffice / MS Word person (but my co-authors but my
co-authors unfortunately are...) so I only stumbled upon this when was
asked to give them a docx... file.

I tried in LibreOffice, and indeed it does not seem to be possible. I
don't know what the convention is, but I don't like that an invald .odt
file is produced. Maybe give a warning about "incompatible features" or
just drop the footnote in the footnote?

Thanks,

Rainer

>
> Thanks,
> Rasmus

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

Centre of Excellence for Invasion Biology
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[O] [BUG] in export to odt -

[Rainer M Krug]

The following .org file produces an invalid .odt file upon export to odt
because of the footnote in the footnote:

--8<---cut here---start->8---
#+TITLE: Footnote in footnote produces invalid .odt
#+AUTHOR: Rainer M. Krug

* A Footnote in a Footnote
Some footnote[fn:2]

* Versions
Org-mode version 8.3.2 (release_8.3.2-161-gd2ac25 @ 
/Users/rainerkrug/.emacs.d/elpa/24.5/org-20151005/)
GNU Emacs 24.5.1 (x86_64-apple-darwin15.0.0, Carbon Version 157 AppKit 1404.13) 
of 2015-11-03 on Rainers-MacBook-Pro.local
Libre Office: Version: 5.0.3.2
  Build ID: e5f16313668ac592c1bfb310f4390624e3dbfb75
  Locale: en-US (en.UTF-8)

* FOOTNOTES

[fn:2] Footnote 2[fn:1]

[fn:1] CHECK!
--8<---cut here---end--->8---

The odt is attached for reference.


Cheers,

Rainer



test.odt
Description: Binary data




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UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
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Re: [O] Org and Citations / References / Bibliography

[Rainer M Krug]

John Kitchin <jkitc...@andrew.cmu.edu> writes:

> Can you send me a minimal org and bib file you are using that doesn't
> work, and how you have it set up?
>
> Does helm-bibtex work for you?
>
> We use org-ref on a daily basis, so it should work.

It does now. I went through the setup process slowly again using the
README.org and the org-ref.org in
[[https://github.com/jkitchin/org-ref]] as guidelines and it worked.

But I could not install any of the "useful libraries", as none of them
seems to be on melpa et al?

Thanks a lot - and org-ref looks really great.

Cheers,

Rainer


P.S.:

Just for reference: I now have the following in my emacs.org file:

*** org-ref
See [[https://www.youtube.com/watch?v=JyvpSVl4_dg][org-ref video]] and 
[[https://github.com/jkitchin/jmax/blob/master/org-ref.org][org-rel github 
site]] for further details (John Kitchin)
#+begin_src emacs-lisp
(use-package ebib
  :ensure t
  )
(use-package dash
  :ensure t
  )
(use-package s
  :ensure t
  )
(use-package f
  :ensure t
  )
(use-package hydra
  :ensure t
  )
(use-package org-ref
  :ensure f
  :load-path "~/.emacs.d/org-ref"
  :config
  ;; README.org in org-ref repo for the why
  (setq reftex-default-bibliography '("~/Documents/Mendeley/bibliography.bib"))
  ;;
  ;; see org-ref for use of these variables
  (setq org-ref-bibliography-notes "~/Documents/Mendeley/notes.org"
org-ref-default-bibliography '("~/Documents/Mendeley/bibliography.bib")
org-ref-pdf-directory "~/iCloud/Mendeley/")
  ;;
  (setq helm-bibtex-bibliography "~/.emacs.d/org-ref/test.bib")
  (setq helm-bibtex-library-path "~/Dropbox/bibliography/bibtex-pdfs")
  ;;
  ;; open pdf with system pdf viewer (works on mac)
  (setq helm-bibtex-pdf-open-function
(lambda (fpath)
  (start-process "open" "*open*" "open" fpath)))
  
  ;; :bind
  ;; You may want to set some convenient keys for working in your bibtex file:
  ;; ("f10" . org-ref-open-bibtex-notes)
  ;; ("f11" . org-ref-open-bibtex-pdf)
  ;; ("f12" . org-ref-open-in-browser)
  )
;; optional but very useful libraries in org-ref
(use-package doi-utils
  :disabled t
  :ensure t
  )
(use-package jmax-bibtex
  :disabled t
  :ensure t
  )
(use-package pubmed
  :disabled t
  :ensure t
  )
(use-package arxiv
  :disabled t
  :ensure t
  )
(use-package sci-id
  :disabled t
  :ensure t
  )
#+end_src

>
> Rainer M Krug writes:
>
>> Hi
>>
>> I have been following the whole discussion about the implementation of a
>> good citation system in org, which is really necessary.
>>
>> At the moment I am again at that point where I would like to include
>> citations in a document and I don't get any citation system to work -
>> neither org-ref[1] nor org's org-reftex-citation nor reftex
>> citation. None of these find anything in a .bib file, I have no overview
>> where I have to specify the bib file and I am frustrated, because it
>> worked some months ago.
>>
>> I would very much like to use org-ref, but I don't even get the supplied
>> examples to work, i.e. find something from the .bib file.
>>
>> Any suggestions what I can do, any simple / minimalistic init.el file
>> which I can merge into my config?
>>
>> Thanks,
>>
>> Rainer
>>
>>
>> Footnotes:
>> [1]  
>> http://kitchingroup.cheme.cmu.edu/blog/2014/05/13/Using-org-ref-for-citations-and-references/
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

-- 
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
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Fax :   +33 - (0)9 58 10 27 44

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Re: [O] Org and Citations / References / Bibliography

[Rainer M Krug]

John Kitchin <jkitc...@andrew.cmu.edu> writes:

> Rainer M Krug writes:
>
>> It does now. I went through the setup process slowly again using the
>> README.org and the org-ref.org in
>> [[https://github.com/jkitchin/org-ref]] as guidelines and it worked.
>>
>> But I could not install any of the "useful libraries", as none of them
>> seems to be on melpa et al?
>
> These should all be in the org-ref distribution, so if you have that in
> your load-path it should work, or add something like   :load-path
> "~/.emacs.d/org-ref" to the optional libaries too.


OK - I had to install key-chord as it is a dependency from jmax-bibtex.
Thanks.

>
> Thanks for sharing your setup. I have not used use-package much, but
> yours looks pretty clean!

Pleasure - that is the reason I started migrating to use-package - its
clean structure and the ability to disable packages by simply adding

,
| :disalbled t
`

and to install via the package manager by adding

,
| :ensure t
`

I am still struggling with larger configurations (like org-mode and ESS, which
have different sections in my emacs.org), but I am getting there.

Cheers,

Rainer

PS: I started using your link for TODO
[[http://kitchingroup.cheme.cmu.edu/blog/2015/04/24/Commenting-in-org-files/]]
and export to todonotes in LaTeX - very nice! 

>
>>
>> Thanks a lot - and org-ref looks really great.
>>
>> Cheers,
>>
>> Rainer
>>
>>
>> P.S.:
>>
>> Just for reference: I now have the following in my emacs.org file:
>>
>> *** org-ref
>> See [[https://www.youtube.com/watch?v=JyvpSVl4_dg][org-ref video]] and 
>> [[https://github.com/jkitchin/jmax/blob/master/org-ref.org][org-rel github 
>> site]] for further details (John Kitchin)
>> #+begin_src emacs-lisp
>> (use-package ebib
>>   :ensure t
>>   )
>> (use-package dash
>>   :ensure t
>>   )
>> (use-package s
>>   :ensure t
>>   )
>> (use-package f
>>   :ensure t
>>   )
>> (use-package hydra
>>   :ensure t
>>   )
>> (use-package org-ref
>>   :ensure f
>>   :load-path "~/.emacs.d/org-ref"
>>   :config
>>   ;; README.org in org-ref repo for the why
>>   (setq reftex-default-bibliography 
>> '("~/Documents/Mendeley/bibliography.bib"))
>>   ;;
>>   ;; see org-ref for use of these variables
>>   (setq org-ref-bibliography-notes "~/Documents/Mendeley/notes.org"
>> org-ref-default-bibliography 
>> '("~/Documents/Mendeley/bibliography.bib")
>> org-ref-pdf-directory "~/iCloud/Mendeley/")
>>   ;;
>>   (setq helm-bibtex-bibliography "~/.emacs.d/org-ref/test.bib")
>>   (setq helm-bibtex-library-path "~/Dropbox/bibliography/bibtex-pdfs")
>>   ;;
>>   ;; open pdf with system pdf viewer (works on mac)
>>   (setq helm-bibtex-pdf-open-function
>> (lambda (fpath)
>>   (start-process "open" "*open*" "open" fpath)))
>>
>>   ;; :bind
>>   ;; You may want to set some convenient keys for working in your bibtex 
>> file:
>>   ;; ("f10" . org-ref-open-bibtex-notes)
>>   ;; ("f11" . org-ref-open-bibtex-pdf)
>>   ;; ("f12" . org-ref-open-in-browser)
>>   )
>> ;; optional but very useful libraries in org-ref
>> (use-package doi-utils
>>   :disabled t
>>   :ensure t
>>   )
>> (use-package jmax-bibtex
>>   :disabled t
>>   :ensure t
>>   )
>> (use-package pubmed
>>   :disabled t
>>   :ensure t
>>   )
>> (use-package arxiv
>>   :disabled t
>>   :ensure t
>>   )
>> (use-package sci-id
>>   :disabled t
>>   :ensure t
>>   )
>> #+end_src
>>
>>>
>>> Rainer M Krug writes:
>>>
>>>> Hi
>>>>
>>>> I have been following the whole discussion about the implementation of a
>>>> good citation system in org, which is really necessary.
>>>>
>>>> At the moment I am again at that point where I would like to include
>>>> citations in a document and I don't get any citation system to work -
>>>> neither org-ref[1] nor org's org-reftex-citation nor reftex
>>>> citation. None of these find anything in a .bib file, I have no overview
>>>> where I have to specify the bib file and I am frustrated, because it
>>>> worked some months ago.
>>>>
>>>> I would very much like to use org-ref, but I don't even get the supplied
>>>> example

Re: [O] Combine tables which are results from calculations?

[Rainer M Krug]

Rick Frankel <r...@rickster.com> writes:

> On Wed, Nov 04, 2015 at 10:03:48AM +0100, Rainer M Krug wrote:
>> Rick Frankel <r...@rickster.com> writes:
>>
>> > On Tue, Nov 03, 2015 at 02:18:05PM +0100, Rainer M Krug wrote:
>> >> Hi
>> >>
>> >> Considering the following example:
>> >
>> > here's a way to do it in ruby. There is probably a way in {emacs,cl}-lisp, 
>> > but
>> > I'm not sure how...
>> >
>> > #+BEGIN_SRC ruby :var a=t1[,0] b=t2[,0] c=t3[,0] :colnames '(a b c)
>> >   r = [a, b, c]
>> >   len = r.collect(&:length).max
>> >   r.each { |l| l.fill('', l.length, len - l.length) }
>> >   a.zip(b, c)
>> > #+END_SRC
>>
>> Thanks - I'll look into this and see if I can do something similar in R
>> or elisp.
>
> Here's a elisp version:
>
> * zip lists
> #+name: a
> | a |
> |---|
> | 1 |
> | 2 |
>
>
> #+name: b
> | b |
> |---|
> | 4 |
> | 5 |
> | 6 |
> | 7 |
> | 8 |
>
> #+name: c
> |  c |
> ||
> |  9 |
> | 10 |
> | 11 |
>
> #+BEGIN_SRC emacs-lisp :var a=a[,0] b=b[,0] c=c[,0] :colnames '(a b c)
>   (let*  ((l (list a b c))
>   (max (apply #'max (mapcar #'length l
> (apply
>  #'mapcar* #'list
>  (mapcar (lambda (x) (append x (make-list (- max (length x)) ""))) l)))
> #+END_SRC

Thanks a lot - I think this should possibly go ito worg?

I'll keep it for reference as I implemented the whole layouting in R.

Thanks,

Rainer

>
>
> rick
>
> Note: previous reply was not to list (whoops) CC'ing the list on this so the
> answer is saved for posterity :).

-- 
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
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Re: [O] Wrong results from R source block when returning a list

[Rainer M Krug]

"Charles C. Berry" <ccbe...@ucsd.edu> writes:

> On Tue, 3 Nov 2015, Rainer M Krug wrote:
>
>> Hi
>>
>> The following code block returns a wrong table / list:
>>
>>
>> #+begin_src R :results value list
>> list(1:10, 1:5)
>> #+end_src
>>
>> #+RESULTS:
>> - (1 1)
>> - (2 2)
>> - (3 3)
>> - (4 4)
>> - (5 5)
>> - (6 1)
>> - (7 2)
>> - (8 3)
>> - (9 4)
>> - (10 5)
>>
>> The result is actually in R:
>
>
> In particular in `org-babel-R-write-object-command' which uses
> write.table() which uses as.data.frame() which dispatches to
> as.data.frame.list() which calls data.frame() where the recycling
> occurs.

Thanks for this info - I thought something along these lines, but this
makes it clear why.

>
> [snip]
>
>> I have no idea if this is a bug or wrong result due to incompatible
>> types (R list and org table)?
>
> If you can't coerce a non-atomic R object to a data.frame and get a
> pleasing result, you need to craft your own solution.

Yup - I did it in R

>
>>
>> Is this mentioned in the manual?
>
> Not that I know of. A comment in `Results Types' in ob-doc-R -
>
> http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html#orgheadline6
>
> - might be helpful.

Yes - thanks,

Rainer

>
> Chuck

-- 
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
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[O] Org and Citations / References / Bibliography

[Rainer M Krug]

Hi

I have been following the whole discussion about the implementation of a
good citation system in org, which is really necessary.

At the moment I am again at that point where I would like to include
citations in a document and I don't get any citation system to work -
neither org-ref[1] nor org's org-reftex-citation nor reftex
citation. None of these find anything in a .bib file, I have no overview
where I have to specify the bib file and I am frustrated, because it
worked some months ago.

I would very much like to use org-ref, but I don't even get the supplied
examples to work, i.e. find something from the .bib file.

Any suggestions what I can do, any simple / minimalistic init.el file
which I can merge into my config?

Thanks,

Rainer


Footnotes: 
[1]  
http://kitchingroup.cheme.cmu.edu/blog/2014/05/13/Using-org-ref-for-citations-and-references/

-- 
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

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