Re: [O] [RFC] Org linting library

2015-05-21 Thread Rainer M Krug
Nicolas Goaziou m...@nicolasgoaziou.fr writes:

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

 There is an example where I get the error:

 * Fitting the kernel to the data
 The parameter which will be fitted can be found in Table [[tab:fitInitial]]

 #+CAPTION: Variables used for the initial fit of the wind profile using the 
 function and the initial values.
 #+LABEL: tab:fitInitial
 | variable   | initial value | remark
|
 |+---+--|

 The cause is the link [[tab:initial]] If I remove everything below and
 including the line #+CAPTION the linting works.

 Fixed. Thank you.


Thanks.

Two more questions:

I get the following warnings:

,
| 10 low   Unknown OPTIONS item @
| 11 low   Unknown OPTIONS item skip
| 11 low   Unknown OPTIONS item LaTeX
| 11 low   Unknown OPTIONS item TeX
`

based on the following lines:

,
| #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:nil -:t f:t *:t :t
| #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
`

The file is not that old - but have these options changed?


and I get

,
|   1821 low   Orphaned affiliated keyword: RESULTS
`

caused by an orphaned

,
| #+RESULTS:
`

But these are created by evaluating a code block which produced no
results - so they are a valid part of the document?

And an error:

I get, in the same document I got the other errors, the following error:

,
| Org linting process starting...
| org-split-string: Wrong type argument: stringp, 292
`

The backtrace is huge - how can I produce a usable backtrace?

Hope this helps,

Rainer



 Regards,

-- 
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] position figures side by side in PDF output

2015-05-21 Thread Zhihao Ding
Thanks a lot Andreas and Rasmus! 
The solution using the subcaption package works best for me. 

Best, 
Zhihao



 On 20 May 2015, at 22:03, Andreas Leha andreas.l...@med.uni-goettingen.de 
 wrote:
 
 Hi Zhihao,
 
 Rasmus ras...@gmx.us writes:
 Hi Zhihao,
 
 Zhihao Ding zhihao.d...@imm.ox.ac.uk writes:
 
 Could anyone give me some advice on how to position figures side by side in 
 PDF output?
 I am trying to write a report, while my figures were all originally 
 produced individually.  I’d like 
 to put them, mostly two, sometimes three, side by side sharing a same 
 caption and label. 
 Below is the syntax I am using now, which can only do one figure. 
 
 Does this thread answer your question?  It would give you individual
 subcaptions, but you need not use them.
 
 https://lists.gnu.org/archive/html/emacs-orgmode/2014-11/msg00548.html
 
 Otherwise you could use e.g. imagemagick to stick together figures.
 
 
 As an alternative you could use a table.
 + easy
 + orgmode only (should work across backends)
 - no scaling of images
 - it is a table for latex (i.e. will appear in list of tables, etc.)
 
 Here is a short example for the table approach and an imagemagick-based
 solution as proposed by Rasmus.
 
 
 --8---cut here---start-8---
 * generate images:noexport:
 #+name: image1
 #+begin_src R :results graphics :file img1.pdf
  plot(1:10)
 #+end_src
 
 #+results: image1
 [[file:img1.pdf]]
 
 #+name: image2
 #+begin_src R :results graphics :file img2.pdf
  plot(1:5)
 #+end_src
 
 #+results: image2
 [[file:img2.pdf]]
 
 * export side-by-side
 
 ** table
 #+caption: stitching side-by-side using tables
 | [[file:img1.pdf]] | [[file:img2.pdf]] |
 
 ** using imagemagick
 
 *** function :noexport:
 #+name: sidebyside
 #+begin_src sh :session none :results file replace :var im1=im1.png :var 
 im2=im2.png :var outname=out.png
  convert $im1 $im2 +append $outname
  echo $outname
 #+end_src
 
 *** test
 #+name: combinedfig
 #+call: sidebyside(im1=img1.pdf, im2=img2.pdf) :results file
 
 #+caption: stitching side-by-side using imagemagick
 #+results: combinedfig
 [[file:out.png]]
 --8---cut here---end---8---
 
 Regards,
 Andreas



Re: [O] use of 'system in ox-odt.el

2015-05-21 Thread Rasmus
Matt Price mopto...@gmail.com writes:

 You are on Gnome, rt?  I think there is a long standing bug in
 gvfs-open (which is called by xdg-open).

 See the following:
 http://lists.gnu.org/archive/html/emacs-devel/2009-07/msg00279.html
 https://bugzilla.gnome.org/show_bug.cgi?id=652262

 I came across this a long time ago trying to investigate why xdg-open
 didn't work when running asynchronously like your example.

   http://thread.gmane.org/gmane.emacs.help/93430

 I think those bug reports describe the problem precisely.  I am also on
 gnome and have much the same problem.

2 minutes research suggest that I cannot tell xdg-open to use another
backend other than through environment variables, viz. BROWSER, DE,
DESKTOP_SESSION.  Unfortunately, I was not able to make this work by just
setting the DESKTOP_SESSION in either the shell starting Emacs or via
setenv.

So I guess on could use an xdg-open alternative or hardcode programs in
mailcap...

Rasmus

-- 
A page of history is worth a volume of logic




Re: [O] [RFC] Org linting library

2015-05-21 Thread Rainer M Krug
Nicolas Goaziou m...@nicolasgoaziou.fr writes:

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

 Two more questions:

 I get the following warnings:

 ,
 | 10 low   Unknown OPTIONS item @
 | 11 low   Unknown OPTIONS item skip
 | 11 low   Unknown OPTIONS item LaTeX
 | 11 low   Unknown OPTIONS item TeX
 `

 based on the following lines:

 ,
 | #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:nil -:t f:t *:t :t
 | #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
 `

 The file is not that old - but have these options changed?

 These options do not do anything. @ and skip have no equivalent.
 TeX and LaTeX are now tex. See (info (org) Export settings).

 and I get

 ,
 |   1821 low   Orphaned affiliated keyword: RESULTS
 `

 caused by an orphaned

 ,
 | #+RESULTS:
 `

 But these are created by evaluating a code block which produced no
 results - so they are a valid part of the document?

 Correct. Note however the low trust on this check. It's just
 a heads-up. Anyway I remove such reports for RESULTS in wip-lint.

 And an error:

 I get, in the same document I got the other errors, the following error:

 ,
 | Org linting process starting...
 | org-split-string: Wrong type argument: stringp, 292
 `

 The backtrace is huge - how can I produce a usable backtrace?

 Usually, only the last top-level function call is useful. 

 It would be better to provide an ECM, tho. The error comes from Babel
 header check. Does 292 ring a bell in a #+HEADER: line?

Addition to my last email: when I close emacs and open it again and try
to linter the ECM, it works - is it possible that there is some caching
which is not cleaned up?

Rainer




 Regards,

-- 
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-mode, tikz and beamer

2015-05-21 Thread Suvayu Ali
On Thu, May 21, 2015 at 04:40:33PM +0200, cédric ody wrote:
 Dear org-mode users,
 
 I have used org-mode for some months now. I find it very useful. I
 have recently used it to prepare mathematic teaching lessons using the
 beamer exporter.
 
 I wanted to combine org-mode and tikz latex's package from latex In
 order to insert some kind of mind-mapping from the headlines between
 the main parts of the lesson. I enclose an example so that you can see
 what I am talking about. Note that you can move forth and back through
 the presentation with hyperlinks. Note also only the chapter Droites
 dans le plan is filled so most of links fail.

Some of the links in that chapter are not working properly I think, but
otherwise it's a very impressive start!  If you post your current shell
script with the Org file, I think others can suggest what is and is not
possible.

To put it in more words, we don't know what you are thinking.  If we can
see the Org source and the shell script, it is easier to understand how
you map Org elements to beamer/tikz environments.

I think you have started a very interesting project!

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.



[O] LOGBOOK entry lands outside LOGBOOK

2015-05-21 Thread Lawrence Bottorff
I'm using the C-c C-z to make what I though would be LOGBOOK entries, but
they seem to appear outside the :LOGBOOK . . . :END: block, even though my
cursor is positioned inside the block. What do I do to keep them inside?

Also, I seem to have created this header:

***   | |  ||

which won't let me remove it, saying it's read only. No other entries are
behaving this way. What have I done and how do I get rid of it?


Re: [O] [RFC] Org linting library

2015-05-21 Thread Rainer M Krug
Nicolas Goaziou m...@nicolasgoaziou.fr writes:

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

 Two more questions:

 I get the following warnings:

 ,
 | 10 low   Unknown OPTIONS item @
 | 11 low   Unknown OPTIONS item skip
 | 11 low   Unknown OPTIONS item LaTeX
 | 11 low   Unknown OPTIONS item TeX
 `

 based on the following lines:

 ,
 | #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:nil -:t f:t *:t :t
 | #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
 `

 The file is not that old - but have these options changed?

 These options do not do anything. @ and skip have no equivalent.
 TeX and LaTeX are now tex. See (info (org) Export settings).

 and I get

 ,
 |   1821 low   Orphaned affiliated keyword: RESULTS
 `

 caused by an orphaned

 ,
 | #+RESULTS:
 `

 But these are created by evaluating a code block which produced no
 results - so they are a valid part of the document?

 Correct. Note however the low trust on this check. It's just
 a heads-up. Anyway I remove such reports for RESULTS in wip-lint.

 And an error:

 I get, in the same document I got the other errors, the following error:

 ,
 | Org linting process starting...
 | org-split-string: Wrong type argument: stringp, 292
 `

 The backtrace is huge - how can I produce a usable backtrace?

 Usually, only the last top-level function call is useful. 

 It would be better to provide an ECM, tho. The error comes from Babel
 header check. Does 292 ring a bell in a #+HEADER: line?

Hi

here is an ECM:

,
| * Matlab code
| 
| #+begin_src octave
| 
| #+end_src
`

Actually, whatever I put there instead of octave, I get the same error.

This is very strange. What is the problem here?

Cheers,

Rainer



 Regards,

-- 
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


signature.asc
Description: PGP signature


Re: [O] [RFC] Org linting library

2015-05-21 Thread Rainer M Krug
Nicolas Goaziou m...@nicolasgoaziou.fr writes:

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

 Two more questions:

 I get the following warnings:

 ,
 | 10 low   Unknown OPTIONS item @
 | 11 low   Unknown OPTIONS item skip
 | 11 low   Unknown OPTIONS item LaTeX
 | 11 low   Unknown OPTIONS item TeX
 `

 based on the following lines:

 ,
 | #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:nil -:t f:t *:t :t
 | #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
 `

 The file is not that old - but have these options changed?

 These options do not do anything. @ and skip have no equivalent.
 TeX and LaTeX are now tex. See (info (org) Export settings).

 and I get

 ,
 |   1821 low   Orphaned affiliated keyword: RESULTS
 `

 caused by an orphaned

 ,
 | #+RESULTS:
 `

 But these are created by evaluating a code block which produced no
 results - so they are a valid part of the document?

 Correct. Note however the low trust on this check. It's just
 a heads-up. Anyway I remove such reports for RESULTS in wip-lint.

 And an error:

 I get, in the same document I got the other errors, the following error:

 ,
 | Org linting process starting...
 | org-split-string: Wrong type argument: stringp, 292
 `

 The backtrace is huge - how can I produce a usable backtrace?

 Usually, only the last top-level function call is useful. 

 It would be better to provide an ECM, tho. The error comes from Babel
 header check. Does 292 ring a bell in a #+HEADER: line?

Well - now it does. The following produces the error:

--8---cut here---start-8---
#+PROPERTY: header-args  :tangle-mode (identity #o444)

* Some code

#+begin_src R :results nons

#+end_src
--8---cut here---end---8---

The problem is the (identity #o444) which is causing the problem.

Here it is,

Rainer



 Regards,

-- 
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


signature.asc
Description: PGP signature


Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Kyle Meyer
Suvayu Ali fatkasuvayu+li...@gmail.com wrote:
 On Thu, May 21, 2015 at 11:41:07AM -0400, Kyle Meyer wrote:
[...]
 You can set org-notmuch-open-function to a function that behaves the way
 you want.  There are probably cleaner ways to handle this, but below
 seems to work.
 
 #+begin_src elisp
   (setq org-notmuch-open-function 'org-notmuch-follow-link-other-window)
 
   (defun org-notmuch-follow-link-other-window (search)
 Like `org-notmuch-follow-link', but use other window.
 (pop-to-buffer (save-window-excursion
  (notmuch-show (org-link-unescape search)
 #+end_src

 I think this (writing your own defun) is the cleanest way to handle
 this.  There is no way for Org to ensure a consistent behaviour for all
 possible link types, there are too many.

Yes, I agree.  It wasn't clear in my original message, but by cleaner
ways, I was referring to the implementation of
org-notmuch-follow-link-other-window.  I don't know if there's a better
way to override switch-to-buffer.

-- 
Kyle



[O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Gregor Zattler
Dear org-moders,

I want to open-link-at-point (C-c C-o) in other window.  With
file links this is standard behaviour (at least with my
configuration).  But I don’t know how to do so with notmuch:
links.  Universal argument won’t help.

Any ideas?

I think there should be key bindings for opening in same window,
other window, other frames regardless of the type of link opened.
Is this doable?

How about:

| open in same window  |   C-c C o |
| open in other window | C-c 4 C-c C o |
| open in other frame  | C-c 5 C-c C o |

?

Ciao, Gregor
-- 
 -... --- .-. . -.. ..--.. ...-.-



Re: [O] org-mode, tikz and beamer

2015-05-21 Thread cédric ody
Thank you for your answer.

Here is the shell script (many comments are in english except the
beginning) and the org file I use. To see how I call it, you can have
a look at the enclosed Makefile. Note that it uses specific
configurations files as well tex macros so it won't work without these
files. I can prepare a short example which generates the tex and pdf
files if needed. The script probably gives for now a good idea. You
can also look at the enclosed generated tex file to see how the tikz
language.

Basically, the shell script looks recursively into the org file and
creates nodes for the tikz headline mindmaps. Thus, there are parent
nodes and children nodes.

During that excursion, two kinds of files are created: the tree
files and the contents files.

The first ones are tex files with tikz mindmaps that must be inserted
at specific locations at the final latex compilation step. One tree
file contains the parent node with all the children files.

The contents files are org files and are converted into tex files
via the org-mode export command in a batch way. In the shell script,
hyperlinks are added to these newly converted tex files.

At the end, the assembly of all these files is done before compiling.

Numbering of sections through the recursive call is important so that
links work properly as you notice. Links allow one to go back and
forth the document. To go back, the idea is to click on the headline.
If a node exists without content, the links sends you the beginning of
the file or something like that.

Cheers,

Cédric


2015-05-21 20:02 UTC+02:00, Suvayu Ali fatkasuvayu+li...@gmail.com:
 On Thu, May 21, 2015 at 04:40:33PM +0200, cédric ody wrote:
 Dear org-mode users,

 I have used org-mode for some months now. I find it very useful. I
 have recently used it to prepare mathematic teaching lessons using the
 beamer exporter.

 I wanted to combine org-mode and tikz latex's package from latex In
 order to insert some kind of mind-mapping from the headlines between
 the main parts of the lesson. I enclose an example so that you can see
 what I am talking about. Note that you can move forth and back through
 the presentation with hyperlinks. Note also only the chapter Droites
 dans le plan is filled so most of links fail.

 Some of the links in that chapter are not working properly I think, but
 otherwise it's a very impressive start!  If you post your current shell
 script with the Org file, I think others can suggest what is and is not
 possible.

 To put it in more words, we don't know what you are thinking.  If we can
 see the Org source and the shell script, it is easier to understand how
 you map Org elements to beamer/tikz environments.

 I think you have started a very interesting project!

 Cheers,

 --
 Suvayu

 Open source is the future. It sets us free.




org2tex.sh
Description: Bourne shell script


coursP.org
Description: Binary data


coursP.tex
Description: TeX document


Re: [O] how to render align environment with mathjax in html-expot

2015-05-21 Thread Rasmus
Hi Max,

Max Linke max_li...@gmx.de writes:

 I would like to use align environments when I export to html. As this
 is nicer for me to align equations.

 When I use them naked like this.

   \begin{align}
   a = b + c \\
   x = y + z
   \end{align}

 the equation does not get rendered at all but the naked text is
 displayed in the html file. Do their exists some options to tell
 org-mode to wrap align environments for mathjax? Or do I have to wrap
 this in some special source block?

It should work out of the box.  Can you reproduce the error from emacs -q?
Which if your version of Org? Do you have internet on your test computer?

Rasmus

-- 
And I faced endless streams of vendor-approved Ikea furniture. . .




Re: [O] [RFC] Org linting library

2015-05-21 Thread Nicolas Goaziou
Rainer M Krug rai...@krugs.de writes:

 Well - now it does. The following produces the error:

 #+PROPERTY: header-args  :tangle-mode (identity #o444)

 * Some code

 #+begin_src R :results nons

 #+end_src

 The problem is the (identity #o444) which is causing the problem.

Fixed. Thank you.

Regards,



[O] how to render align environment with mathjax in html-expot

2015-05-21 Thread Max Linke

Hello

I would like to use align environments when I export to html. As this is 
nicer for me to align equations.


When I use them naked like this.

\begin{align}
a = b + c \\
x = y + z
\end{align}

the equation does not get rendered at all but the naked text is 
displayed in the html file. Do their exists some options to tell 
org-mode to wrap align environments for mathjax? Or do I have to wrap 
this in some special source block?



best Max



Re: [O] Incomplete org-plus-contrib

2015-05-21 Thread Rasmus

Marco Wahl marcowahls...@gmail.com writes:
 Rasmus ras...@gmx.us writes:

 IIUC org-eww is missing because it is not included in branch 'maint'.
 Possibly it is a good idea to put org-eww there.

 In the lisp folder, maint is typically for bug fixes.  I guess for contrib
 it's more flexible.

 So would you recommend to copy org-eww to branch maint...contrib/lisp/?

Good question.  It kind of defies stable, but again, I don't think the
promise of stable necessarily extend to contrib.

Let's see what Bastien says.

—Rasmus

-- 
May contains speling mistake




[O] [PATCH] ob-core: Fix indented cached result returning nil

2015-05-21 Thread Bjarte Johansen
Fix a problem where a source block would return nil oif the result was
cached and it was indented.

* lisp/ob-core.el (org-babel-execute-src-block): Move point to the the
  first character of the result instead of the beginning of the line.

* testing/lisp/test-ob.el
  (test-org-babel/indented-cached-org-bracket-link): Added test to
  to see if the indented cached result returns what it should return.
---
 lisp/ob-core.el |  3 ++-
 testing/lisp/test-ob.el | 16 
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 91bbde4..1f21685 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -652,7 +652,8 @@ block.
 (cache-current-p
  (save-excursion ;; return cached result
(goto-char (org-babel-where-is-src-block-result nil info))
-   (end-of-line 1) (forward-char 1)
+   (end-of-line 1)
+   (forward-char (1+ (current-indentation)))
(let ((result (org-babel-read-result)))
  (message (replace-regexp-in-string
% %% (format %S result))) result)))
diff --git a/testing/lisp/test-ob.el b/testing/lisp/test-ob.el
index f52ff24..55b45ad 100644
--- a/testing/lisp/test-ob.el
+++ b/testing/lisp/test-ob.el
@@ -20,6 +20,22 @@
 
 ;;; Code:
 
+(ert-deftest test-org-babel/indented-cached-org-bracket-link ()
+  When the result of a source block is a cached indented link it
+should still return the link.
+  (should
+   (org-test-with-temp-text
+
+* Test
+  #+pointBEGIN_SRC emacs-lisp :file test.txt :cache yes
+(message \test\)
+  #+END_SRC
+
+  #+RESULTS[f82e11feb0f46907bc5a256a27e9dd81a3876d14]:
+  [[file:test.txt]]
+(string= (concat default-directory test.txt)
+(org-babel-execute-src-block)
+
 (ert-deftest test-org-babel/multi-line-header-regexp ()
   (should(equal ^[ \t]*#\\+headers?:[ \t]*\\([^\n]*\\)$
org-babel-multi-line-header-regexp))
-- 
2.3.2 (Apple Git-55)




Re: [O] [PATCH] ob-core: Fix indented cached result returning nil

2015-05-21 Thread Bjarte Johansen
Thank you for your comments. 

 You need to add TINYCHANGE at the end of the commit message if you
 haven't signed FSF papers yet.
I have already signed the FSF papers when I sent some changes to a 
different Emacs project.

I will shortly send a new patch with the proposed changes.

Regards,
Bjarte




Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Subhan Michael Tindall
Take a look at the following variables:
org-link-frame-setup
org-file-apps

They might get you started in the right direction
Subhan



 -Original Message-
 From: emacs-orgmode-bounces+subhant=familycareinc@gnu.org
 [mailto:emacs-orgmode-bounces+subhant=familycareinc@gnu.org] On
 Behalf Of Gregor Zattler
 Sent: Thursday, May 21, 2015 6:43 AM
 To: emacs-orgmode
 Subject: Re: [O] org-notmuch: how to open-link-at-point in other window?
 
 Hi Leo,
 * Leo Ufimtsev lufim...@redhat.com [21. May. 2015]:
  I usually use my mouse and right click on the link.
 
 Thanks, I have problems, emulation right klick with this old macbook of mine.
 
  C-c C-o opens things in a new application. E.g a picture is opened in
  my image editing application.
 
  Right clicking opens in the right window. C-u C-c C-o also opens
  images in the right side window.
 
 For the key combos this is not the case with notmuch: -links.  I don’t knoiw
 why.
 
 
  In emacs, Window and Frame mean something different. By window, are
  you specifically referring to a new plane, split screen style, on the
  right hand side?
 
 Yes.
 
  As a note, http://emacs.stackexchange.com/ is often a good place for
  questions that have a specific, usually straight forward answer.
 
 Thanks, perhaps I give this a try.
 
 Ciao, Gregor
 --
  -... --- .-. . -.. ..--.. ...-.-


This message is intended for the sole use of the individual and entity to which 
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delete the message.  Thank you.


Re: [O] use of 'system in ox-odt.el

2015-05-21 Thread Matt Price
On May 21, 2015 04:32, Rasmus ras...@gmx.us wrote:

 Matt Price mopto...@gmail.com writes:

  You are on Gnome, rt?  I think there is a long standing bug in
  gvfs-open (which is called by xdg-open).
 
  See the following:
  http://lists.gnu.org/archive/html/emacs-devel/2009-07/msg00279.html
  https://bugzilla.gnome.org/show_bug.cgi?id=652262
 
  I came across this a long time ago trying to investigate why xdg-open
  didn't work when running asynchronously like your example.
 
http://thread.gmane.org/gmane.emacs.help/93430

  I think those bug reports describe the problem precisely.  I am also on
  gnome and have much the same problem.

 2 minutes research suggest that I cannot tell xdg-open to use another
 backend other than through environment variables, viz. BROWSER, DE,
 DESKTOP_SESSION.  Unfortunately, I was not able to make this work by just
 setting the DESKTOP_SESSION in either the shell starting Emacs or via
 setenv.

 So I guess on could use an xdg-open alternative or hardcode programs in
 mailcap...

Did you try this:

 (setcdr (assq 'system org-file-apps-defaults-gnu ) '(call-process
xdg-open nil 0 nil file))

That works for me.


 Rasmus

 --
 A page of history is worth a volume of logic




Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Leo Ufimtsev
I usually use my mouse and right click on the link. 

C-c C-o opens things in a new application. E.g a picture is opened in my image 
editing application. 

Right clicking opens in the right window. C-u C-c C-o also opens images in the 
right side window.

In emacs, Window and Frame mean something different. By window, are you 
specifically referring to a new plane, split screen style, on the right hand 
side?

As a note, http://emacs.stackexchange.com/ is often a good place for questions 
that have a specific, usually straight forward answer.

Thank you

Leo 

- Original Message -
 From: Gregor Zattler telegr...@gmx.net
 To: emacs-orgmode emacs-orgmode@gnu.org
 Sent: Thursday, May 21, 2015 9:09:13 AM
 Subject: [O] org-notmuch: how to open-link-at-point in other window?
 
 Dear org-moders,
 
 I want to open-link-at-point (C-c C-o) in other window.  With
 file links this is standard behaviour (at least with my
 configuration).  But I don’t know how to do so with notmuch:
 links.  Universal argument won’t help.
 
 Any ideas?
 
 I think there should be key bindings for opening in same window,
 other window, other frames regardless of the type of link opened.
 Is this doable?
 
 How about:
 
 | open in same window  |   C-c C o |
 | open in other window | C-c 4 C-c C o |
 | open in other frame  | C-c 5 C-c C o |
 
 ?
 
 Ciao, Gregor
 --
  -... --- .-. . -.. ..--.. ...-.-
 
 

-- 
Leo Ufimtsev | Intern Software Engineer @ Eclipse Team



Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Gregor Zattler
Hi Leo,
* Leo Ufimtsev lufim...@redhat.com [21. May. 2015]:
 I usually use my mouse and right click on the link. 

Thanks, I have problems, emulation right klick with this old
macbook of mine.

 C-c C-o opens things in a new application. E.g a picture is
 opened in my image editing application.
 
 Right clicking opens in the right window. C-u C-c C-o also
 opens images in the right side window.

For the key combos this is not the case with notmuch: -links.  I
don’t knoiw why.


 In emacs, Window and Frame mean something different. By window,
 are you specifically referring to a new plane, split screen
 style, on the right hand side?

Yes.

 As a note, http://emacs.stackexchange.com/ is often a good
 place for questions that have a specific, usually straight
 forward answer.

Thanks, perhaps I give this a try.

Ciao, Gregor
-- 
 -... --- .-. . -.. ..--.. ...-.-



Re: [O] How to elegantly and effectively quote org fragments?

2015-05-21 Thread Nicolas Goaziou
Hello,

alain.coch...@unistra.fr writes:

 Sorry if these are easy questions -- I did spend time with the manual,
 the FAQ, the list archive, and the web.  The best I found is to use an
 org SRC block, but I do not find it satisfactory.  Plus I cannot even
 have it work properly.

You can also use a fixed-width area:

  : * a headline only for the example
  : ** a subheadline
  : text

 (1) Say I have have this in my org file (star in 1st column):

   * a regular headline: writing org examples 

 #+BEGIN_SRC org
   ,* a headline only for the example
   ,** a subheadline
   text
 #+END_SRC

 Is it the best that one can do to quote some org code?  Since I use
 (org-startup-indented t), I would expect to have the corresponding
 indentation.

I'm not sure to understand. `org-indent-mode' is about virtual
indentation, not real one. So, there's no indentation to be inserted.

 Also, if not possible to avoid the escaping commas, I would like to at
 least have them for each line, not only for the headlines. So I would
 like something like this:

   * a regular headline: writing org examples 

 #+BEGIN_SRC org
  ,* a headline only for the example
  ,  * a subheadline
  ,text
 #+END_SRC

 Is (some of) this at all doable?

This is not possible. Escaping rules are explained in (info (org)
Literal examples), fourth footnote.

 (2) Now, if in the org edit buffer I do 'C-c C-d' (org-deadline),
 insert a DEADLINE:, and go back to my org file, the block now looks
 like:

 #+BEGIN_SRC org
   ,* a headline only for the example
   ,** a subheadline
   DEADLINE: 2015-05-21 Thu
   text
 #+END_SRC

 If I do 'M-x org-agenda RET a', I get the following line in the Org
 agenda buffer:

 todo:   Deadline:   a regular headline: writing org examples

 Is this normal?  Since the deadline is part of the block, I would
 expect no entry in the agenda; I tried to escape the DEADLINE with a
 comma, but it does not change anything.  So, is there a way to *quote*
 a DEADLINE:, i.e., without having an associated entry in the agenda?

IIRC, this bug was fixed some months ago on development version.


Regards,

-- 
Nicolas Goaziou



[O] org-notify: can't define an org-notify-add

2015-05-21 Thread Alain . Cochard

Hello.

If I have in my emacs init file the following org-notify setup, as
specified by the org-notify doc (if I understand it correctly):

   (require 'org-notify)
   (org-notify-add 'my-appt '(:time 1h :actions -message
   :period 
30s :duration 20))
   (org-notify-start)

and in my todo.org file:

   * TODO test agenda 
 DEADLINE: 2015-05-21 Thu 17:55
 :PROPERTIES:
 :notify:   my-appt
 :END:  

the behavior I get is the one defined as the default in the
org-notify.el file:

;;; Provide a minimal default setup.
(org-notify-add 'default '(:time 1h :actions -notify/window
 :period 2m :duration 60))

I can override this default in my init file, i.e., replacing
org-notify-add 'my-appt above by org-notify-add 'default, and I
then get my default behavior.

So as far as I can see, everything behaves as if I did not use the
proper syntax for the :PROPERTIES: block (consistently, if I alter it
or remove it completely, I still get the default behavior).

Am I doing something trivially wrong?  Any idea how I could debug
this?  (I have no relevant message in the *Messages* buffer.)

Many thanks in advance.

Org-mode version 8.2.10 (8.2.10-40-gc763fa-elpa @
/home/cochard/.emacs.d/elpa/org-20150518/)
GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 3.14.12) of
2015-04-17 on buildvm-04.phx2.fedoraproject.org



[O] Export code and results in one environment

2015-05-21 Thread Jacob Gerlach
Hello,

I'd like to export a source block and it's results together in one latex
environment. I came up with a solution using the final filter below.

Is there a better way?

Thanks,
Jake

  #+BEGIN_SRC emacs-lisp :exports none :results silent
(defun combine-verb-final-filter (s backend info)
  (when (eq backend 'latex)
  (replace-regexp-in-string end{verbatim}\n*begin{verbatim}

s nil t)))
(add-to-list 'org-export-filter-final-output-functions
'combine-verb-final-filter)
  #+END_SRC

Works, given:
--
#+BEGIN_SRC sh :exports both
echo Hello
#+END_SRC

#+RESULTS:
: Hello
--
Produces (desired effect):
--
\begin{verbatim}
echo Hello

Hello
\end{verbatim}
--


Re: [O] How to elegantly and effectively quote org fragments?

2015-05-21 Thread Alain . Cochard
Nicolas Goaziou writes on Fri 22 May 2015 00:02:

 You can also use a fixed-width area:
  
: * a headline only for the example
: ** a subheadline
: text

Ah, thank you.  If I understand correctly, though, once one does that
(in an SRC org block, say) one looses the ability to edit the block as
org code using org-edit-special (C-c ').

   (1) Say I have have this in my org file (star in 1st column):
  
  * a regular headline: writing org examples 
  
#+BEGIN_SRC org
  ,* a headline only for the example
  ,** a subheadline
  text
#+END_SRC
  
   Is it the best that one can do to quote some org code?  Since I use
   (org-startup-indented t), I would expect to have the corresponding
   indentation.
  
  I'm not sure to understand. `org-indent-mode' is about virtual
  indentation, not real one. So, there's no indentation to be inserted.

I understand that the indentation is virtual; it is just that I would
(ideally) expect for the quoted example to visually look the same as
it does in an org buffer.


   Also, if not possible to avoid the escaping commas, I would like to at
   least have them for each line, not only for the headlines. So I would
   like something like this:
  
  * a regular headline: writing org examples 
  
#+BEGIN_SRC org
 ,* a headline only for the example
 ,  * a subheadline
 ,text
#+END_SRC
  
   Is (some of) this at all doable?
  
  This is not possible. Escaping rules are explained in (info (org)
  Literal examples), fourth footnote.

OK.  I had missed this footnote.  I will live with this, but am still
surprised by this fact -- the SRC org block looks ugly to me.  When we
enter [[xx]] (say) the brackets become invisible, so I had assumed
that a similar mechanism could exist here; I guess there are
advantages to the present situation that I do not see...


   Is this normal?  Since the deadline is part of the block, I would
   expect no entry in the agenda; I tried to escape the DEADLINE with a
   comma, but it does not change anything.  So, is there a way to *quote*
   a DEADLINE:, i.e., without having an associated entry in the agenda?
  
  IIRC, this bug was fixed some months ago on development version.

Very good.  I'll wait.


Thank you very much for the detailed explanations.



[O] [PATCH] org-src.el: Unescape source block on edit

2015-05-21 Thread Kyle Meyer
org-edit-src-code doesn't seem to be unescaping correctly.  For
example, calling org-edit-src-code on

#+begin_src org
  ,* h
#+end_src

puts ,* h, not * h, in the source buffer.  When exiting, ,* is
escaped again, resulting in

#+begin_src org
  ,,* h
#+end_src

The attached patch moves the unescaping call from org-edit-src-code to
org-src--edit-element so that the source string is unescaped
regardless of whether it was passed as an argument or extracted
directly from the buffer.

From a78db0610f769517a146b0a9fc58f81d0381d511 Mon Sep 17 00:00:00 2001
From: Kyle Meyer k...@kyleam.com
Date: Thu, 21 May 2015 23:18:37 -0400
Subject: [PATCH] org-src.el: Unescape source block on edit

* lisp/org-src.el (org-src--edit-element): Unescape code string.
  (org-edit-src-code): Let org-src--edit-element handle unescaping of
  code string.
---
 lisp/org-src.el | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lisp/org-src.el b/lisp/org-src.el
index d82068d..8fcb7aa 100644
--- a/lisp/org-src.el
+++ b/lisp/org-src.el
@@ -380,7 +380,8 @@ (defun org-src--edit-element
 	 (beg (copy-marker (car area)))
 	 (end (copy-marker (cdr area) t))
 	 (old-edit-buffer (org-src--edit-buffer beg end))
-	 (contents (or contents (buffer-substring-no-properties beg end
+	 (contents (org-unescape-code-in-string
+		(or contents (buffer-substring-no-properties beg end)
 (if (and old-edit-buffer
 	 (or (not org-src-ask-before-returning-to-edit-buffer)
 		 (y-or-n-p Return to existing edit buffer ([n] will revert changes)? )))
@@ -833,7 +834,7 @@ (defun org-edit-src-code (optional code edit-buffer-name)
 		  (unless (looking-at [ \t]*$) (insert ind))
 		  (forward-line)
 	  (org-escape-code-in-region (point-min) (point-max
-   (and code (org-unescape-code-in-string code)))
+   code)
   ;; Finalize buffer.
   (org-set-local 'org-coderef-label-format
 		 (or (org-element-property :label-fmt element)
-- 
2.4.1


--
Kyle


[O] org-notify: can't define an org-notify-add

2015-05-21 Thread Alain . Cochard

Sorry I am posting this message again: I made a mistake and it
appeared within an unrelated thread (perhaps it is possible to remove
it from there?)

---


Hello.

If I have in my emacs init file the following org-notify setup, as
specified by the org-notify doc (if I understand it correctly):

   (require 'org-notify)
   (org-notify-add 'my-appt '(:time 1h :actions -message
   :period 
30s :duration 20))
   (org-notify-start)

and in my todo.org file:

   * TODO test agenda 
 DEADLINE: 2015-05-21 Thu 17:55
 :PROPERTIES:
 :notify:   my-appt
 :END:  

the behavior I get is the one defined as the default in the
org-notify.el file:

;;; Provide a minimal default setup.
(org-notify-add 'default '(:time 1h :actions -notify/window
 :period 2m :duration 60))

I can override this default in my init file, i.e., replacing
org-notify-add 'my-appt above by org-notify-add 'default, and I
then get my default behavior.

So as far as I can see, everything behaves as if I did not use the
proper syntax for the :PROPERTIES: block (consistently, if I alter it
or remove it completely, I still get the default behavior).

Am I doing something trivially wrong?  Any idea how I could debug
this?  (I have no relevant message in the *Messages* buffer.)

Many thanks in advance.

Org-mode version 8.2.10 (8.2.10-40-gc763fa-elpa @
/home/cochard/.emacs.d/elpa/org-20150518/)
GNU Emacs 24.5.1 (x86_64-redhat-linux-gnu, GTK+ Version 3.14.12) of
2015-04-17 on buildvm-04.phx2.fedoraproject.org



Re: [O] LOGBOOK entry lands outside LOGBOOK

2015-05-21 Thread Marco Wahl
Hi,

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

 I'm using the C-c C-z to make what I though would be LOGBOOK entries, but
 they seem to appear outside the :LOGBOOK . . . :END: block, even though my
 cursor is positioned inside the block. What do I do to keep them inside?

You could specify that behavior by setting variable
`org-log-into-drawer' accordingly.  This is possible via M-x
customize-variable org-log-into-drawer.

 Also, I seem to have created this header:

 ***   | |  ||

 which won't let me remove it, saying it's read only. No other entries are
 behaving this way. What have I done and how do I get rid of it?

You somehow managed to activate Org's column view.  You get out of it by
pressing 'q' on the special looking header.


HTH,  Marco




Re: [O] LOGBOOK entry lands outside LOGBOOK

2015-05-21 Thread Kyle Meyer
Lawrence Bottorff borg...@gmail.com wrote:
 I'm using the C-c C-z to make what I though would be LOGBOOK entries, but
 they seem to appear outside the :LOGBOOK . . . :END: block, even though my
 cursor is positioned inside the block. What do I do to keep them inside?

Have you set org-log-into-drawer?

 Also, I seem to have created this header:

 ***   | |  ||

 which won't let me remove it, saying it's read only. No other entries are
 behaving this way. What have I done and how do I get rid of it?

It looks related to column view (org-columns).  Can't you remove it
after closing and re-opening the file?

--
Kyle



Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Suvayu Ali
On Thu, May 21, 2015 at 11:41:07AM -0400, Kyle Meyer wrote:
 Gregor Zattler telegr...@gmx.net wrote:
  Dear org-moders,
 
  I want to open-link-at-point (C-c C-o) in other window.  With
  file links this is standard behaviour (at least with my
  configuration).  But I don’t know how to do so with notmuch:
  links.  Universal argument won’t help.
 
 org-notmuch-follow-link calls notmuch-show, which uses switch-to-buffer.
 You can set org-notmuch-open-function to a function that behaves the way
 you want.  There are probably cleaner ways to handle this, but below
 seems to work.
 
 #+begin_src elisp
   (setq org-notmuch-open-function 'org-notmuch-follow-link-other-window)
 
   (defun org-notmuch-follow-link-other-window (search)
 Like `org-notmuch-follow-link', but use other window.
 (pop-to-buffer (save-window-excursion
  (notmuch-show (org-link-unescape search)
 #+end_src

I think this (writing your own defun) is the cleanest way to handle
this.  There is no way for Org to ensure a consistent behaviour for all
possible link types, there are too many.  Org can ensure consistency
only for physical files, and even then when they are opened inside
Emacs.  There is no shortage of links to binary files!

For what it's worth, I have customised notmuch open function to use the
notmuch-tree interface.

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] org-notmuch: how to open-link-at-point in other window?

2015-05-21 Thread Kyle Meyer
Gregor Zattler telegr...@gmx.net wrote:
 Dear org-moders,

 I want to open-link-at-point (C-c C-o) in other window.  With
 file links this is standard behaviour (at least with my
 configuration).  But I don’t know how to do so with notmuch:
 links.  Universal argument won’t help.

 Any ideas?

org-notmuch-follow-link calls notmuch-show, which uses switch-to-buffer.
You can set org-notmuch-open-function to a function that behaves the way
you want.  There are probably cleaner ways to handle this, but below
seems to work.

#+begin_src elisp
  (setq org-notmuch-open-function 'org-notmuch-follow-link-other-window)

  (defun org-notmuch-follow-link-other-window (search)
Like `org-notmuch-follow-link', but use other window.
(pop-to-buffer (save-window-excursion
 (notmuch-show (org-link-unescape search)
#+end_src

--
Kyle



Re: [O] [RFC] Org linting library

2015-05-21 Thread Nicolas Goaziou
Rainer M Krug rai...@krugs.de writes:

 Two more questions:

 I get the following warnings:

 ,
 | 10 low   Unknown OPTIONS item @
 | 11 low   Unknown OPTIONS item skip
 | 11 low   Unknown OPTIONS item LaTeX
 | 11 low   Unknown OPTIONS item TeX
 `

 based on the following lines:

 ,
 | #+OPTIONS:   H:3 num:t toc:t \n:nil @:t ::t |:t ^:nil -:t f:t *:t :t
 | #+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
 `

 The file is not that old - but have these options changed?

These options do not do anything. @ and skip have no equivalent.
TeX and LaTeX are now tex. See (info (org) Export settings).

 and I get

 ,
 |   1821 low   Orphaned affiliated keyword: RESULTS
 `

 caused by an orphaned

 ,
 | #+RESULTS:
 `

 But these are created by evaluating a code block which produced no
 results - so they are a valid part of the document?

Correct. Note however the low trust on this check. It's just
a heads-up. Anyway I remove such reports for RESULTS in wip-lint.

 And an error:

 I get, in the same document I got the other errors, the following error:

 ,
 | Org linting process starting...
 | org-split-string: Wrong type argument: stringp, 292
 `

 The backtrace is huge - how can I produce a usable backtrace?

Usually, only the last top-level function call is useful. 

It would be better to provide an ECM, tho. The error comes from Babel
header check. Does 292 ring a bell in a #+HEADER: line?


Regards,



Re: [O] use of 'system in ox-odt.el

2015-05-21 Thread Rasmus
Matt Price mopto...@gmail.com writes:

 Did you try this:

  (setcdr (assq 'system org-file-apps-defaults-gnu ) '(call-process
 xdg-open nil 0 nil file))

 That works for me.

It works for odt, but not html.

-- 
Slowly unravels in a ball of yarn and the devil collects it