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

[Vikas Rawal]

> 
> pandoc -f latex -t docx test.tex -o test.docx
> 
> I see Org has exported my "W m^{-2}" as "W m$^{\text{-2}}$", which is
> not what I would expect in LaTeX. In OS X Pages.app viewing the docx
> this appears as "W m". In Word it shows up either as just "-2" or "W
> m-2". In Word, the Math shows up with each character as a box (the math
> is just missing in Pages). In Word the figures are missing (they appear
> in Pages).
> 


First, you should differentiate between whether the problem is in Org->LaTeX 
conversion, or in LaTeX->Docx conversion. 

From what you describe above, the problem seems to be in Org->LaTeX conversion. 

For me, $W m^{-2}$ in Org produces correct LaTeX markup, and I get a good docx 
using Pandoc.

Vikas

Re: [O] Export HTML with Free Form Text

[Esben Stien]

Eric Abrahamsen  writes:

> You can do it with the preserve-breaks export option set to t. Either
> "\n:t" in the #+OPTIONS line, or permanently by setting
> org-export-preserve-breaks to t.

Hehe, I knew this would somehow be there;). 

Really great; thanks;)

-- 
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Re: [O] [PATCH] Add author and title to exported PDF properties

[Nicolas Goaziou]

Hello,

Marcel van der Boom  writes:

Thanks for your patch. A few comments follow.

> * lisp/ox-latex.el (org-latex-template): add pdfauthor and pdftitle
> (org-latex-hyperref-template): add placeholders for author and title
> (org-latex-template): adjust default template with author and title

You need full stops at the end of sentences, and upper case letters
after the colons.

>  (defcustom org-latex-hyperref-template
> -  "\\hypersetup{\n pdfkeywords={%k},\n  pdfsubject={%d},\n  
> pdfcreator={%c}}\n"
> +  "\\hypersetup{\n pdfkeywords={%k},\n  pdfsubject={%d},\n  
> pdfcreator={%c},\n pdfauthor={%a},\n pdftitle={%t}}"

Nitpick: the number of space characters after newline characters should
be consistent, even though it wasn't the case before your patch.

> +?a (or (first (plist-get info :author)) "")
> +?t (or (first (plist-get info :title)) "")

This part is buggy. Both (plist-get info :author) and (plist-get
info :title) will return a "secondary list", which is a list of strings
and syntax objects. You usually need to handle these with
`org-export-data', not `first'.

Alas, in this case, `org-export-data' may not be appropriate, as some
objects should be exported differently in these keywords. For example,
you may want to remove footnote references, radio-targets, targets,
links and possibly any LaTeX markup (e.g., are "\textbf{bold}" macros
allowed in these keywords?).

The usual way to achieve this is to create an anonymous export back-end,
derived from `latex', with `org-export-create-backend', and let it
handle specially problematic objects. You then use it within
`org-export-data-with-backend'. See `org-html--format-toc-headline' for
an example.


Regards,

-- 
Nicolas Goaziou

[O] Clock-in in agenda makes some headings with links disappear

[Thomas Morgan]

Dear Org mode hackers,

I came across a bug in Org-mode 8.2.6.  I had an overdue
TODO item in the agenda with a link at the end of the heading
text.  I clocked it in with `I' and the heading text
disappeared; only the link remained visible on that line in
the agenda.

This bug was reproducible for a while and I made the attached
patch which fixed it, but I didn't succeed in making a minimal
test case, and now I'm not able to reproduce it at all.

The problem seemed to be that `(beginning-of-line 0)' was
not moving to the beginning of the line, but between closing
brackets in the link.  I thought this might be related to
`inhibit-field-text-motion', but enabling that didn't help,
nor did using `(forward-line -1)'.  What seemed to solve it
was adding `(beginning-of-line)' after `(forward-line -1)',
as in the patch.

I know this is not a very helpful bug report but thought I'd
send it anyway in case someone else has seen the same problem
and understands what's going on.

Best regards,
Thomas

>From 06cde5027e8ca93d82d14c5c0b46deb3e1c80b25 Mon Sep 17 00:00:00 2001
From: Thomas Morgan 
Date: Tue, 13 May 2014 23:52:48 -0400
Subject: [PATCH] Fix bug mading agenda line disappear on clock-in.

In some cases with a link at the end of the line,
`(beginning-of-line 0)' moves to a position within
the link (between the closing bracket of the link
description and the following closing bracket) and
not to the beginning of the line.

Then the properties at that position in the link
are made the properties of the whole line, and the
entire line disappears.

* lisp/org-agenda.el (org-agenda-change-all-lines): Move backward one
  line and to the beginning of that line as an explicit second step.

TINYCHANGE
---
 lisp/org-agenda.el |3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index e2a0629..428d31f 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -8895,7 +8895,8 @@ If FORCE-TAGS is non nil, the car of it returns the new tags."
 	  (save-restriction
 	(narrow-to-region (point-at-bol) (point-at-eol))
 	(org-agenda-finalize)))
-	(beginning-of-line 0)
+	(forward-line -1)
+	(beginning-of-line)
 
 (defun org-agenda-align-tags (&optional line)
   "Align all tags in agenda items to `org-agenda-tags-column'."
-- 
1.7.10.4

[O] still seeing semi-regular lockups

[Eric Abrahamsen]

Hey there,

After Nicolas made the last round of improvements to the caching
mechanism I got far fewer hangs with Org, but they are still happening.
Maybe once a day or so, on average, editing something in an Org buffer
causes emacs to hang, and my fans to spin up, and there we are until I
kill emacs.

It happens often enough that I guess it's worth running emacs under some
kind of debugger -- at least, I assume that's the best way of catching
the bug. I'm not really sure how to go hunting, though, so if anyone had
any advice in this direction, that would be great.

In the meantime, is there any way of interrupting emacs so it quits
whatever its doing, without having to kill it? I've played around with
sending different signals using "kill", just for fun, but everything
I've tried either does nothing, or kills emacs altogether.

Cheers,
Eric

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

[Christopher Witte]

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

Chris.


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

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

Re: [O] Agenda view in Fortnight mode

[Samuel Loury]

Hi,
Esben Stien  writes:

> Charles Millar  writes:
>
>> (setq org-agenda-span 14)
>
> This specifies this week plus the next week, but is there any way to
> specify this week plus the next week plus the previous week?;)
>
Try this:

--8<---cut here---start->8---
(setq org-agenda-span 14
  org-agenda-start-day "-7d")
--8<---cut here---end--->8---
--
Konubinix
GPG Key: 7439106A
Fingerprint: 5993 BE7A DA65 E2D9 06CE  5C36 75D2 3CED 7439 106A


pgpH14gKeN4iZ.pgp
Description: PGP signature

Re: [O] Agenda view in Fortnight mode

[Esben Stien]

Samuel Loury  writes:

> --8<---cut here---start->8---
> (setq org-agenda-span 14
>   org-agenda-start-day "-7d")
> --8<---cut here---end--->8---

Excellente;)

Thanks..

-- 
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 http://www. s tn m
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   sip:b0ef@   e e 
   jid:b0ef@n n

[O] Bug: Activating org-mode in any buffer recenters (unrelated) selected window. [8.2.6 (release_8.2.6-6-gfc37d1 @ /home/youngfrog/sourcetrees/org-mode/lisp/)]

[Nicolas Richard]

The function `org-overview' calls `recenter' without checking if the
current buffer is actually in the currently selected window. Moreover,
turning on org-mode calls `org-overview' (I guess depending on the
configuration). IOW, turning on org-mode programmatically (e.g. via
find-file-noselect) will recenter whatever window is currently selected.
That's unexpected.

I noticed that because I recently tried org-notify, which uses
find-file-noselect, and the behaviour was very distracting to me. (Side
question : do people live with that or is it just me seeing the weird
behaviour ?)

Anyway, I would suggest to simply remove the call to recenter because I
don't understand why it's there. OTOH if it's there for a reason, then I
suggest something along the line of:
(when (eq
   (current-buffer)
   (window-buffer
(selected-window)))
  (recenter '(4)))

(but then, why the interactive-looking argument ?)

While I am at it, I don't quite understand why (goto-char) is used
*after* recenter (also, why not just save-excursion ?)

Since there are many things I obviously don't understand, I'm not
posting an actual patch but I can do that if someone wants it.

-- 
Nico.

Re: [O] An org password manager

[Colin Baxter]

Dear Jorge,

Many thanks for this. I had forgotten about "define-derived-mode".

Best wishes,

Colin.


> Dear Ramon and Colin,
>
> If you are using an "(add-to-list 'auto-mode-alist ...)" for the gpg
> files, that sets the major mode on. If you want to leave the major mode
> as Org, do not use auto-mode-alist, but instead use a hook:
> (add-hook 'org-mode-hook 'your-function), where your-function should be
> one that checks if the file name ends with gpg and if so turns your
> sensitivity-mode on.
>
> Alternatively, define another major mode:
>
> #+BEGIN_SRC emacs-lisp
>   (define-derived-mode org-but-sensitive-mode org-mode
> ...)
> #+END_SRC
>
> and copy in "..." whatever your sensitive-minor-mode has.
>
> Best,
>
> Jorge.
>
>
>

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

[Vikas Rawal]

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

This is very new. As of now, direct Org->docx conversion does not taken into 
account any LaTeX-specific markup you may have in your Org file. Also, biblatex 
citations are not supported.

If you go Org->LaTeX->docx, it all works fine.

Vikas

Re: [O] An org password manager

[Cayetano Santos]

Hi Jorge,

  Are you aware of this http://git.zx2c4.com/password-store/tree/contrib/emacs 
? It's an api to pass
  and other simple cli tools.

  Hope it helps,

c.

On 11-05-14 01:21:20, Jorge A. Alfaro-Murillo wrote:

Hi! I have been using org for managing passwords for a some time now. In
case someone is interested, the code is in:
https://bitbucket.org/alfaromurillo/org-passwords.el

To consult the database, the code provides a function to open the Org
file with the passwords in Read-Only mode, sets a timer after which the
buffer is killed and provides functions for copying the password without
it getting into the kill-ring. It also provides two types of functions
for generating passwords: strings of random characters, and random words
of the correcthorsebatterystaple-type. The README file in bitbucket has
detailed information about the usage.

If there is interest from the community this can also go to /contrib.

Best,

Jorge.

Re: [O] still seeing semi-regular lockups

[dieter]

hi,

on my machine wanderlust hangs from time to time when i am inside the company 
net and
the proxy has hiccups.
then C-g (sometimes several) usually help.

in the link below i found an interesting variable, debug-on-quit.
when it is set, emacs enters the debugger when you hit C-g.

sendings signal to emacs from external usually only kills it.
the only signal which i am aware of that can be caught is SIGUSR1.
i used to use it to notify emacs about network changes.

hope this helps,
dieter

[1] 
http://www.gnu.org/software/emacs/manual/html_node/elisp/Infinite-Loops.html#Infinite-Loops



> Original Message 
>From: Eric Abrahamsen 
>To: emacs-orgmode@gnu.org
>Sent: Wed, May 14, 2014, 10:36 AM
>Subject: [O] still seeing semi-regular lockups
>
>Hey there,
>
>After Nicolas made the last round of improvements to the caching
>mechanism I got far fewer hangs with Org, but they are still happening.
>Maybe once a day or so, on average, editing something in an Org buffer
>causes emacs to hang, and my fans to spin up, and there we are until I
>kill emacs.
>
>It happens often enough that I guess it's worth running emacs under some
>kind of debugger -- at least, I assume that's the best way of catching
>the bug. I'm not really sure how to go hunting, though, so if anyone had
>any advice in this direction, that would be great.
>
>In the meantime, is there any way of interrupting emacs so it quits
>whatever its doing, without having to kill it? I've played around with
>sending different signals using "kill", just for fun, but everything
>I've tried either does nothing, or kills emacs altogether.
>
>Cheers,
>Eric

[O] Git not working

[Marvin Doyley]

Hi there,

I am trying to pull the latest version of org, but I get the following error 
whenever I try to do so:

fatal: read error: Connection reset by peer

Does anybody now how to resolve this ?

Thanks
M

Re: [O] Update of git repo does not work? Still?

[Charles Millar]

Suvayu Ali wrote:

On Tue, May 13, 2014 at 01:53:01PM +0200, Rainer M Krug wrote:

Is there a problem with git? I can't update via git:

,
| $ git remote -v
| origingit://orgmode.org/org-mode.git (fetch)
| origingit://orgmode.org/org-mode.git (push)
| $ git pull
| fatal: read error: Connection reset by peer
| $ make update
| rm -f
| git checkout
| M etc/R/org_functions.R
| M lisp/ob-R.el
| git remote update
| Fetching origin
| fatal: read error: Connection reset by peer
| error: Could not fetch origin
| make: *** [up0] Error 1
`


I can confirm this.



I just tried (2014-05-14) to update and am still receiving an error message.

rm -f
git checkout
git remote update
Fetching origin
fatal: read error: Connection reset by peer
error: Could not fetch origin
mk/targets.mk:111: recipe for target 'up0' failed
make: *** [up0] Error 1

Org-mode version 8.2.6 (release_8.2.6-959-g08e259 @ 
c:/cygwin/home/owner/.elisp/org-mode/lisp/)


GNU Emacs 24.3.1 (i386-mingw-nt6.0.6002) of 2013-03-17 on MARVIN

---
This email is free from viruses and malware because avast! Antivirus protection 
is active.
http://www.avast.com

Re: [O] [PATCH] Add author and title to exported PDF properties

[Marcel van der Boom]

On wo 14-mei-2014 09:05
Nicolas Goaziou  wrote:

> [...]
>> +   ?a (or (first (plist-get info :author)) "")
>> +   ?t (or (first (plist-get info :title)) "")  
> 

> The usual way to achieve this is to create an anonymous export
> back-end, derived from `latex', with `org-export-create-backend', and
> let it handle specially problematic objects. You then use it within
> `org-export-data-with-backend'. See `org-html--format-toc-headline'
> for an example.
>
Are you saying 'author' and 'title' are problematic? How do they differ
from, say 'subject'? Was this the reason they are not included by
default in the PDF info?

marcel


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Description: PGP signature

Re: [O] [PATCH] Add author and title to exported PDF properties

[Nicolas Goaziou]

Marcel van der Boom  writes:

> Are you saying 'author' and 'title' are problematic? 

I am saying that they need to be treated differently, and with more
care.

> How do they differ from, say 'subject'?

"subject", which refers to :description property, only contains a single
string, no Org syntax. OTOH, TITLE and AUTHOR keywords have their
contents parsed and, as such, can contain parsed objects. E.g.,

  | keyword | value   | property value |
  |-+-+|
  | DESCRIPTION | some *text* | "some *text*"  |
  | TITLE   | some *text* | ("some" (bold ... "text")) |

See also `org-element-document-properties'.

> Was this the reason they are not included by default in the PDF info?

They are not included by default in Org 8 because they were not included
in Org 7 either. I don't know the historical reason, though.


Regards,

-- 
Nicolas Goaziou

Re: [O] org-ref code

[John Kitchin]

I think you are restricted to single characters. That key is used by
reftex, so it would be a limitation in reftex. You can always define your
own function with a key-binding for something specific.

John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Tue, May 13, 2014 at 11:39 PM, Andreas Reuleaux wrote:

> John Kitchin  writes:
>
> > with the most recent org-ref, it should be sufficient to put this in your
> > init file:
> >
> > (org-ref-define-citation-link "textcite" ?I)
> > (org-ref-define-citation-link "citeauthorfull" ?F)
> >
> > this will create a textcite link and create a reftex menu you select with
> > the key I, and the other link with the key F. these should automatically
> be
> > links, and have completion functions. These will get exported as
> > \textcite{label} and \citeauthorfull{label}. The
> > org-ref-define-citation-link function adds the link, creates the
> functions
> > necessary, and adds the types to the right places.
> >
> > You do not need to do the manual additions unless you manually define the
> > link like you did with org-add-link-type.
> >
>
>
> OK, I see, and works fine, thanks.
>
> One minor thing: Am I restricted to single-letter keystrokes
> above ? like:
>
>   I (...?I)
>   F (... ?F)
>   C-t   (... ?\C-t)
>
> I tried to get working something like
>
>  C-r C-t
>
> with something like this
>
>   (... ?(kbd "C-r C-t"))
>
> with no success, but I am unsure, if there is just something simple
> missing like a quote or a backslash, or if it's just not possible
> at this point.
>
> -Andreas
>
>
>

[O] org-clock and org-agenda-files

[Esben Stien]

Is it possible to have org clock table run through all files in
org-agenda-files?

Looking at the manual, I can't find any way to do that.

-- 
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 http://www. s tn m
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Re: [O] org-ref code

[John Kitchin]

I also run emacs 24.3.

nearly my whole setup is here: https://github.com/jkitchin/jmax

If you are on windows, you should be able to clone that repository, and run
jmax.bat which will run the emacs binary in that repository and load the
jmax code which includes org-ref. You may not want to use my setup all the
time, but it might help figure out what is different with your setup.

For Macs or Linux, you just need to run something like "emacs -q -l
path/to/jmax/init.el" to try it out.

John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Tue, May 13, 2014 at 11:58 PM, Andreas Reuleaux wrote:

> Eric,
>
> I don't have auctex installed, and org-ref works fine for me.
>
> But I do run a recent self-compiled emacs 24 (haven't tested yet,
> if it works with my older emacs24 from debian as well),
> and I get updated packages like dash relatively often via cask
> ( https://github.com/cask/cask , http://cask.github.io/ ),
> i. e. I have in my Cask file
>
>   (depends-on "dash")
>
> so it wouldn't have happend to me to have an outdated dash pkg,
> isolating your problem and pointing at what exactly is causing your
> trouble is of course more difficult (and creating a minimal config that
> works for me takes more time than I currently have, sorry).
>
> Hope this helps, nevertheless
>
>
> -Andreas
>
>
>
> Eric S Fraga  writes:
>
> > John,
> >
> > another data point.  When I try to load an org file, once org-ref is
> > loaded, I get the following problem:
> >
> > Debugger entered--Lisp error: (wrong-type-argument stringp nil)
> >   re-search-forward(nil 10001 t)
> >   tex-main-file()
> >   reftex-TeX-master-file()
> >   reftex-tie-multifile-symbols()
> >   reftex-access-scan-info((16))
> >   reftex-parse-all()
> >   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> > (global-auto-revert-mode t) (reftex-parse-all))
> >   org-mode-reftex-setup()
> >   run-hooks(change-major-mode-after-body-hook text-mode-hook
> > outline-mode-hook org-mode-hook)
> >   apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> > outline-mode-hook org-mode-hook))
> >   run-mode-hooks(org-mode-hook)
> >
> > Because of this, org-ref doesn't get initialised properly.
> >
> > Any idea what may be causing this?  Do I need to configure auctex or
> > similar?
> >
> > thanks,
> > eric
>
>
>

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

[Ken Mankoff]

On 2014-05-14 at 01:00, Vikas Rawal  wrote:
>> 
>> pandoc -f latex -t docx test.tex -o test.docx
>> 
>> I see Org has exported my "W m^{-2}" as "W m$^{\text{-2}}$", which is
>> not what I would expect in LaTeX. In OS X Pages.app viewing the docx
>> this appears as "W m". In Word it shows up either as just "-2" or "W
>> m-2". In Word, the Math shows up with each character as a box (the math
>> is just missing in Pages). In Word the figures are missing (they appear
>> in Pages).
>> 
>
> First, you should differentiate between whether the problem is in
> Org->LaTeX conversion, or in LaTeX->Docx conversion.
>
> From what you describe above, the problem seems to be in Org->LaTeX 
> conversion. 
>
> For me, $W m^{-2}$ in Org produces correct LaTeX markup, and I get a good 
> docx using Pandoc.

Yes that equation problem seems to be due to me and Org->LaTeX.

But elsewhere I have

\begin{equation}
x=42
\end{equation}

in Org, which looks just like that in LaTeX, and that appears as just
strange little extended ASCII boxes in MS Word.

  -k.

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

[Vikas Rawal]

> 
> But elsewhere I have
> 
> \begin{equation}
> x=42
> \end{equation}
> 
> in Org, which looks just like that in LaTeX, and that appears as just
> strange little extended ASCII boxes in MS Word.
> 

I am on the latest version of Pandoc, and this works fine for me. 

Am sending you a sample off-list.

Vikas

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

[Vikas Rawal]

> 
> But elsewhere I have
> 
> \begin{equation}
> x=42
> \end{equation}
> 
> in Org, which looks just like that in LaTeX, and that appears as just
> strange little extended ASCII boxes in MS Word.
> 

I am on the latest version of Pandoc, and this works fine for me. 

Am sending you a sample off-list.

Vikas

Re: [O] org-clock and org-agenda-files

[Bastien]

Esben Stien  writes:

> Is it possible to have org clock table run through all files in
> org-agenda-files?
>
> Looking at the manual, I can't find any way to do that.

C-h i d m Org TAB C-s :scope C-s

and look for "agenda" in the lines below.

-- 
 Bastien

Re: [O] org-clock and org-agenda-files

[Esben Stien]

Bastien  writes:

> C-h i d m Org TAB C-s :scope C-s
> and look for "agenda" in the lines below.

Damn, sorry, don't know how I missed that, really. 

Thanks..

-- 
Esben Stien is b0ef@e s  a 
 http://www. s tn m
  irc://irc.  b  -  i  .   e/%23contact
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   jid:b0ef@n n

[O] bug#17484: 24.3.91; Emacs Pretest (emacs-24.3.91.tar.xz) freeze

[Stefan Monnier]

> gdb) xbacktrace
> "avl-tree-delete" (0x54b0)
> "byte-code" (0x55a0)
> "byte-code" (0x5760)
> "org-element--cache-process-request" (0x5990)
> "byte-code" (0x5aa0)
> "org-element--cache-sync" (0x5ce0)
> "org-element-at-point" (0x5e00)
> "byte-code" (0x60d0)
> "org-adaptive-fill-function" (0x6300)
> "fill-match-adaptive-prefix" (0x6480)
> "fill-context-prefix" (0x6620)
> "adaptive-wrap-fill-context-prefix" (0x67d0)
> "adaptive-wrap-prefix-function" (0x6a18)
> "run-hook-with-args" (0x6a10)
> 0x4d89f80 PVEC_COMPILED
> "funcall" (0x6b30)
> "jit-lock-fontify-now" (0x6e38)
> "jit-lock-function" (0x6fc8)
> "vertical-motion" (0xdca8)
> "end-of-visual-line" (0xde08)
> "call-interactively" (0xdfc0)
> "org-end-of-line" (0xe198)
> "call-interactively" (0xe350)
> "command-execute" (0xe478)

> I wonder if it is because `org-adaptive-fill-function' doesn't mix well
> with `adaptive-wrap-prefix-mode'...

As mentioned earlier, the immediate problem is that
org-adaptive-fill-function does not terminate (or at least takes too
long to terminate).

Now, one reason why this might happen here is that
adaptive-wrap-prefix-mode calls org-adaptive-fill-function everywhere,
so it might be called in places where it usually (i.e. when
adaptive-wrap-prefix-mode isn't in use) isn't triggered.


Stefan

Re: [O] org-edit-src-code outside of org

[Hubert Chathi]

On Tue, 13 May 2014 16:49:57 -0400, jorge.a.alf...@gmail.com (Jorge A. 
Alfaro-Murillo) said:

> Hi, I would like to use org-edit-src-code outside of org, I think it
> would be very handy in Message mode, to send messages that contain
> code and edit that code in the proper mode.

[...]

I've been thinking that something like org-edit-src-code might be a
useful alternative to some of the multiple-major-modes tools.

-- 
Hubert Chathi - Email/Jabber: hub...@uhoreg.ca - http://www.uhoreg.ca/
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Fingerprint: F24C F749 6C73 DDB8 DCB8  72DE B2DE 88D3 113A 1368

Re: [O] org-clock and org-agenda-files

[Bastien]

Esben Stien  writes:

> Bastien  writes:
>
>> C-h i d m Org TAB C-s :scope C-s
>> and look for "agenda" in the lines below.
>
> Damn, sorry, don't know how I missed that, really.

No problem!

-- 
 Bastien

Re: [O] Git not working

[Bastien]

Hi Marvin,

Marvin Doyley  writes:

> I am trying to pull the latest version of org, but I get the following
> error whenever I try to do so:
>
> fatal: read error: Connection reset by peer
>
> Does anybody now how to resolve this ?

I cleaned up some processes on the server, it is now back up.
But I'll investigate what when wrong, thanks for reporting this,

-- 
 Bastien

Re: [O] Git not working

[Bastien]

Bastien  writes:

> But I'll investigate what when wrong, thanks for reporting this,

went
-- 
 Bastien

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

[Suvayu Ali]

Hi Vikas,

On Tue, May 13, 2014 at 08:40:13PM +0200, Vikas Rawal wrote:
> > 
> > It seems safer/efficient to focus on making modular documentation that
> > is the definitive *best*/*right* way (and *best* explained) to do
> > something, and then to link to that prolifically.
> > 
> 
> Your points are very valid and expressed convincingly. 
> 
> Writing this document was a result of, first and foremost, a personal urge to 
> write it, and secondly, in view of very specific use cases (my graduate 
> students, to whom I wanted to provide a one-stop shop, before they explore 
> rest of the stuff).
> 
> That said, your arguments that it is not optimal to include such a document 
> as part of documentation on orgmode.org is perhaps right. I can see that 
> maintaining modular non-repetitive content is easier. Long-term maintenance 
> of documentation should be an important concern for something that is under 
> heavy development. 
> 
> Unless others feel differently, I would let the document float around the 
> cyberspace, on my personal website and on github, for anyone to discover and 
> use.

I hate a good resource getting lost in the Internet.  So I would like to
suggest you make a shorter version for Worg, just focusing on the
"producing a complete document part": R, ESS, pandoc, and all.

Of course that requires more of your time and effort.  So how about
using Worg as it is meant to be, copy paste the relevant sections into
worg and collaboratively trim it down to shape?

If people think that is a good idea, I could give this a first shot
sometime next week.

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.

[O] bug#17484: 24.3.91; Emacs Pretest (emacs-24.3.91.tar.xz) freeze

[Daimrod]

Stefan Monnier  writes:

>> gdb) xbacktrace
>> "avl-tree-delete" (0x54b0)
>> "byte-code" (0x55a0)
>> "byte-code" (0x5760)
>> "org-element--cache-process-request" (0x5990)
>> "byte-code" (0x5aa0)
>> "org-element--cache-sync" (0x5ce0)
>> "org-element-at-point" (0x5e00)
>> "byte-code" (0x60d0)
>> "org-adaptive-fill-function" (0x6300)
>> "fill-match-adaptive-prefix" (0x6480)
>> "fill-context-prefix" (0x6620)
>> "adaptive-wrap-fill-context-prefix" (0x67d0)
>> "adaptive-wrap-prefix-function" (0x6a18)
>> "run-hook-with-args" (0x6a10)
>> 0x4d89f80 PVEC_COMPILED
>> "funcall" (0x6b30)
>> "jit-lock-fontify-now" (0x6e38)
>> "jit-lock-function" (0x6fc8)
>> "vertical-motion" (0xdca8)
>> "end-of-visual-line" (0xde08)
>> "call-interactively" (0xdfc0)
>> "org-end-of-line" (0xe198)
>> "call-interactively" (0xe350)
>> "command-execute" (0xe478)
>
>> I wonder if it is because `org-adaptive-fill-function' doesn't mix well
>> with `adaptive-wrap-prefix-mode'...
>
> As mentioned earlier, the immediate problem is that
> org-adaptive-fill-function does not terminate (or at least takes too
> long to terminate).

Ok.

> Now, one reason why this might happen here is that
> adaptive-wrap-prefix-mode calls org-adaptive-fill-function everywhere,
> so it might be called in places where it usually (i.e. when
> adaptive-wrap-prefix-mode isn't in use) isn't triggered.

Is there a way to disable the effect of `inhibit-quit' in `jit-lock' so
C-g interrupt again in order to get an elisp-backtrace with
`debug-on-quit'.

Otherwise, what's the best way to debug this? Looking closer at
`org-adaptive-fill-function'?

-- 
Daimrod/Greg

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

[Axel Kielhorn]

Am 12.05.2014 um 14:57 schrieb Vikas Rawal :

> I have been using Org for writing research papers for a while, gradually 
> improving my set up to be able to exactly produce the output I want. In this 
> process, I have benefited greatly not only from the resources available on 
> the Org-mode website but also from various people who generously provided 
> solutions to my numerous queries on this mailing list. I felt that it may be 
> of some use if I put together all the pieces and document what I was doing.
> 
> I have put the draft for comments at: 
> https://github.com/vikasrawal/orgpaper/blob/master/orgpapers.org

This looks like a workflow I may like.

A few comments:

I tried to export the .org to Latex and failed because it needed
tabulary and threeparttable.

They are used if you use vikas-general.org but as far as i understood the 
document that is just recommended.

I added the line 
#+LaTeX_HEADER: \usepackage{tabulary,threeparttable}
to the document.

Another problem I had are the URLs in the section titles.
They cause problems when running the tex file a second time.

Runaway argument?
{R \(` `\045\BOOKMARK [2][-]{subsection.2.4}{Pandoc}{section.2}\BOOKMARK \ETC.
! File ended while scanning use of \@@BOOKMARK.
 
\par 

You may want to move the URLs from the section title to the body.

You are using straight (") quotation marks in org and the LaTeX export has 
straight quotation marks. Is there a way to convert them to “” or \enquote?

You are using

: #+LaTeX_CLASS_OPTIONS: [garamond]

which results in

\documentclass[garamond]{article}

But garamond is not a valid option for article.

I use this instead
#+Latex_HEADER: \usepackage{tgschola}

I tried ebgaramont, but that font does not contain TS1 support.

Now I have a printable version of your document and will have a closer look.

Greetings
Axel

Re: [O] [PATCH] Add author and title to exported PDF properties

[Marcel van der Boom]

On wo 14-mei-2014 14:48
Nicolas Goaziou  wrote:

> [...]
>> How do they differ from, say 'subject'?  
> 
> "subject", which refers to :description property, only contains a
> single string, no Org syntax. OTOH, TITLE and AUTHOR keywords have
> their contents parsed and, as such, can contain parsed objects. E.g.,
> 
>   | keyword | value   | property value |
>   |-+-+|
>   | DESCRIPTION | some *text* | "some *text*"  |
>   | TITLE   | some *text* | ("some" (bold ... "text")) |
> 
> See also `org-element-document-properties'.
>

Thanks, this section made the click for me. 

I think I sort of assumed that 'LateX codes' in author and title were
just going to be dropped by the hyperref package itself to produce the
properties.

I'm not sure I can find the time to produce a better patch, this is
uncharted territory for me, so it will take some learning effort.

Thanks again,

marcel


signature.asc
Description: PGP signature

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

[Vikas Rawal]

>> 
>> Unless others feel differently, I would let the document float around the 
>> cyberspace, on my personal website and on github, for anyone to discover and 
>> use.
> 
> I hate a good resource getting lost in the Internet.  So I would like to
> suggest you make a shorter version for Worg, just focusing on the
> "producing a complete document part": R, ESS, pandoc, and all.
> 
> Of course that requires more of your time and effort.  So how about
> using Worg as it is meant to be, copy paste the relevant sections into
> worg and collaboratively trim it down to shape?
> If people think that is a good idea, I could give this a first shot
> sometime next week.
> 

It would be wonderful if you could. At least some people seem to think it is 
useful to have a guide of this kind.  If so, improving it together should be 
the way to go.

Vikas

Re: [O] New worg page: Publishing beamer slideshows and articles from one source

[Suvayu Ali]

On Wed, May 14, 2014 at 12:56:35AM +, James Harkins wrote:
> Suvayu Ali  gmail.com> writes:
> 
> > A couple of comments about formatting: the
> > first two footnotes might be better as links from the text.  I propose
> > the attached patch.  If you think this is fine, I'll push it.
> 
> Sure, go ahead.

Done :)

-- 
Suvayu

Open source is the future. It sets us free.

[O] beamer columns and printout

[Seb Frank]

Hi,

I'm interested in using org-mode to generate beamer slides and an
article-like printout (using the article class, usepackage{beamerarticle}
and latex export) from the same source, and I am running into two problems
with the export to article when there are multiple columns.

1.) I often use an empty headline with B_columns tag to allow me to specify
top alignment. E.g.,

#+begin_src org
* :B_columns:
:PROPERTIES:
:BEAMER_env: columns
:BEAMER_opt: T
:END:
** Column 1 :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.35
:END:
** Column 2:BMCOL:
:PROPERTIES:
:BEAMER_COL: 0.6
:END:
#+end_src org

In the printout, this yields an ugly empty section with a number if num:t.
Is there a better way to pass [T] to the title-less columns environment, or
(less preferably) a way to specify a title for the section without it
appearing on the beamer slide?

2.) In the above example, the B_columns and BMCOL tags get exported to the
latex file for the printout (with an error because the underscore is used
outside of math mode). Can these be suppressed?

Thanks,
  Seb

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

[Vikas Rawal]

Thank you Axel for taking the time to test it. I look forward to more comments 
as you look at it. You comments are very useful.

> 
> I tried to export the .org to Latex and failed because it needed
> tabulary and threeparttable.
> 
> They are used if you use vikas-general.org but as far as i understood the 
> document that is just recommended.
> 
> I added the line 
> #+LaTeX_HEADER: \usepackage{tabulary,threeparttable}
> to the document.
> 

vikas-general.org (I already dislike my name being on that file) specifies 
these as part of org-latex-default-package-list, so both tabulary and 
threeparttable should get included by default.

I removed explicit inclusion of these packages from this document and the 
instructions, because I wanted to reduce the work in terms of setting things up.

> Another problem I had are the URLs in the section titles.
> They cause problems when running the tex file a second time.
> 
> Runaway argument?
> {R \(` `\045\BOOKMARK [2][-]{subsection.2.4}{Pandoc}{section.2}\BOOKMARK \ETC.
> ! File ended while scanning use of \@@BOOKMARK.
>  
>\par 
> 
> You may want to move the URLs from the section title to the body.
> 

I thought I had fixed this. But will check again.

> You are using straight (") quotation marks in org and the LaTeX export has 
> straight quotation marks. Is there a way to convert them to “” or \enquote?
> 

Should use 
(setq org-export-with-smart-quotes t)

Will add that to the revised abcd-general.org


> You are using
> 
> : #+LaTeX_CLASS_OPTIONS: [garamond]
> 
> which results in
> 
> \documentclass[garamond]{article}
> 
> But garamond is not a valid option for article.
> 

This is where I got this from

http://orgmode.org/worg/org-contrib/babel/examples/article-class.html#sec-4-3-2

I think it requires mathdesign to be loaded. But I will check.

Vikas

[O] bug#17484: 24.3.91; Emacs Pretest (emacs-24.3.91.tar.xz) freeze

[Stefan Monnier]

> Is there a way to disable the effect of `inhibit-quit' in `jit-lock' so
> C-g interrupt again in order to get an elisp-backtrace with
> `debug-on-quit'.
> Otherwise, what's the best way to debug this? Looking closer at
> `org-adaptive-fill-function'?

You can try `debug-on-event'.

There's jit-lock-debug-mode but it doesn't disable inhibit-quit.
So you'll need to additionally use

   (advice-add 'jit-lock--debug-fontify :around
 (lambda (fun &rest args)
   (with-local-quit (apply fun args

Of course sometimes this doesn't work because jit-lock-debug-mode
changes the way things are executed and the bug may not manifest itself
any more, but it's worth a try.

Another source of info is to

  M-x trace-function RET org-adaptive-fill-function RET
  M-x trace-function RET org-element-at-point RET
  M-x trace-function RET org-element--cache-sync RET
  M-x trace-function RET org-element--cache-process-request RET

Then reproduce the hang, then break the hang somehow (maybe with the
jit-lock-debug hack above, or maybe with debug-on-event, or with C-g C-g
C-g, ...), then look at the *trace..* buffer.


Stefan

[O] *text* in headlines and export to latex

[Seb Frank]

Hi,

Latex export converts *text* to \textbf -- this doesn't work well for
headlines that get turned into section titles as these appear to be bold by
default. Is there a way to change this to \emph in headlines that get
converted to (sub)sections?

Thanks,
  Seb

Re: [O] org-ref code

[Andreas Reuleaux]

OK, thanks.

-Andreas


John Kitchin  writes:

> I think you are restricted to single characters. That key is used by
> reftex, so it would be a limitation in reftex. You can always define your
> own function with a key-binding for something specific.
>
> John

Re: [O] [RFC] [PATCH] ob-core.el: allow the auto-generation of output file names for src blocks.

[Achim Gratz]

Aaron Ecay writes:
> Thanks again for the feedback.  I just pushed the revised patch to master.
>
>>> I think I would prefer the code in this patch to do nothing in this case
>>> (not create a :file value), but for language-specific code that needs a
>>> :file to raise an error to prompt the user to add a name.
>>>
>>
>> Fair enough, especially given that this default will be applied to *all*
>> code blocks, this seems like a reasonable approach.
>
> I went ahead with my suggested approach here.

That breaks the tests for Octave and Maxima; since you're intentionally
not keeping backwards compatibility here this should be fixed in the
tests, I'd think.

Also, I'd think you should be using "user-error" instead of error to
generate the messages.


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

Factory and User Sound Singles for Waldorf Blofeld:
http://Synth.Stromeko.net/Downloads.html#WaldorfSounds

Re: [O] org-ref code

[Eric S Fraga]

On Tuesday, 13 May 2014 at 20:28, John Kitchin wrote:
> interesting. I do have auxtex installed, but I don't think I configure it
> anywhere. I do require reftex and reftex-cite in my init files. I also set
> the default reftex bibliography.
>
> (setq reftex-default-bibliography
> '("~/Dropbox/bibliography/references.bib"))
>
> I will try to reproduce this tomorrow.

Hi John,

In case this helps, if I start emacs with -q and evaluate the contents
of emacs-minimal.el (attached) and then visit orgref.org (attached), I can 
insert a
reference (references.bib also attached) but the resulting latex doesn't
work because bibtex complains about missing bibstyle.  

If I add the LaTeX directive to specify the bibliography style (as the
attached file has), everthing works.  This includes C-u C-c ] asking for
type of citation.  

How do I specify the bibstyle for org-ref?

When I say that everything works, it works with this minimal
configuration but not yet in my full configuration.  But that's my
problem.  Somehow, I am making the latex exporter not handle cite:
links.  Very strange.  I'll get back to you on this in due course!

I am actually using Emacs 24.4, not 24.3.  I'm tracking emacs-snapshot
which is the development version as I like to live dangerously ;-)

thanks again for org-ref,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git
# -*- org-latex-pdf-process: ("pdflatex %b" "bibtex %b" "pdflatex %b" "pdflatex %b") -*-
#+title: test out org-ref
* Introduction
The paper by somebody 
cite:aaltola-2002 is most interesting.  Also, autocite:aaltola-2002 is exciting.
* References

#+latex: \bibliographystyle{acm}
bibliography:references.bib
@Article{aaltola-2002,
  author = 	 {J. Aaltola},
  title = 	 {Simultaneous synthesis of flexible heat exchanger network},
  journal = 	 {Applied Thermal Engineering},
  year = 	 2002,
  volume =	 22,
  number =	 8,
  pages =	 {907-918}
}


emacs-minimal.el
Description: application/emacs-lisp

Re: [O] *text* in headlines and export to latex

[Eric S Fraga]

On Wednesday, 14 May 2014 at 18:00, Seb Frank wrote:
> Hi,
>
> Latex export converts *text* to \textbf -- this doesn't work well for
> headlines that get turned into section titles as these appear to be bold by
> default. Is there a way to change this to \emph in headlines that get
> converted to (sub)sections?

Silly question but: can you not simply use /text/ instead in the
headlines?  Mind you, I think that bold + emph is not pretty... but
that's a personal taste issue!
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

[O] [Latex Export] Influence placement of \maketitle command

[Alexander Baier]

Hello,

I am writing a paper using llncs as the document class. I use the
=\institute= command which has to be placed _above_ the =\maketitle=
command to be considered. But exporting my document always yields a
latex file where =\maketitle= appears above =\institute=. I use
simple #+LATEX: directives to insert =\institute=.

Is there a way for me to influence the placement of =\maketitle= and
thus be able to order those commands "the right way"?

TIA for any pointers,
-- 
Alexander Baier

Re: [O] *text* in headlines and export to latex

[Seb Frank]

Yes -- but that changes it to emph (instead of alert) in beamer export.


On Wed, May 14, 2014 at 7:19 PM, Eric S Fraga  wrote:

> On Wednesday, 14 May 2014 at 18:00, Seb Frank wrote:
> > Hi,
> >
> > Latex export converts *text* to \textbf -- this doesn't work well for
> > headlines that get turned into section titles as these appear to be bold
> by
> > default. Is there a way to change this to \emph in headlines that get
> > converted to (sub)sections?
>
> Silly question but: can you not simply use /text/ instead in the
> headlines?  Mind you, I think that bold + emph is not pretty... but
> that's a personal taste issue!
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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

[Axel Kielhorn]

Am 14.05.2014 um 18:51 schrieb Vikas Rawal :

> 
> Thank you Axel for taking the time to test it. I look forward to more 
> comments as you look at it. You comments are very useful.

I'm new to Emacs, but know LaTeX and Pandoc.
I have a lot of beginner’s questions.
(Configuring emacs is quite difficult: should I use
- custom-set-variable
- starter-kit
- raw elisp in .emacs
)

In your document you are using alt instead of meta.
Not everyone uses alt for meta (especially on the Mac where alt (option) is 
used to access unusual characters).

>> I tried to export the .org to Latex and failed because it needed
>> tabulary and threeparttable.
>> 
>> They are used if you use vikas-general.org but as far as i understood the 
>> document that is just recommended.
>> 
>> I added the line 
>> #+LaTeX_HEADER: \usepackage{tabulary,threeparttable}
>> to the document.
>> 
> 
> vikas-general.org (I already dislike my name being on that file)

How about

config.org ?
config-example.org ?

And ask the user to copy it to $USER.org 

> I removed explicit inclusion of these packages from this document and the 
> instructions, because I wanted to reduce the work in terms of setting things 
> up.

You achieved the opposite.
Now a user *has* to enable the config file.
Otherwise it would be clear that additional packages may be needed which may 
not be part of a minimal TeX Live installation.


>> You are using
>> 
>> : #+LaTeX_CLASS_OPTIONS: [garamond]
>> 
>> which results in
>> 
>> \documentclass[garamond]{article}
>> 
>> But garamond is not a valid option for article.
>> 
> 
> This is where I got this from
> 
> http://orgmode.org/worg/org-contrib/babel/examples/article-class.html#sec-4-3-2
> 
> I think it requires mathdesign to be loaded. But I will check.

Yes, and some additional LaTeX coding.

I'll wait for the next release and have a closer look.

Axel

Re: [O] [Latex Export] Influence placement of \maketitle command

[Nick Dokos]

Alexander Baier  writes:

> Hello,
>
> I am writing a paper using llncs as the document class. I use the
> =\institute= command which has to be placed _above_ the =\maketitle=
> command to be considered. But exporting my document always yields a
> latex file where =\maketitle= appears above =\institute=. I use
> simple #+LATEX: directives to insert =\institute=.
>
> Is there a way for me to influence the placement of =\maketitle= and
> thus be able to order those commands "the right way"?
>
> TIA for any pointers,

If \institute can be placed in the preamble, then using #+LATEX_HEADER
instead of #+LATEX is probably the way to go.

If it has to be in the document body, one way to do it is to redefine
the variable org-latex-title-command in a file-local-variable section
added to the end of your file:

# Local Variables:
# org-latex-title-command: "\\institute{Foo}\\maketitle"
# End:

See

   (info "(emacs) File variables")
   
Nick

Re: [O] org-ref code

[Andreas Reuleaux]

Eric S Fraga  writes:


> How do I specify the bibstyle for org-ref?


I am not sure if I understand your question correctly
and John certainly has more insight here, but I have in
my org document

#+LaTeX_HEADER: \include{ltxhdr}

and within that ltxhdr.tex I have among other config settings

  \usepackage[backend=bibtex,style=authoryear]{biblatex}
  \addbibresource{refs.bib}

I could have written several lines of 

#+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
#+LaTeX_HEADER: \addbibresource{refs.bib}

instead.

There is no specific bibstyle of org-ref (correct, John?), that's the
job of latex, you will be happy if:

* your org mode has clickable citations links,

* let's you insert citations in a comfortably manner

* you can jump between refs and labels etc.

* all of those citations get exported to their latex
  equivalents

If for some reason your citations get exported to latex, say
cite:foo to \cite{foo}, but still don't appear in your
final pdf, than you have to tweek your latex settings,
obviously. - Maybe forgot to call bibtex(8) on your document?

I run these:
* an emacs batch script, tex.el to get the document.tex
  from document.org
* xelatex -8bit -shell-escape document.tex
* bibtex8 document
* xelatex document
  again, etc.

You can check your latex toolchain independently from
your org-ref config.

HTH,
  -Andreas
  

Re: [O] org-ref code

[Sharon Kimble]

Andreas Reuleaux  writes:

> Eric S Fraga  writes:
>
>
>> How do I specify the bibstyle for org-ref?
>
>
> I am not sure if I understand your question correctly
> and John certainly has more insight here, but I have in
> my org document
>
> #+LaTeX_HEADER: \include{ltxhdr}
>
> and within that ltxhdr.tex I have among other config settings
>
>   \usepackage[backend=bibtex,style=authoryear]{biblatex}
>   \addbibresource{refs.bib}
>
> I could have written several lines of 
>
> #+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
> #+LaTeX_HEADER: \addbibresource{refs.bib}
>
> instead.
>
> There is no specific bibstyle of org-ref (correct, John?), that's the
> job of latex, you will be happy if:
>
> * your org mode has clickable citations links,
>
> * let's you insert citations in a comfortably manner
>
> * you can jump between refs and labels etc.
>
> * all of those citations get exported to their latex
>   equivalents
>
> If for some reason your citations get exported to latex, say
> cite:foo to \cite{foo}, but still don't appear in your
> final pdf, than you have to tweek your latex settings,
> obviously. - Maybe forgot to call bibtex(8) on your document?
>
> I run these:
> * an emacs batch script, tex.el to get the document.tex
>   from document.org
> * xelatex -8bit -shell-escape document.tex
> * bibtex8 document
> * xelatex document
>   again, etc.
>
> You can check your latex toolchain independently from
> your org-ref config.
>
> HTH,
>   -Andreas

That seems a very long winded way round things! For your information
this is a batch script that I'm using for generating a PDF in pure
latex, and all I have to do is to cd to the directory where the
files are, and then just enter "pdfbuild" in the command-line. It
does all the rest itself, and you could easily adapt it for your
circumstances
--8<---cut here---start->8---
#!/bin/bash
set -e
#set -x

#variables
filename="uh2014"

#
xelatex $filename
biber $filename
biber $filename
xelatex $filename 
biber $filename
xelatex $filename 
makeindex $filename
makeindex $filename
xelatex $filename
makeglossaries $filename
xelatex $filename
xelatex $filename
--8<---cut here---end--->8---

It handles and generates the references, the glossary, and the index
as well as the body of the document. 

All you have to do is enter your "foo.tex" where foo is the name of
your generated tex file, and then let the script take over.

Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
my git repo = https://bitbucket.org/boudiccas/dots
TGmeds = http://www.tgmeds.org.uk
Debian testing, Fluxbox 1.3.5, emacs 24.3.91.1


signature.asc
Description: PGP signature

Re: [O] org-ref code

[Andreas Reuleaux]

Well, I know how to write shell scripts,
and have something similar encoded in a shake file
(haskell make replacement), for that matter,
but prefer to have xelatex not called 5 times
during every little development step.
Anyway thanks a lot.

My point here really was, that org-ref and
the latex chains are separate and can be
separately tested.

-Andreas


Sharon Kimble  writes:

> Andreas Reuleaux  writes:
>
>> Eric S Fraga  writes:
>>
>>
>>> How do I specify the bibstyle for org-ref?
>>
>>
>> I am not sure if I understand your question correctly
>> and John certainly has more insight here, but I have in
>> my org document
>>
>> #+LaTeX_HEADER: \include{ltxhdr}
>>
>> and within that ltxhdr.tex I have among other config settings
>>
>>   \usepackage[backend=bibtex,style=authoryear]{biblatex}
>>   \addbibresource{refs.bib}
>>
>> I could have written several lines of 
>>
>> #+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
>> #+LaTeX_HEADER: \addbibresource{refs.bib}
>>
>> instead.
>>
>> There is no specific bibstyle of org-ref (correct, John?), that's the
>> job of latex, you will be happy if:
>>
>> * your org mode has clickable citations links,
>>
>> * let's you insert citations in a comfortably manner
>>
>> * you can jump between refs and labels etc.
>>
>> * all of those citations get exported to their latex
>>   equivalents
>>
>> If for some reason your citations get exported to latex, say
>> cite:foo to \cite{foo}, but still don't appear in your
>> final pdf, than you have to tweek your latex settings,
>> obviously. - Maybe forgot to call bibtex(8) on your document?
>>
>> I run these:
>> * an emacs batch script, tex.el to get the document.tex
>>   from document.org
>> * xelatex -8bit -shell-escape document.tex
>> * bibtex8 document
>> * xelatex document
>>   again, etc.
>>
>> You can check your latex toolchain independently from
>> your org-ref config.
>>
>> HTH,
>>   -Andreas
>
> That seems a very long winded way round things! For your information
> this is a batch script that I'm using for generating a PDF in pure
> latex, and all I have to do is to cd to the directory where the
> files are, and then just enter "pdfbuild" in the command-line. It
> does all the rest itself, and you could easily adapt it for your
> circumstances
> #!/bin/bash
> set -e
> #set -x
>
> #variables
> filename="uh2014"
>
> #
> xelatex $filename
> biber $filename
> biber $filename
> xelatex $filename 
> biber $filename
> xelatex $filename 
> makeindex $filename
> makeindex $filename
> xelatex $filename
> makeglossaries $filename
> xelatex $filename
> xelatex $filename
>
> It handles and generates the references, the glossary, and the index
> as well as the body of the document. 
>
> All you have to do is enter your "foo.tex" where foo is the name of
> your generated tex file, and then let the script take over.
>
> Sharon.

Re: [O] org-ref code

[John Kitchin]

Good. I am glad to hear you are making some progress!

you have to specify the bibliography style for latex export somewhere in
the document. You can use a bibliographystyle link for bibtex, eg.
bibliographystyle:unsrt. That will get exported to
\bibliographystyle{unsrt}. That link does not do anything but export to
latex. or you can simply put \bibliographystyle{unsrt} above the
bibliography link. For any other thing like biblatex, just put the code
that specifies the style where it belongs, e.g. in the header with
#+latex_header: or at the end with the raw latex commands. Not all
documents require a style, article classes do, but the revtex4-1 class, for
example defines the style for you.

I wonder if you are adding another cite link later that overrides my cite
link. do the other citation links export ok, e.g. autocite, citeyear,
etc...?

John

---
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Wed, May 14, 2014 at 2:17 PM, Eric S Fraga  wrote:

> On Tuesday, 13 May 2014 at 20:28, John Kitchin wrote:
> > interesting. I do have auxtex installed, but I don't think I configure it
> > anywhere. I do require reftex and reftex-cite in my init files. I also
> set
> > the default reftex bibliography.
> >
> > (setq reftex-default-bibliography
> > '("~/Dropbox/bibliography/references.bib"))
> >
> > I will try to reproduce this tomorrow.
>
> Hi John,
>
> In case this helps, if I start emacs with -q and evaluate the contents
> of emacs-minimal.el (attached) and then visit orgref.org (attached), I
> can insert a
> reference (references.bib also attached) but the resulting latex doesn't
> work because bibtex complains about missing bibstyle.
>
> If I add the LaTeX directive to specify the bibliography style (as the
> attached file has), everthing works.  This includes C-u C-c ] asking for
> type of citation.
>
> How do I specify the bibstyle for org-ref?
>
> When I say that everything works, it works with this minimal
> configuration but not yet in my full configuration.  But that's my
> problem.  Somehow, I am making the latex exporter not handle cite:
> links.  Very strange.  I'll get back to you on this in due course!
>
> I am actually using Emacs 24.4, not 24.3.  I'm tracking emacs-snapshot
> which is the development version as I like to live dangerously ;-)
>
> thanks again for org-ref,
> eric
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

Re: [O] [Latex Export] Influence placement of \maketitle command

[Alexander Baier]

On 2014-05-14 21:01 Nick Dokos wrote:
> Alexander Baier  writes:
>
>> Hello,
>>
>> I am writing a paper using llncs as the document class. I use the
>> =\institute= command which has to be placed _above_ the =\maketitle=
>> command to be considered. But exporting my document always yields a
>> latex file where =\maketitle= appears above =\institute=. I use
>> simple #+LATEX: directives to insert =\institute=.
>>
>> Is there a way for me to influence the placement of =\maketitle= and
>> thus be able to order those commands "the right way"?
>>
>> TIA for any pointers,
>
> If \institute can be placed in the preamble, then using #+LATEX_HEADER
> instead of #+LATEX is probably the way to go.

Of course! Somehow I totally forgot about the LATEX_HEADER
directive. With this, everything works fine!

> If it has to be in the document body, one way to do it is to redefine
> the variable org-latex-title-command in a file-local-variable section
> added to the end of your file:
>
> # Local Variables:
> # org-latex-title-command: "\\institute{Foo}\\maketitle"
> # End:

Oh, the title-command is a variable, that is nice.

Thank you very much,
-- 
Alexander Baier

Re: [O] org-ref code

[Eric S Fraga]

On Wednesday, 14 May 2014 at 20:03, Andreas Reuleaux wrote:
> Eric S Fraga  writes:
>> How do I specify the bibstyle for org-ref?

[...]

> There is no specific bibstyle of org-ref (correct, John?), that's the

That's what I wanted to confirm.  And it has been confirmed (by both you
and another email from John).  Thanks.
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: [O] Export to iCalendar only not DONE, scheduled tasks?

[Arun Persaud]

Hi

On 05/10/2014 07:55 AM, Chris Poole wrote:
> On Mon, May 5, 2014 at 11:08 PM, Arun Persaud  > wrote:
> 
> pretty sure this can be done. I export only events to an ics file that
> have a start and an end date and are not in a certain category. For this
> I use
> 
> 
> That's great, thank you. I have this, but it doesn't work:
> 
> (defun filter-scheduled-todo-tasks (content backend info)
>   "Filter iCalendar export to include only TODO tasks that are
> not done, but which are scheduled or have a deadline."
>   (when (eq backend 'icalendar)
> (if (and (org-entry-is-todo-p)
>  (not (org-entry-is-done-p))
>  (or (org-get-scheduled-time (point))
>  (org-get-deadline-time (point
> content nil)))
> 
> ... called with:
> 
> (let ((org-export-filter-final-output-functions
>  '(filter-scheduled-todo-tasks)))
> (org-icalendar-combine-agenda-files))

had another look and org-export-filter-final-output-functions is the
wrong function to use. I'm not really using the ical export anymore and
when the org exporter got updated a while ago, I apparently didn't
update this correctly. Sorry about that.

I think the correct way is probably something like:

(defun filter-scheduled-todo-tasks (data backend info)
   ; add check for backend
  (org-element-map data 'headline 'my-debug info)
  data)

(defun org-mycal-export ()
  (let ((org-export-filter-parse-tree-functions
'(filter-scheduled-todo-tasks)))
(org-icalendar-combine-agenda-files)))

the filter function is called before each entry is transcoded into ical
format and gets the whole parse tree. You can then loop through the
parse tree with org-element-map looking at each headline (not 100% sure
if headline is the correct thing to use). Each headline has for example
properties set that you can use to filter. You can access them using
things like:

(defun my-debug (e)
(message "+")
(message (buffer-substring (org-element-property :begin e)
(org-element-property :end e)))
(message "--")
(message "%S" (org-element-property :raw-value e))
(message "-- todo")
(message "%S" (org-element-property :todo-keyword e))
(message "-- todo type")
(message "%S" (org-element-property :todo-type e))
(message "-- tags")
(message "%S" (org-element-property :tags e))
(message "-- level")
(message "%S" (org-element-property :level e))
(message "*"))

To ignore a headline, I think, you can mark it using

(org-export-ignore-element headline info)

where headline would be the same as argument 'e' in my-debug, but I
haven't played around with this yet. I found

http://searchcode.com/codesearch/view/48068680

which uses the function and perhaps you can get an idea how things work
from it.

Arun

Re: [O] still seeing semi-regular lockups

[Eric Abrahamsen]

die...@schoen.or.at writes:

> hi,
>
> on my machine wanderlust hangs from time to time when i am inside the company 
> net and
> the proxy has hiccups.
> then C-g (sometimes several) usually help.
>
> in the link below i found an interesting variable, debug-on-quit.
> when it is set, emacs enters the debugger when you hit C-g.

Whatever's going on here isn't network-related, it's pretty clearly
triggered by making editing changes to an org buffer. It's also
unsalvageable with C-g, or this whole thing would be much simpler!
There's an ongoing thread between Daimrod and Stephen that might
actually be the same issue, I'll check that out.

> sendings signal to emacs from external usually only kills it.
> the only signal which i am aware of that can be caught is SIGUSR1.
> i used to use it to notify emacs about network changes.

Good to know, thanks!

> hope this helps,
> dieter
>
> [1] 
> http://www.gnu.org/software/emacs/manual/html_node/elisp/Infinite-Loops.html#Infinite-Loops
>
>
>
>> Original Message 
>>From: Eric Abrahamsen 
>>To: emacs-orgmode@gnu.org
>>Sent: Wed, May 14, 2014, 10:36 AM
>>Subject: [O] still seeing semi-regular lockups
>>
>>Hey there,
>>
>>After Nicolas made the last round of improvements to the caching
>>mechanism I got far fewer hangs with Org, but they are still happening.
>>Maybe once a day or so, on average, editing something in an Org buffer
>>causes emacs to hang, and my fans to spin up, and there we are until I
>>kill emacs.
>>
>>It happens often enough that I guess it's worth running emacs under some
>>kind of debugger -- at least, I assume that's the best way of catching
>>the bug. I'm not really sure how to go hunting, though, so if anyone had
>>any advice in this direction, that would be great.
>>
>>In the meantime, is there any way of interrupting emacs so it quits
>>whatever its doing, without having to kill it? I've played around with
>>sending different signals using "kill", just for fun, but everything
>>I've tried either does nothing, or kills emacs altogether.
>>
>>Cheers,
>>Eric

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

[Vikas Rawal]

> 
>> 
>> Thank you Axel for taking the time to test it. I look forward to more 
>> comments as you look at it. You comments are very useful.
> 
> I'm new to Emacs, but know LaTeX and Pandoc.
> I have a lot of beginner’s questions.
> (Configuring emacs is quite difficult: should I use
> - custom-set-variable
> - starter-kit
> - raw elisp in .emacs
> )
> 

You could use either. 

I think starter-kit is a good choice. You will be up and running in no time. 
Just put it in place. 

If you are using the starter kit, you should create a sub-directory inside 
.emacs.d with your username. Any .org file or .el file you keep inside will be 
evaluated when you start emacs. 

If you put my config file in that sub-directory, you are good to go as far as 
my basic set up goes.

In addition, you could have your personal config files for whatever additional 
you want.

This is not necessarily “optimal”, but it will be quick and clean. As you 
learn, you can customise to make it optimal to your needs.

> In your document you are using alt instead of meta.
> Not everyone uses alt for meta (especially on the Mac where alt (option) is 
> used to access unusual characters).
> 
>>> I tried to export the .org to Latex and failed because it needed
>>> tabulary and threeparttable.
>>> 
>>> They are used if you use vikas-general.org but as far as i understood the 
>>> document that is just recommended.
>>> 
>>> I added the line 
>>> #+LaTeX_HEADER: \usepackage{tabulary,threeparttable}
>>> to the document.
>>> 
>> 
>> vikas-general.org (I already dislike my name being on that file)
> 
> How about
> 
> config.org ?
> config-example.org ?
> And ask the user to copy it to $USER.org 
> 

Yes, one of these, I guess. I want to leave $user.org for additional personal 
configurations that the person may want to do.

>> I removed explicit inclusion of these packages from this document and the 
>> instructions, because I wanted to reduce the work in terms of setting things 
>> up.
> 
> You achieved the opposite.
> Now a user *has* to enable the config file.
> Otherwise it would be clear that additional packages may be needed which may 
> not be part of a minimal TeX Live installation.
> 

May be I should specify the packages that are being called, so the user can 
make sure those are installed or modify the config file. But I prefer the basic 
set of LaTeX packages being called by default rather than being added in every 
file.

Vikas