[O] Emacs batch and bbdb Issue

[Aric Gregson]

Hello,

I have cron set up to send me an email with my org calendar each morning
as follows:

/usr/local/bin/emacs --batch -l ~/.emacs --eval '(org-batch-agenda a
org-agenda-span (quote day))'

It works fine unless Gnus starts running. When that happens, bbdb is
taken by Gnus and then the emacs --batch gets stuck because it wants to
know if emacs should steal the bbdb file.

I use diary in org. I am not sure if there is a way to not use bbdb file
and still use diary? Is there a way to make stealing the bbdb file the
default for emacs upon start-up?

Thanks, Aric

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[O] Source Code Header Not Honored in Exportation?

[Aric Gregson]

Hello,

I am trying to export via org-odt and do not want some of the R source
run during export. For these blocks I have the following:

#+begin_src R :eval no

However, it seems that they are still being evaluated, despite having
refreshed the local set-up. Is this not the correct header to tell org
not to evaluate the code block?

Thanks, Aric

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Re: [O] Source Code Header Not Honored in Exportation?

[Aric Gregson]

Aric Gregson aorc...@mac.com writes:

 I am trying to export via org-odt and do not want some of the R source
 run during export. For these blocks I have the following:

 #+begin_src R :eval no

 However, it seems that they are still being evaluated, despite having
 refreshed the local set-up. Is this not the correct header to tell org
 not to evaluate the code block?

It seems that the file was actually not getting refreshed. Closing and
opening the file caused the headers to be noticed and the evaluation was
not carried out, just as desired. 

Thanks, Aric

Re: [O] Repeat task a fixed number of times

[Aric Gregson]

Bastien b...@gnu.org writes:

 SabreWolfy sabrewo...@gmail.com writes:

 How do I indicate that the event should be repeated monthly for 6 months
 only? Time-shift?

 FWIW, this is a frequently requested feature and I will propose
 something other than cloning headlines for the next major Org version.

I entirely agree. Thus far I have been pulling my hair out getting diary
sexp statements to work. They do, but unless you understand how to write
them, it is time consuming searching the web for instructions.

Thanks, Aric

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Re: [O] Excluding habits from Diary?

[Aric Gregson]

Aric Gregson aorc...@mac.com writes:

 The main improvement for me would be to repress the introduction of
 habits into the diary output. I have not been able to accomplish this
 thus far, and am unsure of how I might go about trying to do so.

The way I have worked around this is to set the habits to show only for
the present day in the agenda. They are then not exported into the diary
calendar unless you export the present day. This works just fine. 

Aric

[O] Excluding habits from Diary?

[Aric Gregson]

Hello,

I have recently found that I can combine my org-mode
calendar/scheduling/todo with the Emacs diary to output to latex via
cal-tex.el. This is fantastic, despite a few nagging issues.

The main improvement for me would be to repress the introduction of
habits into the diary output. I have not been able to accomplish this
thus far, and am unsure of how I might go about trying to do so.

To integrate org-mode with the diary I simply have the following at the
top of my diary:

%%(diary-sunrise-sunset)
%%(diary-lunar-phases)
%%(org-diary)

Thanks in advance, Aric

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Re: [O] MobileOrg

[Aric Gregson]

That's what I was looking for. Didn't realize I could do that...

Thanks, Aric

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Re: [O] MobileOrg

[Aric Gregson]

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

 org-mobile.el which is responsible for the sync has a custom var defined
 called 'org-mobile-files-exclude-regexp' which should exlude files that
 match.

OK. I've tried to play with this, but clearly my understanding of emacs
and regex is inadequate for this. Ideally I would like to exclude all of
the files except for two, agenda.org and organizer.org. Alternatively,
is there a way to list all files you want excluded in the regex match
pattern?

I tried [[:name.of.file:]][[:name.of.another:]] but it didn't like
that. I can exclude a single file just by putting it's name in, but I am
not clear on how to make a list of files to exclude. 

Thanks, Aric

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Re: [O] BBDB and Org

[Aric Gregson]

Eric Abrahamsen e...@ericabrahamsen.net writes:

 Ah, check the variable bbdb-read-only then -- it's for precisely this
 situation.

Exactly what I was looking for! Thank you.

Aric

[O] BBDB and Org

[Aric Gregson]

Hello,

I am just wondering if there is a way to get org mode to stop playing
with bbdb. Because I use both gnus and org, it is a bit of a hassle to
have org always pulling bbdb away from gnus when I create an agenda. I
have taken out all reference to bbdb and org in my start-up files. I
don't use anniversary any longer (could not get it to work properly with
version 3 of bbdb, despite some help from the list) and really don't see
why org needs it. Any idea of how to turn it off? 

Thanks, Aric

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Re: [O] BBDB and Org

[Aric Gregson]

Eric Abrahamsen e...@ericabrahamsen.net writes:

 I'm also not sure what you mean by org pulling bbdb away from gnus --
 are you running two separate instances of emacs?

Yes, that is precisely what I am doing. I tend to work in the Emacs
instance running org mode and use the other just for email. Too much
blocking if I do it all in one instance. Plus, previously there were
lots of crashes, but things do appear more stable now.

Thanks, Aric

Re: [O] BBDB and Org

[Aric Gregson]

Thanks Charles. I may try this again. I have had lots of issues moving
From v2 to v3 of bbdb. Still problems with Gnus, but workable at this
point.

Aric


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Re: [O] Org Agenda and BBDB File

[Aric Gregson]

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

 I think your impression is correct, assuming that org-agenda-file-regexp
 has not been modified:

Thanks Nick. So I am left trying to figure out why org agenda creation
keeps pulling in the bbdb file.

Aric

[O] Org Agenda and BBDB File

[Aric Gregson]

Hello,

I am wondering if it is possible to get org-mode to stop asking to read
the bbdb file when creating the new agenda. It is a bit annoying because
GNUS in another instance of emacs generally has the file. 

I have seemingly removed any calls to bbdb in my org set-up (initially
used it for anniversaries, but now doesn't appear to work in bbbd v3). I
now have no dates that need to be looked at for agenda creation in org
mode.

If I have  '(org-agenda-files (quote (~/org))) and the bbdb file is in
this directory, it is then used by org mode to create the agenda? My
impression was that only files ending in '.org' in the directory were
used. 

Thanks, Aric

Re: [O] MobileOrg

[Aric Gregson]

Hello,

I was wondering if it is possible to export only some of the org files
for mobileorg? Like have a list of included or excluded files?

Thanks, Aric

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Re: [O] MobileOrg

[Aric Gregson]

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

 org-mobile.el which is responsible for the sync has a custom var defined
 called 'org-mobile-files-exclude-regexp' which should exlude files that
 match.

Thanks very much. I'll give this a try again. Would be nice to have on
the phone once and a while. For computer syncing I find github to work
very well. 

Thanks, Aric

Re: [O] [ANN] ELPA package for ODT and JabRef exporters

[Aric Gregson]

Jambunathan,

I have tried to install this. I even created a blank .emacs file as you
suggested. Everything appears to be fine with the exception of 

C-h v org-odt-styles-dir
C-h v org-odt-schema-dir

These do not appear as options for me. I'm not sure if that matters.

Thanks, Aric

[O] Habits and Diary Type Dates?

[Aric Gregson]

Hello,

I believe that what I want to do will not work, but I thought I would
ask. I have a habit that I want to do on certain days of the week
only. I had the date in the org file set as the following:

#+begin_src org
%%(memq (calendar-day-of-week date) '(2 3 0))
#+end_src 

While it shows up on the calendar on the correct dates, it will not
cycle like a habit should. It will actually move to a DONE
state. Changing the date format back to an org date type format seems to
solve the problem.

Is there a work-around? 

Thanks, Aric

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[O] GPG Files and Agenda

[Aric Gregson]

Hello,

I have a gpg encrypted org file in my org directory that I have tracked
time on. I would like this to show up in the Agenda view when I create
it and have logging on, but it seems that logged time from the gpg file
is not included in the agenda. I have loaded the module org-crypt, but
that does not seem to do anything different. I should note that I
encrypted it outside of org-mode, I used just the emacs 'Encrypt-file'
function. 

Must the file be encrypted from within org mode? Or is this just
something you cannot do? 

Thanks, Aric

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Re: [O] Habits and Diary Type Dates?

[Aric Gregson]

--On January 29, 2014 9:18:57 PM -0800 Josiah Schwab jsch...@gmail.com 
wrote:



I have a habit that I only do on weekdays, and the workaround that I
ended up using was to have separate copies of the task for each day of
the week that I want to do it.


Thanks, I read the link. Sounds like they are just not meant to work that 
way.


Aric

Re: [O] Citations and references in ODT

[Aric Gregson]

--On January 19, 2014 11:16:53 AM +0530 Jambunathan K 
kjambunat...@gmail.com wrote:



Are you still stuck here or you made some repairs and stuck elsewhere.

...

IMO, starting from scratch (i.e., an empty .emacs) and installing Org
via M-x list-packages is a sure way to have a working setup with minimal
fuss.


Yes, still stuck here. All works fine so long as I don't try to use your 
modified files, thus I imagined it was due to some error when installing 
your modified files for org, which it must be. I will look through and 
reinstall again and see what I can find. Otherwise, works well enough now 
without the ox-jabref.el.


Aric

Re: [O] How to write medical journal articles with org-mode

[Aric]

Jambunathan K kjambunathan at gmail.com writes:

 regcl regcl at channing.harvard.edu writes:
 
  org  latex  pandoc  docx ?
 
 Too many moving parts.  

I agree. I tried this with a relatively simple export, albeit with tables and
figures and references,  and pandoc choked on the latex and I was not
able to figure out what the problem was.  

 Pick a workflow that has minimum dependencies - even if that means
 throwing Emacs out the Windows.

For collaboration it is actually easier to do just that. Keep all of your R
files and latex files in the directory and pound out the draft in odt/doc. 

Now trying org as a 'master' document to hold the latex (only tikz, no
other reason to use at this point) and R code.  I can easily produce draft
documents in odt - doc for collaborators. The challenge will be the
references on a unix computer. For mac and windows I don't think it is
a problem at that point. 

A 'more mature' markdown exporter would help for medical writing.

Aric

Re: [O] Citations and references in ODT

[Aric Gregson]

Ken Mankoff mank...@gmail.com writes:

 Aric, perhaps you could add markdown support using export filters? I have
 just come across this feature and it looks useful.

 http://thread.gmane.org/gmane.emacs.orgmode/74816/focus=74876

I'll give this a try, but my lisp knowledge is nil. I can pretty easily
change the references to latex format with a search and replace, but I
am running into issues going from latex to docx with pandoc. Will
probably need to explore this option here more and wait to see if
Jambunathan has any ideas as to why his exporter is not working with my
set-up.

Thanks, Aric

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Re: [O] Citations and references in ODT

[Aric Gregson]

Jambunathan K kjambunat...@gmail.com writes:

 This will be an one-off change, so I am hesitant to consider this.
...
 I am interested in considering all suggestions or use-cases that extends
 or improves upon the current practice. 

Clearly for me, this would not be a one off change...

Thanks, Aric

Re: [O] Citations and references in ODT

[Aric Gregson]

Jambunathan K kjambunat...@gmail.com writes:

 C-h v org-version

org-version is a variable defined in `org.el'.
Its value is 8.2.5c

 M-x find-library org-loaddefs

;;; org-loaddefs.el --- autogenerated file, do not edit
;;
;;; Code:

;;;### (autoloads (org-babel-mark-block org-babel-previous-src-block
;;  org-babel-next-src-block org-babel-goto-named-result 
org-babel-goto-named-src-block
...

 M-x find-library ox

;;; ox.el --- Generic Export Engine for Org Mode

;; Copyright (C) 2012-2014 Free Software Foundation, Inc.

;; Author: Nicolas Goaziou n.goaziou at gmail dot com
;; Keywords: outlines, hypermedia, calendar, wp

;; This file is part of GNU Emacs.
...

 M-x find-library ox-odt

;;; ox-odt.el --- OpenDocument Text Exporter for Org Mode

;; Copyright (C) 2010-2013 Free Software Foundation, Inc.

;; Author: Jambunathan K kjambunathan at gmail dot com
;; Keywords: outlines, hypermedia, calendar, wp
;; Homepage: http://orgmode.org

;; This file is part of GNU Emacs.
...

 M-x find-library ox-jabref

;;; ox-jabref.el --- JabRef Citation Processor for Orgmode

;; Copyright (C) 2013 Jambunathan K kjambunathan at gmail dot com

;; Author: Jambunathan K kjambunathan at gmail dot com
;; Keywords: outlines, hypermedia, calendar, wp
;; Homepage: http://orgmode.org
;; Version: 8.0.6

;;; Commentary:

 Quick start guide:
;;
;; 1. Install [[http://jabref.sourceforge.net/][JabRef]]
;;
;;This module is tested with version JabRef-2.9.2.jar.
;;
...

 M-x list-load-path-shadows org

I am not able to put in the org. It just runs after the command and does
not allow options. Sorry for the large output. 

/fitz/home/aorchid/.emacs.d/gnus/lisp/sasl-ntlm hides 
/usr/local/share/emacs/24.3/site-lisp/flim/sasl-ntlm
/fitz/home/aorchid/.emacs.d/gnus/lisp/hmac-md5 hides 
/usr/local/share/emacs/24.3/site-lisp/flim/hmac-md5
/fitz/home/aorchid/.emacs.d/gnus/lisp/md4 hides 
/usr/local/share/emacs/24.3/site-lisp/flim/md4
/fitz/home/aorchid/.emacs.d/gnus/lisp/sasl-cram hides 
/usr/local/share/emacs/24.3/site-lisp/flim/sasl-cram
/fitz/home/aorchid/.emacs.d/gnus/lisp/hex-util hides 
/usr/local/share/emacs/24.3/site-lisp/flim/hex-util
/fitz/home/aorchid/.emacs.d/gnus/lisp/sasl-digest hides 
/usr/local/share/emacs/24.3/site-lisp/flim/sasl-digest
/fitz/home/aorchid/.emacs.d/gnus/lisp/hmac-def hides 
/usr/local/share/emacs/24.3/site-lisp/flim/hmac-def
/fitz/home/aorchid/.emacs.d/gnus/lisp/ntlm hides 
/usr/local/share/emacs/24.3/site-lisp/flim/ntlm
/fitz/home/aorchid/.emacs.d/gnus/lisp/sasl hides 
/usr/local/share/emacs/24.3/site-lisp/flim/sasl
/fitz/home/aorchid/.emacs.d/gnus/lisp/sha1 hides 
/usr/local/share/emacs/24.3/site-lisp/flim/sha1
/fitz/home/aorchid/.emacs.d/gnus/lisp/smime hides 
/usr/local/share/emacs/24.3/site-lisp/semi/smime
/fitz/home/aorchid/.emacs.d/gnus/lisp/utf7 hides 
/usr/local/share/emacs/24.3/site-lisp/wl/utf7
/fitz/home/aorchid/.emacs.d/gnus/lisp/hex-util hides 
/usr/local/share/emacs/24.3/lisp/hex-util
/fitz/home/aorchid/.emacs.d/gnus/lisp/password-cache hides 
/usr/local/share/emacs/24.3/lisp/password-cache
/fitz/home/aorchid/.emacs.d/gnus/lisp/format-spec hides 
/usr/local/share/emacs/24.3/lisp/format-spec
/fitz/home/aorchid/.emacs.d/gnus/lisp/color hides 
/usr/local/share/emacs/24.3/lisp/color
/fitz/home/aorchid/.emacs.d/gnus/lisp/md4 hides 
/usr/local/share/emacs/24.3/lisp/md4
/fitz/home/aorchid/.emacs.d/gnus/lisp/dns-mode hides 
/usr/local/share/emacs/24.3/lisp/textmodes/dns-mode
~/.emacs.d/remember/remember hides 
/usr/local/share/emacs/24.3/lisp/textmodes/remember
~/.emacs.d/org-mode/lisp/ob-picolisp hides 
/usr/local/share/emacs/24.3/lisp/org/ob-picolisp
~/.emacs.d/org-mode/lisp/org-eshell hides 
/usr/local/share/emacs/24.3/lisp/org/org-eshell
~/.emacs.d/org-mode/lisp/org-capture hides 
/usr/local/share/emacs/24.3/lisp/org/org-capture
~/.emacs.d/org-mode/lisp/ob-keys hides 
/usr/local/share/emacs/24.3/lisp/org/ob-keys
~/.emacs.d/org-mode/lisp/org-archive hides 
/usr/local/share/emacs/24.3/lisp/org/org-archive
~/.emacs.d/org-mode/lisp/ob-asymptote hides 
/usr/local/share/emacs/24.3/lisp/org/ob-asymptote
~/.emacs.d/org-mode/lisp/org-mouse hides 
/usr/local/share/emacs/24.3/lisp/org/org-mouse
~/.emacs.d/org-mode/lisp/org-agenda hides 
/usr/local/share/emacs/24.3/lisp/org/org-agenda
~/.emacs.d/org-mode/lisp/ob-lob hides 
/usr/local/share/emacs/24.3/lisp/org/ob-lob
~/.emacs.d/org-mode/lisp/ob-js hides /usr/local/share/emacs/24.3/lisp/org/ob-js
~/.emacs.d/org-mode/lisp/ob-gnuplot hides 
/usr/local/share/emacs/24.3/lisp/org/ob-gnuplot
~/.emacs.d/org-mode/lisp/org-loaddefs hides 
/usr/local/share/emacs/24.3/lisp/org/org-loaddefs
~/.emacs.d/org-mode/lisp/ob-fortran hides 
/usr/local/share/emacs/24.3/lisp/org/ob-fortran
~/.emacs.d/org-mode/lisp/ob-scheme hides 
/usr/local/share/emacs/24.3/lisp/org/ob-scheme
~/.emacs.d/org-mode/lisp/org-plot hides 
/usr/local/share/emacs/24.3/lisp/org/org-plot
~/.emacs.d/org-mode/lisp/ob-sh hides /usr/local/share/emacs/24.3/lisp/org/ob-sh

Re: [O] Org Export to ODT Problem Files

[Aric Gregson]

Jambunathan K kjambunat...@gmail.com writes:

 You are looking for this

 (custom-set-variables
  '(org-odt-display-outline-level 0))

Thanks, Aric

Re: [O] Export tikz Figures Issue

[Aric]

Andreas Leha andreas.leha at med.uni-goettingen.de writes:
 
 Works for me if I add ':results raw file'.  Not sure, this is the
 'official' solution, though.

That works beautifully, thank you very much!

Aric

Re: [O] Citations and references in ODT

[Aric Gregson]

Ken Mankoff mank...@gmail.com writes:

 I find the ODT export very useful. Working on another document imported
 from LaTeX I have a lot of \citep{} and \citet{} in addition to \cite{}. Is
 it possible for ox-jabref.el to support this even if it does not
 distinguish between the T and P?

On a similar note, would it be possible to add support for the markdown
style of references?

[@Authoryear; @anotherauthoryear]

I have so many like this across files.

Thanks, Aric

Re: [O] Citations and references in ODT

[Aric Gregson]

 I have found this useful for converting latex export to doc[x]

Thanks for that idea, I will give that a try as well. 

Thanks, Aric

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Re: [O] Citations and references in ODT

[Aric Gregson]

Ken Mankoff mank...@gmail.com writes:

 3) I put MathToWeb.jar in the unit test folder. However, if I run
 java -jar MathToWeb.jar I get the following error. I have an email
 in to the MathToWeb developer/maintainer about this

 $ java -jar mathtoweb.jar
 Exception in thread main java.lang.UnsupportedClassVersionError:
 mathtoweb/engine/MathToWeb : Unsupported major.minor version 51.0

I had the same issue and the author of mathtoweb quickly got back to me
with it being an incompatibility with java 6. I installed OpenJDK7 on my
machine and it worked just fine!

Aric

Re: [O] Org Export to ODT Problem Files

[Aric Gregson]

Jambunathan K kjambunat...@gmail.com writes:

 2. MathToWeb

Pro: Uses MathML

Con: MathToWeb is new kid on the block.  May prove to be problematic
with more complex formulae.

If ltx-mathml conversion is problematic for some equations, you can
create ODF files (OpenDocumentFormula files created with
LibreOffice Math) by hand and insert an Org link to them.

Yes, this works very well for me. There is an issue with export of
$\geq$ that the author is looking into. 

   4. Figure and table references are by section, sort of like old
 fashioned latex.

For me, I am not writing a book or anything very long, just
manuscripts. Thus, I would prefer just to label each figure in order and
each table in order. I would therefore get Figure 1, Figure 2, etc and
Table 1, Table 2, etc in the order of appearance in the text. There is
no reference to section that way. 

Maybe this is something that can be set in my odt reference file for
exporting? I have not yet investigated that.

Thanks, Aric

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Re: [O] Org Export to ODT Problem Files - Latex Equations Work

[Aric Gregson]

Bastien b...@gnu.org writes:

 can you give more details about your setup? 

I am using the mathtoweb function and so far so good. Here is what I
have and what I understand of it, but I could be wrong about why it is
working. 

The file has this header:

#+OPTIONS:   LaTeX:t 

I have this in my .emacs file:

;; to convert latex equations to mathml for ODT export
; uses mattoweb (http://www.mathtoweb.com/cgi-bin/mathtoweb_home.pl)
(setq org-latex-to-mathml-convert-command
  java -jar %j -unicode -force -df %o %I
  org-latex-to-mathml-jar-file
  ~/.emacs.d/mathtoweb.jar)

Now it just works after updating to Java 7. 

 This could well deserve a link to worg/org-hacks.org!

Yes, some of those files are outdated and it has been somewhat
challenging to find all the needed info in one place. 

Thanks, Aric

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Re: [O] Citations and references in ODT

[Aric Gregson]

Jambunathan,

Thanks for posting your instructions and links again. I followed the
instructions and am receiving the following error on export attempt:

OpenDocument export failed: Symbol's function definition is void:
org-element-cache-reset

I also receive this error the first time that I try to open an org
file. I can open the file if I try another time. 

Thanks, Aric

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Re: [O] Citations and references in ODT

[Aric]

Ken Mankoff mankoff at gmail.com writes:

 And this 2013 post saying yes https://lists.gnu.org/archive/html/emacs-
orgmode/2013-07/msg00969.html

 But I'm not sure if that 2013 code is part of the latest ELPA distribution, 
or if there is extra work to get it set up on my system.

It does not appear to be, as I just did download the updated org-mode 
distribution. I mistakenly only copied in the ox-jabref.el and could not get 
it to function. But now I see there are several other files that need to be 
updated as well. 

If this could become functional, it may avoid export to markdown, but 
modifying the formats will need to be easily accomplished like csl. I look 
forward to getting a functional bibliographic system going for odt files.

aric

 

Re: [O] Org Export to ODT Problem Files - Latex Equations Work

[Aric]

I just wanted to update that I am able to export latex equations from Org 
mode files directly to ODT files via the MathtoWeb program. Works very well. 
Removes one hurdle to using ORG and ODT instead of markdown. 

thanks,

Re: [O] Org Table Export to Markdown Table Question

[Aric]

Alan L Tyree alantyree at gmail.com writes:

 Org is so nice to use for authoring that I can't give it away. I have a 
 book manuscript due in May and currently all my citations are using the 
 [[cite: key]] format with ox-bibtex. It is far from satisfactory and I'm 
 sure that May will see me tearing my hair out (what little is left).

Yes, I hear you. I am trying to avoid this by using the [@nameYear] style for 
markdown hoping that a final export to markdown for bibliography will not go 
horribly wrong. But that is probably not a fair assumption. 

Aric

[O] No Export Tag Not Working?

[Aric]

Hello,

I am certainly doing something wrong with regards to the EXCLUDE_TAGS. I 
believe the default is noexport. I have the following in a subtree:

*** subtree
:PROPERTIES:
:TAGS: noexport
:END:
  blah, blah, blah. 

The subtree is still exported during html export. I have tried to look at the 
option 'org-export-exclude-tags' but it appears to be an unknown variable in 
my set-up. Is there some module that must be loaded to get this option? Am I 
tagging the subtree incorrectly? Must #+EXCLUDE_TAGS be set in every file?

Using Org 8.2.5c.

Thanks in advance, Aric

Re: [O] No Export Tag Not Working?

[Aric Gregson]

t...@tsdye.com (Thomas S. Dye) writes:

 Section 7.2, Special properties, says that TAGS shouldn't be used as a key
 in the properties drawer. Chapter 6, Tags, explains that tags occur at
 the end of the headline. 

Thank you for pointing that out. I'll give that whirl.

aric

[O] Export tikz Figures Issue

[Aric]

I apologize for the sudden flurry of postings, but I am finding some great 
solutions within Org. 

I have very happily managed to find the more recent references to babel 
latex and tikz figures with the imagemagick conversion, and this works 
absolutely beautifully within the Org mode buffer. 

I have not been successful in exporting the image (html or odt) however. I 
can export it if I create a link to the generated png image, rather than 
leaving it to the results section like I can with latex. Here is an example:

Working R:

#+name: fig:bplotil8staph
#+headers: :results graphics :file /somewhereelse/bplotil8staph.png
#+begin_src R 
bwplot(il.8 ~ impression,)
#+end_src

#+CAPTION: Plot demonstrating significantly increased IL-8 levels during /S. 
aureus/ pneumonia as compared to colonization. 
#+RESULTS: bplotil8staph
[[file:/somewhereelse/bplotil8staph.png]]

Note that this link is generated by the R output and I can see the image 
along with the caption in both Org buffer and exported files. 

Not working so well LaTeX:

#+name: fig:markovdesc
#+headers: :imagemagick yes :iminoptions -density 600 :imoutoptions -
geometry 800 
#+headers: :file /somewhereelse/plot_markovModel.png :fit yes
#+begin_src latex  :buffer no :packages '(( tikz)) 
\usetikzlibrary{shadows,arrows,automata,decorations.text,shapes,snakes,fit}
\tikzstyle{ball} = [circle,shading=ball,minimum size=1cm] 
\begin{tikzpicture}[-,=stealth',shorten =1pt,auto,node distance=4.2cm]
  \tikzstyle{everystate}=[draw=black,thick,scale=1,align=center]
  \node [state,initial,text width=4em,align=center,ball,text=black,ball 
color=green!70!black,drop shadow] (A){{\small Post-
Transplant State 1}};
  \node [state,align=center,text width=4em,ball,text=black,ball 
color=purple!70,drop shadow]  (B)  [right of=A]  {{\small BOS 
~~~State 2}};
\path (A) edge [bend left] node[above]   {{\small $\lambda_{12}(t)$ 
Covariates~$HR_{12}$}} (B);
  \node[state,align=center,text width=4em,ball,text=black,ball 
color=blue!50,drop shadow](C)  [below=2.6cm,right=1cm] 
{{\small Death ~~~State 3}};
\path (A) edge [] node[left] {{\small $\lambda_{13}(t)$ 
Covariates~$HR_{13}$}} (C);
\path (B) edge [] node[right] {{\small $\lambda_{23}(t)$ 
Covariates~$HR_{23}$}} (C);
\end{tikzpicture}
#+end_src

#+CAPTION: Basic idea of the model demonstrating the transition states. 
#+RESULTS: fig:markovdesc
#+BEGIN_LaTeX
[[file:/fitz/Rworkarea/gnr/new_work/staph/plot_markovModel.png]]
#+END_LaTeX

For the LaTeX there is no image in the exported buffers and the in-text link 
to the image is not active at all. Things only work for latex tikz in the 
Org buffer. 

What am I doing wrong? Or do I need to create a manual link to the file?

Thanks so much for suggestions. 

aric

Re: [O] Org Table Export to Markdown Table Question

[Aric Gregson]

--On January 9, 2014 11:58:37 AM -0500 Rick Frankel r...@rickster.com 
wrote:



I'm not sure why you are using markdown as an intermediate file
format. Org will export to latex, pdf (via latex) and openoffice odt
(which can be exported from open/libre office to doc/docx.).


I had originally tried because of problems with the odt exporter, which 
appears to have been fixed with the recent release, as noted previously. 
Markdown is still extremely useful for formatting references/bibliographies 
with bibtex and csl. Latex is not as useful because it is nearly impossible 
to share latex files with those using Word and most journals in my field do 
not accept latex files.


Thanks, Aric

[O] Org Table Export to Markdown Table Question

[Aric]

Hello,

I am trying to use org-mode now with R code in it to write manuscripts. That 
does unfortunately mean that it must be eventually exported to some doc 
format. I have been able to export to markdown and everything looks good in 
markdown (even previewed on github) with the exception of latex code which is 
not converted. However, using pandoc to convert the markdown to docx, the 
tables are not converted properly (all a single column). 

I realize this is a pandoc problem, but since markdown supports tables, is it 
possible to have Org export the tables into markdown as markdown tables 
rather than html tables? Also, is there a way for latex code to be converted 
prior to markdown export?

Thanks, Aric

[O] Org Export to ODT Problem Files

[Aric]

Hello,

I need to get a file into doc or docx format and can export from org into 
ODT. However, the odt file cannot be opened by LibreOffice to convert. I can 
open the file and it displays very well in both Calligra and Nisus Writer (on 
mac). The problem is that Calligra cannot save in doc format and the file 
crashes Nisus whenever I try to save it, whether I am trying to save in odt 
or doc. I have figures and long tables in the document. 

Is this an issue others have had or is it perhaps something within this file 
that is causing the problem?

Re: [O] Org Export to ODT Problem Files

[Aric Gregson]

Bastien b...@gnu.org writes:

 What version of Org and Emacs are you using?
 M-x org-version RET

8.2.1-dist

 M-x emacs-version RET

24.3.1 freebsd-amd64

Thanks, Aric

-- 
~O
/\_,
###-\  |_
(*) / (*)

Re: [O] Org Export to ODT Problem Files

[Aric]

Bastien bzg at gnu.org writes:

 Please try with Org 8.2.5 or later, an issue with multiple figures
 not showing up in LibreOffice 4.1.x has been fixed.

Thank you, I will give this a try.

aric

Re: [O] Org Export to ODT Problem Files

[Aric]

Thank you very much for the upgrade notice. The export to ODT from org-mode 
works very well now. There are pluses and minuses it seems between pandoc and 
org export.

Org export -
  1. Includes figures and tables
  2. Includes pretty code mark-up
  3. Lacks latex code export
  4. Figure and table references are by section, sort of like old fashioned 
latex.
  5. Author list and title are in appropriate places

Pandoc html (from org) to odt -
  1. Includes tables
  2. Does not include figures
  3. Does not include pretty code mark-up
  4. Has latex code properly exported (i.e., $\geq$ is = sign)
  5. Figure and table references are as 'expected', first table is 1, then 2, 
etc.
  6. author list is at end of file

I can cut and paste the heavy math latex portions from a pandoc export, but 
is there a setting that I am missing about latex code being interpreted on 
export to odt?

Thanks very much, Aric

[O] org-mobile-pull date completed for habits

[Aric]

Hello,

I am new to using org-mobile with org and I have a question about how 
habits are handled with the org-mobile-push and pull operations. I hope 
this is a proper list to post. What is happening is that the completed date/
time for a habit is being given as the date/time of org-mobile-pull rather 
than the date/time completed on the mobile device or even the sync date/
time. I would think this is not the desired behaviour? I suspect that I 
have something set incorrectly.

I sync using Dropbox now and the Android MobileOrg version. I am on FreeBSD 
so I must use webdav to manually sync my local folder with Dropbox. 

In my .emacs file:

(add-to-list 'auto-mode-alist '(\\.org$ . org-mode))
(require 'org-mobile)
(setq org-directory ~/org)
(setq org-mobile-inbox-for-pull ~/org/pulled.org) 
(setq org-mobile-directory ~/Dropbox/MobileOrg)

Two examples in my agenda.org file:

** TODO item XY
SCHEDULED: 2013-10-25 Fri 21:00 .+1d-2013-10-27 Sun
- State TODO   from[2013-10-17 Thu 12:37]
:PROPERTIES:
:STYLE:habit
:ID:   e46dc0f1-3765-11e3-87d2-003048f9fb84
:LAST_REPEAT: [2013-10-24 Thu 20:43]
:END:

** TODO XXYY 
SCHEDULED: 2013-10-23 Wed .+1d/3d
- State DONE   from TODO   [2013-10-17 Thu 19:31]
- State DONE   from TODO   [2013-10-16 Wed 19:02]
- State STARTEDfrom TODO   [2013-10-16 Wed 18:12]
:PROPERTIES:
:STYLE:habit
:ID:   43be99e1-33a9-11e3-87d2-003048f9fb84
:LAST_REPEAT: [2013-10-22 Tues 10:30]
:END:

The only file that changes between syncs is a file called 'mobileorg.org', 
which I never created. It resides in the '~/Dropbox/MobileOrg' only. I have 
tried to look at this file, but I can see nothing in it. When I run org-
mobile-pull it notes that there are X number of edits and it changes the 
proper events to done state. The only problem is that the date/time of 
completion is the date/time of org-mobile-pull command rather than the date/
time actually completed.

Perhaps using habits to schedule recurring events is not the way to go? Any 
suggestions/pointers would be greatly appreciated. 

Thanks,