Re: [O] Enabling another language in org-babel

2014-07-31 Thread Jay Kerns
Dear Ista,

I don't know if Bastien has already responded to your private message
(if so, please disregard this), but for what it's worth, it looks like
you are doing everything right to me.  I am not an org-mode developer
so I can't speak with 100% certainty, but it looks like a permissions
issue on the side (read: your key hasn't been added just
quite yet) and nothing on your side.

Good luck, and best wishes.

On 07/30/14 12:47, Ista Zahn wrote:
 I've made the suggested changes, with the exception of the part of
 Emacs bit,  as this should go in contrib not core.
 I asked Bastien privately about getting access to the git repository,
 but will ask here as well: When I run 'git clone' I get a response saying
 Permission denied (publickey).
 fatal: Could not read from remote repository
 Does that mean my key wasn't properly added, or did I miss some required 
 On Tue, Jul 29, 2014 at 10:36 AM, Bastien wrote:
 Hi Ista,

 some comments on the code below.

 Ista Zahn writes:

 ;; Copyright (C) 2014 Ista Zahn
 ;; Author: Ista Zahn, based on ob-julia.el by G. Jay Kerns, and ob-R.el
 ;; by Eric Schulte and Dan Davison

 You need to reformat this -- see files with multiple authors in Org or
 in Emacs.

 ;; This file is not part of GNU Emacs.

 We plan to add this to Org's core, so this will be part of Emacs.

 ;; Stata and ESS are required.

 Maybe add some links for the requirements.

 (defcustom org-babel-stata-command inferior-STA-program-name
   Name of command to use for executing stata code.
   :group 'org-babel
   :version 24.4
   :package-version '(Org . 8.0)

 This needs to be 8.3

 ;; The following was a very complicated write object command
 ;; The replacement needs to add error catching
 ;(defvar org-babel-stata-write-object-command 

 Maybe simply remove this, or make it more readable.

 Thanks in advance for this contribution!


Re: [O] Enabling another language in org-babel

2014-06-24 Thread G. Jay Kerns
Great work, Ista!


G. Jay Kerns, Ph.D.
Youngstown State University

On 06/24/14 15:52, Ista Zahn wrote:
 I just hacked up a rudimentary ob-stata.el by replacing julia with
 stata in ob-julia.el by G. Jay Kerns (and making a few other minor
 tweaks). Only :results output works (no graphics, no :results
 value). In short it's in pretty rough shape, but it does work for some
 basic things. Perhaps someone with better emacs-lisp can polish it up.
 The code is available at
 On Tue, Jun 24, 2014 at 8:05 AM, Rainer M Krug wrote:
 Eric Schulte writes:

 Brendan Halpin writes:

 Does there exist any documentation on extending org-babel to another

 Hi Brendan,

 There is a template [1] which may be filled out to add support for a new
 language.  More generally simply defining a function named
 `org-babel-execute:foo' will cause babel to try to execute foo code
 blocks using that function.  See the template for existing
 `org-babel-execute:*' functions.

 Relatedly, is anyone working on adding Stata coverage to org-babel?

 I'm not but who knows.  If you do add support for Stata please consider
 contributing it to Org-mode (see [2]).

 stata should be not to difficult to add, as ESS supports stata and I
 would guess that most functions would be the same (or very similar)








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

 Centre of Excellence for Invasion Biology
 Stellenbosch University
 South Africa

 Tel :   +33 - (0)9 53 10 27 44
 Cell:   +33 - (0)6 85 62 59 98
 Fax :   +33 - (0)9 58 10 27 44

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


 Skype:  RMkrug

 PGP: 0x0F52F982

Re: [O] Org sources and PDF files on Worg

2013-05-22 Thread Jay Kerns
On Wed, May 22, 2013 at 3:04 AM, Bastien wrote:
 Hi Jay and Marc,


 Don't want to steal your work :)  Just thought I would fix this
 because I may be the one who broke things by forgetting to compile
 at some point.  I checked the scripts in ~/bin/ and they do compile
 normally.  Also, I removed the FORCE flag in (defun publish-worg ...)
 so that publishing does not republish everything.


Thanks, Bastien, yes, this helps a lot.


Re: [O] formatting org-babel output

2013-05-22 Thread Jay Kerns
Hi Joe,

On Wed, May 22, 2013 at 7:18 AM, Joe Bogner wrote:
 I am using org-mode and babel with R for reproducible research. I
 would like certain numbers in the output tables to be formatted for
 easier reading - such as eliminating decimals and adding commas for


Have you considered doing your formatting in R before it ever gets to
the org table?  The format function is very powerful. For instance,

 format(163328361.2423, nsmall = 2, big.mark =,)
[1] 163,328,361.24

Just an idea.


Re: [O] R plots always exported to Rplots.pdf

2013-05-22 Thread Jay Kerns
Hi Greg,

On Wed, May 22, 2013 at 8:23 AM, Greg Slodkowicz wrote:


 This is what my code block looks like:

 #+NAME: pvals_waw
 #+BEGIN_SRC R :file fig1.png :exports results
 pvals = read.table(waw_data.txt, header=T)
 plot(pvals$pvalue, pvals$length)

Have you tried (something like) this?

 #+BEGIN_SRC R :exports results :results graphics :file fig1.png

I hope this helps,


Re: [O] Org sources and PDF files on Worg

2013-05-21 Thread Jay Kerns
Hello Viktor,

On Tue, May 21, 2013 at 2:13 PM, Viktor Rosenfeld wrote:

 I recently wrote a tutorial for the ox-koma-letter exporter [1] which
 includes a link to an Org file [2] file and a PDF file [3] as examples.
 The files are checked into the Worg repository, but they are not
 available online. Is there something I have to do to enable this? At
 first I thought the problem was related to the switchover to the new
 exporter, but the issue persists.

 Also, an old version of the tutorial at an old address [4] is still
 online even though I've changed the location in the git repository. How
 can I delete this version?



I believe I can give a partial answer: it looks like Worg isn't
publishing right now, which suggests that there was a recent commit
which broke things.  The search for the problem begins.  Once the
error is identified and fixed, then things should get back to normal.

I've copied Marc on this message - we'll see if we can track the problem down.

Thanks for the report.

Jay Kerns

G. Jay Kerns, Ph.D.
Youngstown State University

Re: [O] How to get BibTeX to work with Org mode LaTeX export?

2013-05-18 Thread Jay Kerns
Hi Omid,

On Sat, May 18, 2013 at 4:40 AM, Omid wrote:
 - The \bibliographystyle and \bibliography commands are at the end of the
 - The question is about how to get Org mode to do the whole job, as there is
 a command for it which is supposed to do exactly that but it doesn't.

Have you tried (something like) the following in your init file?

(setq org-latex-pdf-process (quote (texi2dvi --pdf --clean --verbose
--batch %f bibtex %b texi2dvi --pdf --clean --verbose --batch %f
texi2dvi --pdf --clean --verbose --batch %f)))

You can read more about this variable (and customize it) with

C-h v org-latex-pdf-process RET

I hope this helps,


Re: [O] I merged worg-new-exporter into worg.git master

2013-05-14 Thread Jay Kerns
Dear Bastien,

On Tue, May 14, 2013 at 8:25 AM, Bastien wrote:
 Hi all,

 now both and Worg are published from Org 8.0.

 I merged worg-new-exporter into worg.git master, and updated
 the emacs.el file on the server -- many thanks again to those
 involved in this move.

 Marc and Jay: please let me know if you need more information
 on monitoring the publication process.

That's great news!  Thanks for all of your work on this, Bastien.


Re: [O] Org LaTeX export not setting default title?

2013-05-08 Thread Jay Kerns
Hi Dan,

On Wed, May 8, 2013 at 6:06 AM, Daniel E. Doherty wrote:

 I just upgraded to 8.02, so I am trying out the new exporter.  Nice.

 A little nit.  When I export a minimal org file, it should use the
 name of the file or buffer as the title if I set nothing in #+TITLE:,
 but it seems not to.


I am writing to say that I observe the same behavior that you do so it
isn't something unique to your setup.  I will let others say what
Org's new exporter  should do in this case, but let me point out that
if you insert the default export template with

C-c C-e # d TAB RET

Then the file name (with extension removed) is inserted in the #+TITLE
field and exported to the LaTeX buffer.  I understand, though, that
this probably isn't what you meant by minimal org file.



Re: [O] [Worg] [New Exporter] invalid time specification

2013-04-29 Thread Jay Kerns
On Mon, Apr 29, 2013 at 3:41 AM, Nicolas Goaziou wrote:

 This should be fixed. Thanks for reporting it.

Confirmed - thank you.


Re: [O] worg-new-exporter successful publish locally

2013-04-28 Thread Jay Kerns
Dear Achim,

On Sat, Apr 27, 2013 at 11:43 AM, Achim Gratz wrote:


Thank you for looking into this.  The worg-local-init.el is a great
idea! Thanks, also, for confirming successful publish - that's great

I have a question, a comment, and some information to add to my earlier

1. I set up worg-local-init.el as you recommended and everything goes
   smoothly until here:

| Publishing file /home/jay/git/worg/ using
| Loading cc-langs...
| Symbol's function definition is void: nil

Now, I have opened (with the same emacs -Q as above but
without batch) and it exports successfully to HTML from the
interactive dispatcher.  Do you have any idea what the problem might

2. If I don't do batch but instead publish interactively with M-x
   publish-worg, the error doesn't appear but then near
   the end I get

org-publish-get-base-files: Wrong type argument: stringp, (concat
worg-base org-contrib/bibtex/)

I haven't had time to look deeper into this to see what's going on,
but I thought you might like to know.

3. I've been working on that invalid time format problem we've been having
   and I think I might have identified where the problem is.  I will
   write about it in another message.

Thanks again.


[O] [Worg] [New Exporter] invalid time specification

2013-04-28 Thread Jay Kerns
Hello there,

I've noticed people mentioning on the list that there is a problem
with Worg not publishing, something about an invalid time
specification. Having been publishing Worg locally myself, I noticed
that I was getting a similar error when it came time to construct the  My workaround at the time was to set autositemap nil
in the emacs.el related to Worg, but with Achim's recent improvements
to emacs.el I thought I'd try to track down what's going on.  Here is
what I found:

If I reset autositemap t in worg-init.el (presumably the same
setting as the Worg server) then near the beginning of interactive
publish I get the following:

| Generating tree-style sitemap for Sitemap for project worg-pages [11 times]
| org-publish-format-file-entry: Invalid time specification

Doing `toggle-debug-on-error' yields (I'm deleting most of it)

| Debugger entered--Lisp error: (error Invalid time specification)
|   format-time-string(%Y-%m-%d 2010-04-24 Sat)
|   org-publish-format-file-entry(%t

If I fix the #+DATE: in to 2010-04-24 and
republish, then I don't get an error until the next file with the same
problem.  :-)  Here are the files that generate these errors:

- exporters/beamer/ [2013-03-13 Wed]
- org-tutorials/  2011-06-02 Thu
- org-tutorials/  2011-02-28 Mon
- org-tutorials/   2013-03-12 Di
- org-tutorials/ 2010-04-24 Sat
- org-tutorials/ 2011-03-30
- 2013-04-22 Mon

I have modified the dates on each of those files in the
worg-new-exporter branch and am able to publish successfully even with
autositemap t.  I am not 100% sure that this is the same problem
Worg is having, but if not then it's one heck of a coincidence.

Rather than push my changes to worg-new-exporter, though, maybe this
is something to be fixed somewhere else?  What I mean is, the
default #+DATE: inserted by `C-c C-e # default RET' is a date that
looks like -YY-ZZ Foo, and that's the same kind of date which
looks to be tripping up Worg.

I hope this helps with tracking down the problem,


P.S. It looks like I can fix the date with even 2013-03-13 Wed, so
maybe it's the   which is causing the problem.

Re: [O] worg-new-exporter successful publish locally

2013-04-28 Thread Jay Kerns
On Sun, Apr 28, 2013 at 3:12 PM, Achim Gratz wrote:


 I've fixed it on Worg.

Confirmed - thanks!


Re: [O] worg-new-exporter successful publish locally

2013-04-28 Thread Jay Kerns
On Sun, Apr 28, 2013 at 4:21 PM, Achim Gratz wrote:
 Achim Gratz writes:

 I've fixed this, not that I would know exactly how… :-)

Confirmed again, and thanks again!  I'm really starting to warm up to
this batch publishing approach, it's quite handy.


[O] worg-new-exporter successful publish locally

2013-04-27 Thread Jay Kerns
Hi there,

The new Worg branch publishes for me without error under Org-mode
version 8.0.1 (release_8.0.1-24-g92f372).  I updated the existing
emacs.el (underlying Worg, IIUC) to the Org 8.0 exporting/publishing
syntax. You can see the latest draft in


which lives in the top-level directory. To test the publish yourself
you'd need to customize the base/publishing directories for your local
machine and then do

emacs -Q -l /path/to/worg/worgtest-init.el

followed by

M-x publish-worg

There are changes to some files which are necessary for a successful
publish and which are detailed at the bottom of this email. Have a
look in FIXME.

Given the successful publish locally, I went through and updated all
remaining in-buffer settings that I could find (HTML_HEAD, etc.).  To
the best of my knowledge, everything is DONE, notwithstanding the
comments below.

1. I didn't work on at all.
2. Successful export/publish doesn't say anything about the content
   and/or outdated info in the pages.



  - Error: Invalid time-stamp specification
  - The error here has to do with an undocumented function that I
can't figure out.
  - Status: disabled auto-sitemap in publish-alist

  - content is out of date, but exports without error
  - Status: updated in-buffer settings but otherwise unchanged

  - content is out of date, but exports without error
  - Status: updated buffer settings but otherwise unchanged

- org-contrib/babel/
  - Error: local variables in and header-args.html
- eval: org-babel-default-header-args:Python
- if I hit n then Emacs hangs until C-g
- Status: moved to FIXME

- org-tutorials/org-R/
  - Error: none, really, it takes a really long time to export but
succeeds eventually.
  - Status: unchanged, but somebody might investigate the reason for
this extended export time, maybe it's just because the file is so

- org-configs/
  - export of this single file takes 1.5 hrs on my laptop
  - I don't know why
  - Status: moved to FIXME

- The following appear to set file local variables
  - code/org-info-js/
  - code/org-info-js/org-slides/
  - org-contrib/
  - org-contrib/
  - org-contrib/babel/examples/
  - Status updated in buffer settings, but otherwise unchanged.
Thought you might like to know.

Re: [O] worg-new-exporter successful publish locally

2013-04-27 Thread Jay Kerns
HI Thorsten,

On Sat, Apr 27, 2013 at 4:40 AM, Thorsten Jolitz wrote:
 Jay Kerns writes:

 Hi Jay,

 I started this page, so I kind of 'own' it, but the local variable has
 been added later, not by me, probably by Eric Schulte, because he is
 mentioned as second author.

 | - org-contrib/babel/
 |   - Error: local variables in and header-args.html
 | - eval: org-babel-default-header-args:Python
 | - if I hit n then Emacs hangs until C-g
 | - Status: moved to FIXME


Sounds good - thanks for the background info. IIRC I didn't modify
that file because I really didn't know anything else to do other than
delete the bit at the bottom which seemed to be causing the trouble,
so instead, it appeared better to ask people more competent than me to
take a look at it.  Certainly Eric (CC:'ed now) would be one of those,
among many, many others.  :-)


Re: [O] Updating Worg: call to Worg authors

2013-04-25 Thread Jay Kerns

First: thanks to Nicholas Goaziou and Thorsten Jolitz. There is
a bunch of work already completed - indeed, out of the 83
currently existing headlines, 63 are marked DONE.

But there is a lot of updating that remains.  And the longer the
process continues, the further the two branches will diverge so all
the more difficult the eventual merge of the two branches will be.

Moving forward, I would like to start marking *.org files DONE if they
export cleanly on my machine with no change. To this end, it occurred
to me that just because a file exports cleanly on *my* machine doesn't
necessarily mean that it would be OK on Worg. (This occurred to me
when I noticed Babel code evaluating during export, something not
permitted on Worg).

For testing purposes, we should be using a minimal config, consistent
with the one on Worg, right? This let me to here:

Though that one, of course, has a bunch of extra stuff which isn't
relevant for the time being (publishing, etc.). In addition, that one
is not necessarily compatible with Org 8.0 and the new exporter.

I've made a first stab at a minimal init file, copy-pasted below. I've
also put a soft copy called


which lives right beside in the top-level of the
worg-new-exporter branch. It would seem that the new asynchronous
export would make it relatively easy to test files uniformly and
minimally for Org 8.0 by doing something like

$ emacs -Q -l ~/git/worg/worgtest-init.el

and testing from there.

Here are my questions:

1. Is this overkill?
2. Is there something extra/missing in worgtest-init.el?
3. Anything I should be asking but amn't?


#+BEGIN_SRC emacs-lisp
 '(org-modules (quote (org-jsinfo)))
   (quote ((org-tags-column . -80)
   (org-export-html-style . link rel=\stylesheet\
type=\text/css\ href=\stylesheet.css\ /)
   (org-export-html-style-extra . link rel=stylesheet
href=\org-faq.css\ type=\text/css\ style type=\text/css\
   (org-export-html-style . link rel=stylesheet
href=\freeshell2.css\ type=\text/css\ style type=\text/css\
.tag { color: red; font-weight:bold}/style)

(add-to-list 'load-path ~/git/org-mode/lisp/)
(add-to-list 'load-path ~/git/org-mode/contrib/lisp/)

(show-paren-mode 1)
(menu-bar-mode 0)

(require 'org)
(require 'htmlize)

(setq org-export-in-background t)
(setq org-export-async-init-file ~/git/worg/worgtest-init.el)
(setq org-export-async-debug t)

(setq org-export-default-language en
  org-export-html-extension html
  org-export-with-timestamps nil
  org-export-with-section-numbers nil
  org-export-with-tags 'not-in-toc
  org-export-skip-text-before-1st-heading nil
  org-export-with-sub-superscripts '{}
  org-export-with-LaTeX-fragments t
  org-export-with-archived-trees nil
  org-export-highlight-first-table-line t
  org-export-html-style-include-default nil
  org-export-htmlize-output-type 'css
  org-startup-folded nil
  org-export-allow-BIND t
  org-export-babel-evaluate nil
  org-confirm-babel-evaluate nil)

Re: [O] Updating Worg: call to Worg authors

2013-04-25 Thread Jay Kerns
On Thu, Apr 25, 2013 at 7:18 PM, Jay Kerns wrote:

 First: thanks to Nicholas Goaziou and Thorsten Jolitz. There is

That should have been Nicolas; I apologize.


[O] Updating Worg: call to Worg authors

2013-04-23 Thread Jay Kerns
Hello there,

I started some work on this and pushed a worg-new-exporter branch to
Worg.  I followed Carsten's advice which I will repeat here for

Given an existing Worg repository obtained by

$ git clone

Everybody else can hook onto this branch with

$ git checkout --track -b worg-new-exporter origin/worg-new-exporter

and then work in this branch and push it whenever they want.  Note you
will need commit access to the worg repository at; see
here for more info:

After checking out the worg-new-exporter branch you will find a file

in the root of the repository.  This file has headlines for every
single file/directory on Worg current as of last night some
time. has TODO entries so we can keep track of what is
DONE, what is TODO, what is INPROGRESS, etc. We can also add AUTHOR
properties, etc, to help the update proceed smoothly.


- Please checkout the worg-new-exporter branch and update those files
  which are yours.
- Please mark DONE or INPROGRESS files in
- If you cannot or are not able to update your files, please say so on
  the mailing list so other volunteers can update them instead.
  Alternatively, you can mark your files as ABANDONED in

If you know of ways to streamline this update process, please feel
free to speak up and/or move forward with it immediately.  There are
~700 files on Worg to be checked, so we have a nontrivial job ahead
of us.

Thanks to John Hendy for some offlist brainstorming and advice - I
think is much better as a result.


P.S. I did a once-over to mark obvious things like *.png, *.pdf,
etc. as DONE.  I tried to be sparing to avoid false positives, though
I could have made some mistakes. Please fix any errors you find.

P.P.S. I inadvertently deleted a few directory names from the list when
I first started work.  This should be harmless, but if you notice
something missing feel free to add it back for completeness.

Re: [O] Gentoo ebuild for app-emacs/org-mode-8.0.1

2013-04-22 Thread Jay Kerns

On Sun, Apr 21, 2013 at 4:00 PM, Christoph LANGE wrote:
 Hi all,

 Gentoo users may find my ebuild for app-emacs/org-mode-8.0.1 useful.
 Please download it from and let's hope
 this ebuild (or alternatively Emacs 24.4) will be included with Portage
 soon (subscribe to to
 track the progress).

 Thanks to Bastien et al. for version 8!



Thank you for this work!  It's very helpful.  May it have a speedy
Portage review.

Best wishes,


Re: [O] New maintainer

2013-04-22 Thread Jay Kerns
On Mon, Apr 22, 2013 at 6:27 AM, Julian M. Burgos wrote:
 I echo all the thanks that other people already gave.  My digital life
 orbits around org-mode, so thanks to everyone who contributed to this
 project.  Keep it up!!


I have been watching these multiple messages go by trying to find a
space to get a word in edgewise, but instead of waiting longer let me
just say now:  I am sorry to see you step down, Bastien, but also, I
am happy about your bright future ahead.  Congratulations! on a job
very well done!



Re: [O] Release 8.0

2013-04-22 Thread Jay Kerns
On Sun, Apr 21, 2013 at 9:25 AM, Bastien wrote:
 Hi Memnon,

 Memnon Anon writes:

[ snip ]

Quick question: is it true, now that Org 8.0 has been released, that
the engine which publishes Worg is now Org 8.0, too?  In other words,
is it now safe to publish to Worg all of that stuff which was written
compatible with the new exporter, without breaking Worg in the



Re: [O] uniborg

2013-04-18 Thread Jay Kerns
On Thu, Apr 18, 2013 at 6:22 AM, Bastien wrote:


 Also, I uploaded the SVG version of the new logo, it's under CC by-sa
 if people want to use/modify it:

Thanks - looks great. I still get the same 404 Not Found on
uniborg.svg, but I wouldn't classify that as mission-critical.


[O] uniborg

2013-04-16 Thread Jay Kerns

I remember reading a discussion some time ago about Org, and the
Borg, and unicorns with mechanical faceplates, Resistance is
futile, etc. Here is one interpretation of a uniborg:

Feel free to improve it, embellish it, play with it, modify it, add captions,...


P.S. It appears that Worg isn't publishing SVG images (is that
right?), only my PNG in being published. If this is indeed the case,
would it be possible to add the extension svg to
org-publish-attachment in the worg publishing setup?  I looked for
that setup file but didn't find it.

Re: [O] Inline code in tables?

2013-04-11 Thread Jay Kerns
Dear John,

On Thu, Apr 11, 2013 at 6:56 PM, John Hendy wrote:
 I  have a table like so:

Please see the responses by Eric S. and Charles B. in the following thread:

I hope this helps,


Re: [O] R code block on Worg

2013-04-09 Thread Jay Kerns
Dear Nick,

On Tue, Apr 9, 2013 at 8:18 PM, Nick Dokos wrote:
 The example I used earlier came from


I seem to have overlooked your earlier message - sorry about that.  As
far as doing R stuff with Org I am afraid that ob-doc-R is a bit
behind all of the many, many released changes of recent weeks.  Some
time back I updated an extended document (originally written by Erik
Iverson) to work with the new exporter.  You can find all of that

I recommend working through the *.org file and looking at the *.pdf
and *.html files for comparison.  It goes through a whole bunch of
things, and there is a ggplot2 example, too.

I hope to eventually migrate that over to Worg but thought it best to
wait for Org-8.0's release.  Perhaps you may find something useful
there in the meantime.

I hope this helps,

P.S. If you find yourself walking further down the R path you might be
interested in IPSUR.  It is written in org so you'd feel right at

Re: [O] scaling the text in the results block of some code chunk when exported using LaTeX

2013-03-18 Thread Jay Kerns
Hello Shripad,

On Mon, Mar 18, 2013 at 7:44 PM, shripad sinari wrote:


 Is there a way for me to define the scaling of the text within the results
 block when this is exported  using latex?


I don't know of a way to scale /within/ the code block, but does
this work instead?

#+NAME: foo
#+BEGIN_SRC R :session :exports results :results output org replace :tangle yes
print(list.files(recursive = T, pattern = *.xls*))

#+RESULTS: foo
[1] 20130304 Some Spreadsheet/20130215 XXX_CB edited for
sample classification.xls
[2] 20130304 Some Spreadsheet/20130215 XXX_CB edited for
sample classification.xls
[4] 20130304 Some Spreadsheets/20130215  samples
results final.xlsx
[5] 20130304 Some Spreadsheets/20130215  results
[6] 20130304 Some Spreadsheets/20130304  samples
results 121109_Rep Aliqs Highlighted.xlsx

I learned just yesterday that the 'naming code blocks' trick is very
handy for things like this.  Here is halfway through the thread where
this was discussed:

See also John Hendy's comments later in the thread.

I hope this helps,


Re: [O] org-babel src block generated graphics included twice if CAPTION is added

2013-03-17 Thread Jay Kerns
Greetings Li,

On Sun, Mar 17, 2013 at 9:10 AM, Li Bowen wrote:

 If #+CAPTION is added, the figure will be included in the exported pdf
 file twice.

 #+begin_src R :exports both :results graphics :file img.pdf

 #+CAPTION: Some description

For that particular example maybe the quickest way to get rid of the
extra figure (that is caption-less) would be to use :exports code
instead of :exports both.

I hope this helps,


Re: [O] org-babel src block generated graphics included twice if CAPTION is added

2013-03-17 Thread Jay Kerns
On Sun, Mar 17, 2013 at 6:21 PM, Nick Dokos wrote:


 I think the best way to deal with problems like this is to name your code 
 blocks (and results blocks).


I can't speak for Li, but it works on my system and I like Nick's
solution better than mine.



Re: [O] Publish to html issue

2013-03-16 Thread Jay Kerns
Dear Igor,

On Sat, Mar 16, 2013 at 7:12 PM, Igor Kupczyński wrote:
 Dear List,

 I try to set up a simple org -- html publishing system.

 (setq org-publish-project-alist
   :base-directory ~/tmp/org/
   :publishing-directory ~/tmp/html
   :section-numbers nil
   :table-of-contents nil
   :publishing-function org-publish-org-to-html
   :style link rel=\stylesheet\


Would you please try keeping everything the same except for the
following change:

:publishing-function org-html-publish-to-html

Then (after restart) open one of the *.org files in your ~/tmp/org
directory and do the keybinding C-c C-e P p.  It should do some
thinking and there should be (at least one) *.html file(s) in

Also, please see the following information on Worg which has lots of
updates/changes that haven't made it to the manual yet:

I hope this helps,


[O] hall of fame, i.e. Org fortunes

2013-03-15 Thread Jay Kerns

In another thread, Bastien proposed a sort of Hall of Fame
where we could keep track of excellent (or otherwise exemplary) posts
to this list.  I like this idea.  I've only been closely following the
list since the new exporter's release after an extended hiatus,
though; that's been,
what, a few weeks?  In other words, I do not have a large
catalogue in my mental RAM of excellent posts at the moment.

Those of you who are interested in this idea, when you see or
have seen an excellent (or otherwise exemplary) message to the
list, would you please say something, bring some attention to it?
In this way maybe fewer great messages will slip through the cracks.


P.S. I'm thinking a good place for this might be the mailing
list page on Worg, maybe an additional headline towards the
bottom.  Sound good?

Re: [O] Syntax of Org Babel :results header argument

2013-03-15 Thread Jay Kerns

On Fri, Mar 15, 2013 at 1:30 PM, shripad sinari wrote:


I am happy with the current behavior, but
that isn't to say it couldn't possibly be improved or that I
disagree with Sebastien's suggestions.  It did take me quite some
time to figure out what the heck was going on with it all, but
now that I know, I like it a lot.

Few comments:

- :results graphics makes the list even longer, yes?  :-) I'm not
  sure that every language supports it and I don't believe it's
  currently in the manual. And I don't think it directly affects
  what Sebastien is asking about.

- Out of the myriad combinations, I only use a few regularly.

- I hope that a change, if any, would be mindful of
  brevity. Particularly with inline src blocks, it is much
  shorter to write

  : SRC_foo[:results value scalar raw append]{blah}

  than it is to write

  : SRC_foo[:results_collect value :results_type scalar
:results_handling append :results_wrapper raw]{blah}

  (or however it would be decided to handle that).


Re: [O] posting guide?

2013-03-14 Thread Jay Kerns

 FWIW, +1

 +2 :)

Fair enough.  I agree that time shouldn't be wasted on lone users, and
that includes me:;a=commitdiff;h=933d17d268a1618d9244c12014403a05c05c5a25



Re: [O] posting guide?

2013-03-14 Thread Jay Kerns
Reading my message again, it doesn't say what I wanted it to say, and
it sounds in my head not in the way I wanted it to sound.  Let me try
again, with more words:

That's totally fine by me, I meant it when I said OK if you don't
want to do that, and I don't want a silly thing like a posting guide
idea of mine to be wasting people's time any more than I want
malicious comments from hostile lone users to be wasting people's

I hope that sounds better; it is closer to what I meant.

Sorry for the noise,


[O] posting guide?

2013-03-13 Thread Jay Kerns
The past few days have reminded me of something somebody famous
once said [1]. I can already see work being done to protect the
community for the future, yet I believe there is more we might do
to be even stronger.

I understand and appreciate Bastien's stated position regarding
moderator controls [2], and in that particular case I think he
did the right thing. At the same time, I do not possess his
seemingly superhuman level of patience, temperance, and couth.

Yes, I can add people to my SPAM filter (which I did, BTW), but
that action protects only *me*.  It does not protect the
community. Further, my later blissful ignorance means I am
unavailable to respond to future threats, so malicious
individuals are left to run rampant and destroy everybody else
still hanging around.  Of course, if *everybody* agrees to divert
to SPAM then we're all set.

That's my point: I propose that we, as a community, come to some
sort of consensus as to what un/acceptable behavior is and an
accepted mechanism of response.  One way to accomplish this is
with a posting guide. I have some thoughts about this:

1. It should be written and maintained by the community. On
Worg, for instance.

2. It should be minimal. Posting guides sometimes go overboard,
to the extent that they can be (and sometimes are) used as a
weapon.  I do *not* propose that.  If we insist on 1) then I
trust the community to handle it with care.

3. It should contain things which help new users draft messages
that are informative and targeted to whatever problem they're
having, things they might not have known otherwise (things like
M-x org-version, M-x toggle-debug-on-error, etc.).

4. I think we can all agree that messages like this [3] should
not be tolerated, ever, under any circumstances.  If a person
resorts to ad hominem attacks of this sort (or similar)
then (s)he should promptly be shown the door.  Period.  As far as
I am concerned, that's pretty much the only thing I can't
stomach, but maybe the larger community considers other subjects
to be off-topic or unwelcome on the list.  That would be for the
community to decide.

All the above is a long-winded way to say that every community
has some /minimum/ standards and expectations of conduct,
otherwise we're just a bunch of people standing around in the
same (virtual) place.  To date, these expectations have lived
unspoken or scattered around in emails here or there.  I propose
that we come together in a community-driven way to define when
it's time to say Welcome! and when it's time to say, Get

I understand that there are valid arguments against posting
guides, not the least of which including what I said above in 2).
Maybe this community doesn't want a posting guide.  OK.  But even
in that case we've at least agreed that we don't want a posting
guide and can get back to work.

If we *do* decide that a minimal posting guide makes sense, then
it wouldn't be of much use unless there are those among us willing
to enforce it when individuals maliciously disregard the
agreement of the community.  I would probably have been one of
those people had I known there was some consensus about what is
OK and what isn't.  Now is the time to decide.

I have a mental first draft of things that could go in one, but
there's no point moving forward if there isn't a general feeling
that this would be something good to do.  And, I'd like the Org
old-timers to feel free to take the reins and run with it if they
so choose.




G. Jay Kerns, Ph.D.
Youngstown State University

Re: [O] posting guide?

2013-03-13 Thread Jay Kerns
Dear Andreas,

On Wed, Mar 13, 2013 at 3:59 PM, Andreas Röhler wrote:

 Hi Jay,

 if you permit my opinion as a kind of guest-reader for years: don't think
 it's needed.
 IMO it was an accident. Hopefully the person will recover and present it's
  excuses some weeks or month later.

 Expect org-mode users being decent people by virtue of these fine thing
 Really don't assume that might happen next years again.

Of course, I permit your opinion, and thanks for chiming in.  I
personally do not believe that Jambunathan's recent behavior was an
accident, but that is just my opinion.  And I do not hold any ill will
toward the man: I wish him the very best - some place far, far away
(for a while).

As Org grows there will be additional newbies (hopefully hundreds!)
and additional hostile individuals (hopefully epsilon).  Those are the
two categories targeted by this proposal.


Re: [O] posting guide?

2013-03-13 Thread Jay Kerns
Dear Bastien,

On Wed, Mar 13, 2013 at 4:33 PM, Bastien wrote:
 Hi Jay,

 Well, I would not invest too much time on this, personally.

No, you don't seem to be bothered at all; those attacks seem to
wash off you like water off a duck's back, or scandals off of Bill
Clinton's resume.  ;-)

 From experience, such a drafting process takes a lot of time.  And at
 the end, you're not always sure that the whole community comes: to an
 agreement... only the ones who care, who are obviously not the ones
 the guidelines want to reach.

Drafting takes about five seconds. In fact, let me do one right now:

Please note that messages to the emacs-orgmode list are expected
to be civil and focused toward our mutual interest of Org
mode. /Ad hominem/ or other attacks of a personal nature will not
be tolerated by the community.

Any strenuous objections?

 Why not trying another approach and have a hall of fame for great
 posts sent on this lists?  Examples of good/thorough explanations,
 example of detailed bug reports, etc.  It would be both encouraging
 and educating, maybe.

 What do you think?

I think that's a great idea!, actually.  My mental catalogue of
excellent posts probably isn't as extensive as yours, but even
just last night I got a great response that fits a Hall of Fame
in my book. Surely there must be other people who got a great
response to some question they asked at some point in their past.


Re: [O] posting guide?

2013-03-13 Thread Jay Kerns
Dear Tom,

Perfect - that's just what I'm looking for.  And that's exactly what I'll

On Mar 13, 2013 6:16 PM, Thomas S. Dye wrote:

 Aloha Jay,

 Jay Kerns writes:

  That's my point: I propose that we, as a community, come to some
  sort of consensus as to what un/acceptable behavior is and an
  accepted mechanism of response.  One way to accomplish this is
  with a posting guide. I have some thoughts about this:
  1. It should be written and maintained by the community. On
  Worg, for instance.

 Worg has a brief description of the mailing list, including list

 It tries to stay away from prescription, and it deliberately avoids
 mentioning all the bad behaviors that can be found on mailing lists.

 Please feel free to edit so it suits!

 All the best,

 Thomas S. Dye

Re: [O] posting guide?

2013-03-13 Thread Jay Kerns
On Wed, Mar 13, 2013 at 8:34 PM, Robert Horn wrote:

 I share Bastien's opinion.  My experience with community building is
 that describing and rewarding exemplary behavior is much more useful
 than attempting to set strict rules of behavior.  You need some basic
 rules, but then emphasize describing excellence.

 It's much better for people trying be be like her, because everyone
 respects and honors her, rather than following some set of detailed

 R Horn

You know, I don't disagree with any of that.

Re: empty words, in my view, the measure of any statement is the
veracity of the person who says it, or in this case, the resolve
of the community who lives by it.

Or not.  :-)

After having reviewed the paragraph on the Worg page that Tom
mentioned, it is clear that there already exists a
community-driven place to give guidance about what is
considered (un)acceptable behavior on this list.

As promised, I added a sentence to that paragraph: Ad hominem
comments are out of place and will not be tolerated by the
community.  If one of you feels this is inconsistent with Org's
spirit, feel free to delete my change (it is a wiki, after all).
No hard feelings.  Honest.

Time to get back to work.  Thanks to all who contributed to the


Re: [O] [bug] new beamer exporter always adds default width to graphics

2013-03-12 Thread Jay Kerns
Dear James,

On Tue, Mar 12, 2013 at 9:25 AM, James Harkins wrote:

 Apologies if this was previously reported. I read the digest, so I
 might not have seen the most recent e-mails. I took a quick glance at
 gmane's archive and didn't readily see anything.

 The width attribute for beamer graphics is not handled properly at
 present (current master).

 The org file contains:

 #+ATTR_LaTeX: :options width=6cm

 In the .tex file, I see:


 Two widths appear: the one that I wanted, and the default that I was
 trying to override. LaTeX obeys the one that I didn't want.

 The problem is somewhere between HEAD and this commit (i.e., 8cc6c13
 is a good commit; head is bad):

 commit 8ee6c13c7fd6eacc2e8c2ace8054f8aac3548966
 Author: Bastien Guerry
 Date:   Sat Feb 23 13:47:44 2013 +0100
 Fix typo: an headline - a headline.

 Please fix. Thanks.

Yes, the same thing happened to me too, and yes, there was a change
recently, and here is a link to the discussion about it:

I believe you can do the following to get what you were expecting:

#+ATTR_LaTeX: :width 6cm

I hope this helps,


Re: [O] inline Babel calls in math environments and table cells

2013-03-12 Thread Jay Kerns

I went back and spent some time to rethink how I was approaching my
problem.  Instead of inline src blocks like this:

\( SRC_R{blah} \)

or this

| SRC_R{blah} |

or even this


I could get by doing noweb substitution like this:

#+NAME: foo

then elsewhere

#+BEGIN_SRC latex :noweb yes
Here is a bunch foo() of LaTeX markup

This method works. I think it would be cool if it were possible to
evaluate inline src blocks all over the place but on the other hand
there are other tools which might be better suited for that kind of
work. At least for the time being.  :-)


Re: [O] Create course material with org-mode

2013-03-12 Thread Jay Kerns

On Tue, Mar 12, 2013 at 12:47 PM, Marcin Borkowski wrote:
 Dnia 2013-03-11, o godz. 23:02:46
 Marcin Borkowski napisał(a):


Many comments.

- You can set up a single org file with tagged headings, like this:
  * These are my slides   :slide:
  * These are my Lecture Notes  :lecture:
  * Here are Exam questions:exam:
  * Here be Exercises :exer:
  * Organisation of everything:organ:

- Then when it comes time to export you can do the
  #+EXCLUDE_TAGS: slide exam exer organ
  which will export your lecture notes.

- Set up a PROPERTY line for each heading to tangle to different
  places (if desired), like this:
  * Organisation of everything:organ:
  :tangle:   organ.R

- Beamer is a case all its own.  It might be easier to have a
  single big Beamer org file which has all slides and then another
  org file(s) for everything else.  Maybe I'm wrong, though; try it!

- Org publishing is very powerful.  You can set up assorted
  publishing projects to do almost /anything/.

- I have some example org-publishing setup from some time ago.  I
  haven't updated these to the new exporter but it can at least
  give you an idea about what used to be possible:

- Regarding exams/quizzes, at first I used LaTeX, then moved to
  LyX a long time ago, then managed to get an example Org file
  working, then it stopped working (and it seemed easier to do with
  LyX anyway), so I went back to LyX, but now the new exporter is
  out, so after reading your message I went back to see if I
  could get the old example working again, and I did!

- My personal workflow is to put the book in one org file, then
  lecture notes in another org file, then grades in another org
  file. YMMV.

- The book is a lengthy org file which is still in the much
  lengthier process of conversion to the new exporter.

Good luck and best wishes.


Re: [O] inline Babel calls in math environments and table cells

2013-03-12 Thread Jay Kerns
Dear Chuck,

On Tue, Mar 12, 2013 at 10:31 PM, Charles Berry wrote:

[snip extended brew example]

Whoa. That opens up a lot of possibilities I really hadn't thought
about before. *Thank you*.


Re: [O] ox-html.el removal

2013-03-11 Thread Jay Kerns
On Mon, Mar 11, 2013 at 3:11 AM, Achim Gratz wrote:

 Nevertheless my suggestion to the Org community is to respect your wish
 and move these two files to contrib...


I have to say I think Achim is really on the right track, here.  Also
for those interested in a bit of historical irony check out the commit
history of ox-html.el in black and white:

In particular, the following was committed by Jambunathan K on
2012-02-18 with commit message, org-e-html: New HTML exporter - a
first attempt.

diff --git a/EXPERIMENTAL/org-e-html.el b/EXPERIMENTAL/org-e-html.el
new file mode 100644
index 000..7079b5f
--- a/dev/null
+++ b/EXPERIMENTAL/org-e-html.el
@@ -0,0 +1,4902 @@
+;;; org-e-html.el --- HTML Back-End For Org Export Engine
+;; Copyright (C) 2011-2012 Free Software Foundation, Inc.
+;; Author: Nicolas Goaziou n.goaziou at gmail dot com
+;; Keywords: outlines, hypermedia, calendar, wp
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; GNU General Public License for more details.


Re: [O] ox-html.el removal

2013-03-11 Thread Jay Kerns
Dear Carsten,

I certainly support your position.  And if *anybody's* wishes should
be honoured, I would think yours should be at the top of that list,
along with the wishes of the other (at least) 4 copyright holders' of


On Mon, Mar 11, 2013 at 4:58 AM, Carsten Dominik wrote:

 On 11.3.2013, at 05:08, Jambunathan K wrote:

 Even if my combative positioning doesn't amount to anything much, I want
 to throw in a little friction by the way of Bastien and the current
 release.  I am stating my purpose in no uncertain terms - yes it is to
 delay the release or cause confusion.

 I don't think there is any confusion pertaining to the 8.0 release.  These 
 files were brought into the Org-mode repository, marked as GPL from the 
 start, so there are no formal issues including them in 8.0 in their current 
 form.  Wether ox-odt.el should be moved to contrib as per Achims suggestion I 
 don't know.   I would object moving ox-html.el, it contains a lot of variable 
 definitions, documentation strings and code I and others wrote, even if you 
 have made the interface with org-elemets.

 We will see in how far the FSF will follow your arguments and what will 
 happen when we merge 8.0 into the Emacs distribution.  So I don't see a 
 reason to hold up the 8.0 release.  With respect to Emacs, we will have time 
 to resolve the issue one way or another.

 - Carsten

[O] inline Babel calls in math environments and table cells

2013-03-11 Thread Jay Kerns

I am in the process of updating materials to the new exporter in
anticipation of Org 8.0.  It appears that inline SRC blocks are not
being evaluated in table cells and math environments in the new
exporter, for instance, something like this:

\( SRC_R[:exports results]{2+3} \)

or like this:

| SRC_R[:exports results]{2+3} |

Is the above intentional?  I am reading the Org Syntax document and it
looks like inline Babel calls are objects.  It also looks like the
pair \(...\) is a LaTeX fragment (also an object).  At the beginning
of the section it says, Most objects cannot contain objects.  And it
also says right above that, Objects can be found in... table cells.
If my reading of the syntax is correct then it would look like the
latter example is meant to be supported while the former example is

Am I reading that correctly?

Thank you,


P.S. I've tried all possible settings of #+OPTIONS and of :mode
settings in the #+attr_latex line for the table.

P.P.S. Best-case scenario for me would be both examples supported, but
if not then I am willing to live with it or try to write something
that will support it.

Re: [O] inline Babel calls in math environments and table cells

2013-03-11 Thread Jay Kerns
Let me make clear: I'm talking about on export to LaTeX the code
blocks aren't evaluated.  I can execute in the buffer and everything
works fine.


On Mon, Mar 11, 2013 at 4:54 PM, Jay Kerns wrote:

 I am in the process of updating materials to the new exporter in

Re: [O] inline Babel calls in math environments and table cells

2013-03-11 Thread Jay Kerns
Hello there,

On Mon, Mar 11, 2013 at 5:26 PM, Eric Schulte wrote:

 Hi Jay,

 This sounds like a question about the new exporter which is beyond my

 However, code blocks may be called from Org-mode tables, using the `sbe'
 [1] macro.

 Hope this helps,

Thank you.  Yes, it definitely helps; I hadn't heard about sbe - very
cool!  I played with your suggestion and here is a working example
(for the archives):

#+BEGIN_SRC R :session *R*
A - matrix(sample(100, size = 6), nrow = 2)

| 51 | 77 | 63 |
| 65 | 20 | 56 |

#+name: foo
#+BEGIN_SRC R :session *R*

|   || 63 |
|   |||
#+TBLFM: @1$3='(sbe foo (m 1) (n 3))

Now I can frame my question better about the new exporter: what I am
asking about is whether it is planned to ever be possible to do
something like this (and get the same exported results):

#PROPERTY: :exports results
#PROPERTY: :results output

|   || SRC_R{A[1,3]} |
|   ||   |


Re: [O] [BABEL] the julia language

2013-03-04 Thread Jay Kerns
Dear Bastien,

On Mon, Mar 4, 2013 at 12:53 PM, Bastien wrote:
 Hi Jay,

 thanks a lot for ob-julia.el!

 Can I add it to contrib/babel/langs in org-mode.git right now?

 For code in contrib/ we don't need authors to assign their copyright
 to the Free Software Foundation, and support for more languages for
 Babel is always great.

 Let me know.

Yes, of course.  Thank you!

 Also, if you want to edit Worg, can you send me your public key?

I did that some time ago - I am all set for Worg.

 To go through the FSF copyright assignment process, please fill in
 this form:

 When the FSF confirms it's fine, we will be able to incorporate
 ob-julia.el into Org's core.



By all means, thank you!

 PS: I'm on ArchLinux, it was a bit weird to run ~$ yaourt -S julia :)



[O] [BABEL] the julia language

2013-03-03 Thread Jay Kerns

Maybe you've heard about the relatively new language, julia [1]?
The ESS team added support for it some months back [2] and they've
been working on it more recently even [3]. It seemed natural to
investigate Babel support for julia and after quite a bit of fiddling
with ob-R.el I believe I've sorted out the major pieces:


There's an ob-julia.el file which is the meat, then and files for testing, plus
an file in case you're new to julia and would like
to learn more. For testing you'd need a recent installation of julia
[2] and you'd need an almost bleeding-edge version of ESS [4].  By the
way, it was written under the development branch of Org so if you
haven't updated recently you might need that too.

LaTeX/HTML/Beamer export is working, C-c C-c evaluation of code
chunks, plotting figures (need the Winston package), etc.  Session
evaluation is required at least for the time being.

If you see ways to improve it I'd appreciate any feedback.



G. Jay Kerns, Ph.D.
Youngstown State University

Re: [O] [BABEL] the julia language

2013-03-03 Thread Jay Kerns
Dear Eric,

On Sun, Mar 3, 2013 at 2:05 PM, Eric Schulte wrote:
 Hi Jay,

 Having read through and scanned ob-julia.el I have to
 say this looks great.  Thanks for sharing!

I should be saying Thanks to you!  Org Babel is truly great work; I
use it almost every day of my life.

 Would you be willing to contribute ob-julia.el to the Org-mode

Yes, of course, it would be an honor to give back to the Org
community.  And I'm not just saying that.

 I don't see you listed as an Org-mode contributor (see
 [1]), so to do so you would likely have to complete the FSF copyright
 attribution.  Please let me (and more importantly Bastien) know if this
 is something you'd like to do, so we can help get julia support into

OK, I'll get started on that right away.

 Additionally, it would be nice for your excellent introduction to be
 added to worg, and for julia to be listed as a supported babel language
 (see [2]).

Thanks for the kind words, and I would be happy to contribute to worg.
 I've been sitting on my hands about worg so far because I'm scared
I'm going to break it with something that isn't compatible with the
old exporter.  In an earlier message Bastien indicated that Org 8.0
might be coming out in a few weeks (thanks, Bastien!) and I've been
trying to wait for it patiently.

In the meantime, maybe I'll check out the maintenance branch and dig
up those old configurations to get the ball rolling on my side.


Re: [O]

2013-02-22 Thread Jay Kerns

On Fri, Feb 22, 2013 at 3:55 AM, Andreas Röhler wrote:
 Coming upon this tutorial, which seems excellent for beginners

 maybe move from FIXME into common place?


Yes, I agree, that's an excellent one, and a person can find another
version of it here:

Coincidentally, just last week I was working on this (fixing broken
links, etc) mostly with an eye to update with recent developments and
make compatible with the new exporter.  I contacted the original
author a couple days ago to see if he would like to incorporate those
updates, but I haven't heard back from him.

Unfortunately my updated draft is on my computer at home so I would
have to wait until later this evening before I could share the
updates.  (If there's interest, of course.)


Re: [O]

2013-02-22 Thread Jay Kerns
On Fri, Feb 22, 2013 at 5:04 PM, Andreas Röhler wrote:
 Am 22.02.2013 22:58, schrieb Achim Gratz:

 Andreas Röhler writes:

 IMHO it would be great if Jay moves it already at place. As it's a
 doku basically, giving a nice entry into a lot of things. If exporting
 is not perfect yet, it's not at the core here, we may fix it step by
 step.  Also we might gather bug-reports that way.

 The thing with Worg is that it is auto-published to HTML whenever a
 change is pushed, so if something doesn't export cleanly, it will break
 all of Worg.  So, if the document does in fact export without error to
 HTML with the latest maint version of Org it could be moved, otherwise


 Ahh, thanks for the explanation,


Hmm... thanks for the heads-up, Achim.  I usually work on the master
branch and I haven't actually checked that what I did is compatible
with the maint branch.  I will checkout the maint branch and make sure
everything exports smoothly.


Re: [O]

2013-02-22 Thread Jay Kerns
On Fri, Feb 22, 2013 at 8:49 PM, Jay Kerns wrote:

 Hmm... thanks for the heads-up, Achim.  I usually work on the master
 branch and I haven't actually checked that what I did is compatible
 with the maint branch.  I will checkout the maint branch and make sure
 everything exports smoothly.


Alright, here goes: it looks like the maint branch does not yet
include the new exporter (ox-latex.el and such).  The whole point of
my working on this to begin with was to get something compatible with
the new exporter, so rather than go back all over again to make
something work with something that's set to be outdated in the coming
months (weeks?) anyway, I'd rather sit tight on the work done so far
and patiently look forward to the new exporter's merge from master to

In the meantime, the latest updated draft (little more than some
tweaks of Erik Iverson's original work) is here:

I've confirmed just now that it successfully exports to PDF/HTML under
the new exporter based on a freshly pulled org from git mere minutes
ago.  There's still work to be done, and I welcome
suggestions/corrections in the balance of time between now and when
some rendition of this can safely land on Worg.


Re: [O] org-export-babel-evaluate and :exports none

2013-02-18 Thread Jay Kerns
Dear Ista,

On Mon, Feb 18, 2013 at 1:22 PM, Ista Zahn wrote:
 Hi all,

 Just checking to see if anyone was able to reproduce this or if I am
 the only one with this problem.


I just make update2'ed, followed your recipe, but my tmp.tex did not
incorrectly have the exported source block.  So, I guess I can't
reproduce, unfortunately.

Jay Kerns

Re: [O] [ANN] Merge of new export framework on Wednesday

2013-02-06 Thread Jay Kerns

The new exporter just arrived in my git repository and I wanted to say
Congratulations! but even more importantly, THANK YOU.  Kudos on a
job very well done, if not 100% complete yet.  I have been looking
forward to this for quite some time, now.

I would like to extend my Congratulations and THANK YOU to the rest of
the Org-mode community/team as well, not limited to Nicolas, though
this happens to be the occasion of the new exporter's release.

Org-mode (and GNU-Emacs more generally, and Free software more
generally than that) has changed my life, and by extension those who
live and work near me, in my view, for the better.  Cheers, and may we
share many good days ahead.

Jay Kerns

On Sun, Feb 3, 2013 at 2:00 PM, Nicolas Goaziou wrote:

Re: [O] Formatting R output

2012-09-10 Thread G. Jay Kerns
Dear Erich,

comments inline below.

 From: Neuwirth Erich erich.neuwirth at
 Subject: Formatting R output
 Newsgroups: gmane.emacs.orgmode
 Date: 2012-09-10 12:12:00 GMT

 I am using org-mode with R.
 I already wrote a message about formatting inline code some time ago.
 After working more with R in org-mode (which I _really_ like) I have some
 questions and/or suggestions.

 1) a mild annoyance.

 src_R{1+1} inserts the result 2 in the output. In fact, it inserts =2=.
 When one runs the file repeatedly, org-mode does not remove older results.
 So if I replace src_R{1+1} by src_R{2+2} and do not remove the last output,
 My file will contain

 src_R{2+2} =4= =2=

 Also, If I run the inline code segment by C-c C-c one, the org file ail 
 contain just 1
 correct result, bit if afterwards I export the file (to LaTeX or html),
 the exported file will have 2 copies of the result.

 Is there anything the developers can do about this?

I can confirm that if a person does not remove old output but changes
input to the inline code segment then the exported file will have both
the correct output plus the (old) incorrect output.  My strategy to
avoid this is use C-c C-c sparingly just to check whether the output
is as expected, then always erase output.  If I am going to use an org
file with C-c C-c a lot (for a lecture, say), then I keep a copy for
exporting clean and separate from the one I am going to do a lot of
C-c C-c'ing with.  YMMV.

 2) formatting inline output.
 As discussed above, using inline code produces something like
 src_R{2+2} =4=

 In some cases, I would like the result to be not on fixed font.
 Currently, I to not see a way of removing the equal signs before and after 
 the result,
 they seem to be added by org itself, therefore I cannot use trickery in R to 
 remove them.
 Could the developers think of an option which would allow to get the result
 without the bracketing equal signs?

I think you can fix this with inline code-segment header arguments
which will override buffer-wide or system wide settings.  So, for
example, you could do

src_R[:results raw]{2 + 2}

which will return 4 and not =4=.

I hope this helps,


G. Jay Kerns, Ph.D.
Associate Professor
Mathematics and Statistics

Re: [O] how to both :body-only t and :table-of-contents t

2011-09-23 Thread G. Jay Kerns
Dear Jan

On Fri, Sep 23, 2011 at 3:51 AM, Jan Böcker wrote:

 Hi Jay,

 I faced the same problem about a year ago.
 See this thread in the mailing list archive:

 The HTML exporter will refuse to include a TOC if body-only is t; the
 atom exporter and a send HTML messages with Wanderlust hack relied on
 that behaviour, which is why this was not changed in the official Org

 You can either apply the one-line patch I included in the linked thread
 or ask Ian Barton about his solution using jQuery he mentioned at the
 end of that thread.


Thanks; I was afraid it was going to be something like that, and am
appreciative that I don't need to reinvent this particular wheel.  My
previous workaround was to export once with TOC, copy-paste the TOC
bit to the org-file in a #+BEGIN_HTML block, then export again with
:body-only t.  But each run takes a couple of hours (another question
for another day), which is a pain, and not convenient should the
document structure change.

I noticed in the thread that Carsten mentioned writing a hook that
strips the other stuff.  Don't have much experience writing hooks, but
there should be a way to write a custom publishing function just like
the current one which strips everything but the TOC.  I'll use your
patch while I continue thinking about it.

Thanks again.

[O] how to both :body-only t and :table-of-contents t

2011-09-21 Thread G. Jay Kerns
Dear Org Mode list,

First: congratulations on Org mode; it is truly dynamite.

I am publishing a project to HTML for the purposes of Jekyll
post-processing.  For this, I need to set :body-only t so I can put
the YAML frontmatter at the top of my file.  However, I would also
like to have the TOC exported (only), right after the body tag,
which it correctly does whenever :body-only isn't t.

In other words, it looks like I am obliged to :body-only t which cuts
out header/footer/TOC or I can NOT do :body-only t which will give me
the TOC plus a bunch of extra stuff.

My question:  is it possible to do what I want?  Is there some sort of
YAML {{ page.toc }} that I'm missing somewhere, or is there some
combination of publishing options that I've missed that will export an
org file to an HTML file that looks like this:

layout: default
title: whatever

div id=table-of-contents
h2Table of Contents/h2
div id=text-table-of-contents
lia href=#sec-1blah blah blah /a/li
lia href=#sec-2blah blah blah /a/li

Rest of exported content here?

Thanks for any advice, and again, THANK YOU to the Org Mode team.