[Orgmode] [bug] small problem with tags in HTML export with H:1 option set

[Erik Iverson]

See the following .org file for an explanation, I think it's a
small bug...

==

#+TITLE: HTML Export with #+OPTIONS: H:1 set
#+STYLE:  p {color: red; font-family:sans-serif;} 

#+OPTIONS: h:1 toc:nil
* Here is a headline, no space between it and subsequent text
This text is red.

New paragraph, also red.
** A second-level headline, no space between headline and subsequent
Oops? This line not in any HTML tag, not red.

But this is red.


** A second-level headline, one space between headline and subsequent text

Now it's red.

And so is this.


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Re: [Orgmode] Bibtex and latex export

[Erik Iverson]

Rafael,

I asked the same question last week :).

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg30073.html


I've just now looked into the org-latex.el file, and found:

(defcustom org-latex-to-pdf-process
  '("pdflatex -interaction nonstopmode -output-directory %o %f"
"pdflatex -interaction nonstopmode -output-directory %o %f")
  "Commands to process a LaTeX file to a PDF file.
This is a list of strings, each of them will be given to the shell
as a command.  %f in the command will be replaced by the full file name, %b
by the file base name (i.e. without extension) and %o by the base directory
of the file.
The reason why this is a list is that it usually takes several runs of
pdflatex, maybe mixed with a call to bibtex.  Org does not have a clever
mechanism to detect which of these commands have to be run to get to a 
stable

result, and it also does not do any error checking.

Alternatively, this may be a Lisp function that does the processing, so you
could use this to apply the machinery of AUCTeX or the Emacs LaTeX mode.
This function should accept the file name as its single argument."
  :group 'org-export-pdf
  :type '(choice (repeat :tag "Shell command sequence"
  (string :tag "Shell command"))
 (function)))


Looks like you can just customize that variable, easy!

--Erik


Rafael Calsaverini wrote:
Hi there, 

I'm trying to use org-mode to compose latex documents and I'm having a 
problem with bibtex. When I export to pdf with C-c C-e p, pdflatex runs 
and everything works gracefully with respect to the latex code (the 
output is even prettier than I used to have patience to do only with 
latex), but bibtex isn't called. 

I've  tried to fiddle with org-exp-bibtex, which is nice, but apparently 
it don't call bibtex either. 

I've tried to edit the function that calls pdflatex to include a call to 
bibtex, but to be honest I know zero about lisp, so I couldn't even edit 
a simple list of commands. :P (I must be the only emacs user in the 
world that can't write or read lisp... it would be swell if I could use 
haskell to extend emacs instead of lisp :P). 

How should I go about automatically including a call to bibtex whenever 
I want to export my org document as a pdf?


Thanks for your time, and sorry to bore you with simple questions...
---
Rafael Calsaverini
Dep. de Física Geral, Sala 336
Instituto de Física - Universidade de São Paulo

rafael.calsaver...@gmail.com 
http://stoa.usp.br/calsaverini/weblog
CEL: (11) 7525-6222
USP: (11) 3091-6803





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Re: [Orgmode] Worg updating?

[Erik Iverson]

Hello,

Worg now publishes the results of its publishing script, at:

http://orgmode.org/worg/publishing.txt

I had Bastien install R for an update to the R docs that I'm doing,
and it appears to work when he does a manual publish.  But I think
the problem is that R is not in the path of whatever user is running
the automated script, you can see the last line is complaining
about that.

I think that's the only fix needed, just get R in the path of
that script.

Sorry if my request has caused this issue, but having R on there
will be nice.  The export file its bombing on isn't even mine,
so someone else appears to be wanting to use it as well.

John Hendy wrote:

Still not all is well...

http://orgmode.org/worg/org-contrib/babel/examples/org-babel-gnuplot.org

---
[jwhe...@bigbang ~]$ ls 
Worg/org-contrib/babel/examples/org-babel-gnuplot.org 
 
Worg/org-contrib/babel/examples/org-babel-gnuplot.org 


---

Exists 
in git, not on Worg.



John

On Fri, Sep 17, 2010 at 11:32 AM, Tom Dye > wrote:


Aloha all,

Thanks to whoever fixed links on Worg.  It appears that Worg isn't
updating itself now, though.

All the best,
Tom

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[Orgmode] exporting to a specified directory

[Erik Iverson]

Hello,

Can you set some option in an org-mode buffer telling the
exporter to write the HTML and PDF versions of the document
in a specific directory?  I know the publishing mechanism
does this, just wondering if there is a simple variable
to set per file to set this on export, or do I need to
set up a publishing project?

Thanks!
Erik

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Re: [Orgmode] Ditaa usage

[Erik Iverson]

On 09/22/2010 08:08 AM, Juri Artamonov wrote:

Hello John,

if I add what you provided then I have

"Warning (initialization): An error occurred while loading
`c:/emacs/.emacs.d/init.el':
Symbol's function definition is void: org-babel-do-load-languages"

message.


From your previous post, looks like you're using a fairly old version
of org-mode.  using source code blocks like ditaa is much simplified
in org-mode 7.01, so just upgrade to that and you'll be all set.




I have added this for now:

(setq org-ditaa-jar-path "~/lib/ditaa0_9.jar")

(setq org-babel-load-languages (quote ((emacs-lisp . t)
  (dot . t)
  (ditaa . t)
  (R . t)
  (python . t)
  (ruby . t)
  (gnuplot . t)
  (clojure . t)
  (sh . t

In result I don't have error message on initialization but after export
I have at least area with where the lines are shown exactly the same as
I wrote in org file but without any converting to the image.

Maybe I need something to install additionally or add something else to
the configuration?

Thank you,
   Juri.

On Wed, Sep 22, 2010 at 3:23 PM, John Hendy mailto:jw.he...@gmail.com>> wrote:

Do you have the necessary lines for babl as described here:
http://orgmode.org/worg/org-contrib/babel/languages.php#configure

Namely:



;;active Babel languages
(org-babel-do-load-languages
  'org-babel-load-languages
  '((gnuplot . t)
(ditaa . t)
))


You don't have to have gnuplot... just put whatever languages you
want in the form "language . t" and you're set.

See if that helps.


John

On Wed, Sep 22, 2010 at 7:06 AM, Juri Artamonov
mailto:jartamo...@gmail.com>> wrote:

Hello Guys,

I'm still learning how to correctly configure orgmode. One of
the items is ditaa usage.

I have the following in my org file.

#+begin_src ditaa :file task_states.png :cmdline -r -s 0.8
  ++   +-+   ++
  ||   | |   ||
   +--+  TODO  +-->+  NEXT   +-->+  DONE  |
   |  | cRED   |   |  cBLU   |   | cGRE   |
   |  +--+-+---+   +--+---+--+   ++

#+end_src

#+results:
file:task_states.png

init.el
contains reference to ditaa library.

(setq org-ditaa-jar-path "~/lib/ditaa0_9.jar")

Could you please tell me what else do I need to configure in
order to have graphics in result of exporting the file into HTML?

Thank you,
 Juri.


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Re: [Orgmode] Re: does #+PROPERTY still exist ?

[Erik Iverson]

On 09/22/2010 10:13 PM, Vincent Belaïche wrote:

Hello all,

Thanks for all the feedback. I am using Org-mode version 6.33x which is
the latest on emacs CVS repository --- that may be outdated as emacs is
using bazaar now.



Yes, very outdated.  Orgmode 7.01 was released over two months ago now.

You can get the latest from http://orgmode.org

It is a very simple installation, just download and add a couple
directories to your load-path.

You can also get the latest from git, which is what I do.


What is not working is

1. Auto-completion of `#+PROP' does not work
2. `C-c C-x p' does not work.

Look at the following example:

--8<-coupez ici--début-->8---
#+PROPERTY: toto_ALL 1 2 3

* test

Then I type here `C-c C-x p'
--8<-coupez ici---fin--->8---

2.1 The completion at `Property:' prompt does not propose `toto'
2.2 The completion at `Value:' prompt does not propose 1 2 or 3


Hope that this clarifies the issue.

   Vincent.

PS-1: Where can I get the latest org-mode ?
PS-2: Sorry for my first email contained an error, setting properties
before the 1st heading does not work.



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Re: [Orgmode] Org-mode screencasts

[Erik Iverson]

Richard,

First of all, your MobileOrg screencasts are very nice.
In my opinion, keeping things high-level and showing
the major features are what is important.  In a way,
they are commercials for the product, and I think the
best way to entice people into trying the product is to
make them say "Wow" when viewing the video.

I would be happy to help but would need to know the
software requirements.  Is it easy to make these under
Linux?

Richard Moreland wrote:

Hi All,

I think it would be helpful to create a series of screencasts to
demonstrate Org-mode.  The screencasts I've made for MobileOrg[1,2]
seem to have helped users get started quickly.  There are so many
powerful features of Org-mode that are difficult to visualize yourself
using until you can see them in action.  It may also help draw in new
users who otherwise wouldn't quite get it.

Some topics that may be interesting:

- Org-mode in action, demonstrating common tasks like capture,
restructuring a tree, refiling, etc.
- Babel
- Integration with other tools (Gnus, WL, Firefox, etc)
- Clocking/reporting
- Export capabilities
- Power user showing their streamlined configurations
- ...?

I'd like to collect all of the videos in one place, unify them with
some similar (but simple) production, with each of the videos having a
page that links to documentation, Worg, example dotfiles, comments,
etc to help the user take it further on their own.

I'd be happy to host the videos if bandwidth is a concern on the
orgmode.org site.  I've also already purchased the necessary software
to record/edit the videos.  But I'm looking to the community for ideas
on topics as well as individuals who would be willing to record the
videos or at least help me work up a script with key talking points so
I could do the recording and narration.

What do you think?  Anyone interested in helping?

Thanks,
Richard

[1] http://mobileorg.ncogni.to/screencasts/MobileOrg-Dropbox-OSX/
[2] http://ncogni.to/mobileorg/overview.mov

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Re: [Orgmode] wrap sourcecode?

[Erik Iverson]

On 09/23/2010 07:11 PM, Matt Price wrote:

This may be an odd request, but is it possible to wrap sourcecode
blocks?  attached is the org source for the following page, rendered by
wordpress using html generated by org2blog:
http://www.hackinghistory.ca/lab-01-understanding-html/
You can see that without wrapping, the source goes right off of the
page.  Is there anything I can do to fix that? Do I need to define the
"src" and "example" classes in css somewhere, in order to get horizontal
sliders?  Or can I set an option in the html export that will make this
easier for me?


You can see from the generated HTML that those classes have already
been assigned



so you just need to provide the appropriate style.  There are several
ways to accomplish that, see "CSS Support" in the manual if memory
serves.

--Erik

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Re: [Orgmode] Re: Org-mode screencasts

[Erik Iverson]

On 09/23/2010 07:45 PM, Richard Moreland wrote:

I jumped the gun a bit and decided to put together a video showing the very 
basics.  It seems overly simple when I re-watch it, but I think it is helpful 
for those who are unsure how to get started with the basics of Org-mode.

http://ncogni.to/org-screencasts/1-basics/

Feedback is welcome, these were the least exciting topics to cover, but I 
wasn't sure how to really wow new users without overwhelming them.  I figured 
that taking it step by step with short, clear episodes covering special topics 
would be a good start.



One more thought, if it's easy to edit the screencast, throw in a bit about
headline folding.  Just show how easy it is to collapse and expand the
different headlines.


-Richard

On Sep 23, 2010, at 6:47 PM, Charles Cave wrote:


Richard Moreland  ncogni.to>  writes:
I think it would be helpful to create a series of screencasts to
demonstrate Org-mode.


Great idea!  I would he happy to record a couple of screencasts
based on tutorials I have written. Currently I am preparing
a tutorial on date trees and capturing notes to a journal.

I am a Windows user and a screencast tool I use is
http://www.screenr.com - from Articulate.
This allows screencasts up to 5 minutes to be recorded
then hosted on their website.

Charles







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Re: [Orgmode] Re: Org-mode screencasts

[Erik Iverson]

On 09/23/2010 07:45 PM, Richard Moreland wrote:

I jumped the gun a bit and decided to put together a video showing the very 
basics.  It seems overly simple when I re-watch it, but I think it is helpful 
for those who are unsure how to get started with the basics of Org-mode.

http://ncogni.to/org-screencasts/1-basics/

Feedback is welcome, these were the least exciting topics to cover, but I 
wasn't sure how to really wow new users without overwhelming them.  I figured 
that taking it step by step with short, clear episodes covering special topics 
would be a good start.



Really nice, agree that the intro is the least exciting.

But even starting with agendas in the next one, the more interesting things
can be shown.

Great job!

So with the software you use, you can go and insert/delete/edit voice into the
presentation once it's complete, or if you want to change the wording in one
part, do you have to record the whole thing over again?  I assume you can change
it, but don't know if the Linux tool has that capability.


-Richard

On Sep 23, 2010, at 6:47 PM, Charles Cave wrote:


Richard Moreland  ncogni.to>  writes:
I think it would be helpful to create a series of screencasts to
demonstrate Org-mode.


Great idea!  I would he happy to record a couple of screencasts
based on tutorials I have written. Currently I am preparing
a tutorial on date trees and capturing notes to a journal.

I am a Windows user and a screencast tool I use is
http://www.screenr.com - from Articulate.
This allows screencasts up to 5 minutes to be recorded
then hosted on their website.

Charles







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Re: [Orgmode] Re: Org-mode screencasts

[Erik Iverson]

On 09/23/2010 10:09 PM, John Hendy wrote:

Wow, Richard. That was sweet. You even have a pleasing "screencaster's
voice."


Agreed with John.  Your voice is perfect for this, and you have
good timing and delivery.




My only thought was along the lines of what one should assume about
org-mode viewers. Familiarity with emacs? No knowledge of emacs? I only
got into emacs because I found org-mode, so my only thought there is
that I might not even have known what "meta" was... I can't recall, but
did you clarify meta = alt on Win/Linux and Command on Mac?

Stuff like that might be helpful. Obviously these won't all be done on a
Mac and some unfamiliar with it might wonder what the Command and carat
symbols are on their own keyboards?

As Erik said -- folding and perhaps adjusting in and out (meta +
left/right). Also, it seems that only the meta or control functions show
up as keystrokes. For example, I thought you said "M-n s" and "M-n w" to
narrow on the tree and then widen the view but I only ever saw one part
of that flash on the screen.

Great, great job. Loved it and think this is exactly what Org could use.
I have a co-worker who just got emacs and org-mode up on his computer
and would love to have something this simple and clear-cut.


Great work, again.
John

On Thu, Sep 23, 2010 at 9:54 PM, Erik Iverson mailto:er...@ccbr.umn.edu>> wrote:

On 09/23/2010 07:45 PM, Richard Moreland wrote:

I jumped the gun a bit and decided to put together a video
showing the very basics.  It seems overly simple when I re-watch
it, but I think it is helpful for those who are unsure how to
get started with the basics of Org-mode.

http://ncogni.to/org-screencasts/1-basics/

Feedback is welcome, these were the least exciting topics to
cover, but I wasn't sure how to really wow new users without
overwhelming them.  I figured that taking it step by step with
short, clear episodes covering special topics would be a good start.


Really nice, agree that the intro is the least exciting.

But even starting with agendas in the next one, the more interesting
things
can be shown.

Great job!

So with the software you use, you can go and insert/delete/edit
voice into the
presentation once it's complete, or if you want to change the
wording in one
part, do you have to record the whole thing over again?  I assume
you can change
it, but don't know if the Linux tool has that capability.


-Richard

On Sep 23, 2010, at 6:47 PM, Charles Cave wrote:

Richard Moreland ncogni.to <http://ncogni.to>>
  writes:
I think it would be helpful to create a series of
screencasts to
demonstrate Org-mode.


Great idea!  I would he happy to record a couple of screencasts
based on tutorials I have written. Currently I am preparing
a tutorial on date trees and capturing notes to a journal.

I am a Windows user and a screencast tool I use is
http://www.screenr.com - from Articulate.
This allows screencasts up to 5 minutes to be recorded
then hosted on their website.

Charles







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[Orgmode] publishing orgmode to a CMS

[Erik Iverson]

Does anyone have any general advice or comments regarding
the publishing of org-mode documents to a CMS?

I'm thinking of the case where I have HTML files generated
by Org-mode, and want to publish it Worg-style, but would
prefer to publish to a system with comments/RSS/etc.

If anyone has done that, I'd love to hear your experience,
which CMS software you chose, and how it is working for you.

Thanks,
Erik

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Re: [Orgmode] [babel] creating simple vectors in R

[Erik Iverson]

Hello,

Dan Davison wrote:

I'd appreciate opinions from R users on the following org-babel-R
details:



I use R daily, with and without org-mode, but have never investigated
these features of passing tables and Lisp lists to source blocks, but
it looks interesting.  More below.


Currently, Org tables, and lisp lists, are converted into data frames
when they are sent from Org to R, and we have no way to create simple
vectors such as c(1,2). I'd like to know whether users of org and R
would approve of the following change that makes simple R vectors
possible, or have other suggestions related to these issues.

With the patch below, there would be two ways to create a simple vector
in R. The most direct way is to pass a non-nested lisp list:

#+begin_src R :var x='(1 2) :results output
str(x)
#+end_src

CURRENT OUTPUT:
#+results:
: 'data.frame': 1 obs. of  2 variables:
:  $ V1: int 1
:  $ V2: int 2

NEW OUTPUT:
#+results:
:  num [1:2] 1 2



What happens with "non-atomic" lists that contain mixed types?
They could either be turned into a vector of the lowest common
type, e.g., '(1 "hi") is turned into a character vector, or this
could be turned into an R list.  Then you'd be going from
Lisp List -> R list data types.


In addition, because babel's table-indexing code produces a non-nested
list when taking a one-dimensional slice, this would be another
situation in which a vector rather than data frame is created:

#+tblname: input-tab
| 1 | 3 |
| 2 | 4 |

#+begin_src R :var x=input-tab[0,] :results output
str(x)
#+end_src

CURRENT OUTPUT:
#+results:
: 'data.frame': 1 obs. of  2 variables:
:  $ V1: int 1
:  $ V2: int 3

NEW OUTPUT:
#+results:
:  num [1:2] 1 3

There's a possible argument that that's slightly at odds with R, since,
in R, a single row slice of a data frame is still a data frame.



Yes, only since data.frames may and almost always do contain
mixed types.  Which goes back to the first question about the
behavior of this code when there are mixed types.  I think for
this case, if you're taking a single row of an org-table,
turning it into a vector is an OK thing to do, and
is something I probably would rarely do.  For columns,
I definitely think it's an OK thing to do, and it's more likely
I'd be passing in a single column of an org-table as opposed
to a single row.

In R, for columns, subsets of data.frames only return data.frames
with certain indexing styles, and even then,
setting drop = TRUE will return a vector.

> df1 <- data.frame(a = 1:10, b = 2:11)

> is.vector(df1$a)
[1] TRUE

> is.vector(df1[["a"]])
[1] TRUE

> is.vector(df1[, "a"])
[1] FALSE

> is.vector(df1[, "a", drop = TRUE])
[1] TRUE


A related issue is translating an Org table into a matrix rather than a
data frame in R. This can be done explicitly with a call to as.matrix in
the user's code, but if anyone feels that it would be helpful for babel
to automate this then do say so.

Dan


diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c709064..4b49af5 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -141,16 +141,18 @@ This function is called by `org-babel-execute-src-block'."
 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
   "Construct R code assigning the elisp VALUE to a variable named NAME."
   (if (listp value)
-  (let ((transition-file (org-babel-temp-file "R-import-")))
-;; ensure VALUE has an orgtbl structure (depth of at least 2)
-(unless (listp (car value)) (setq value (list value)))
-(with-temp-file transition-file
-  (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
-  (insert "\n"))
-(format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", 
as.is=TRUE)"
-name (org-babel-process-file-name transition-file 'noquote)
-   (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
-   (if rownames-p "1" "NULL")))
+  (if (listp (car value))
+ (let ((transition-file (org-babel-temp-file "R-import-")))
+   (with-temp-file transition-file
+ (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
+ (insert "\n"))
+   (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", 
as.is=TRUE)"
+   name (org-babel-process-file-name transition-file 'noquote)
+   (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" 
"FALSE")
+   (if rownames-p "1" "NULL")))
+   (format "%s <- %s"
+   name
+   (concat "c(" (mapconcat 'org-babel-R-quote-tsv-field value ",") 
")")))
 (format "%s <- %s" name (org-babel-R-quote-tsv-field value
 
 (defvar ess-ask-for-ess-directory nil)


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Re: [Orgmode] Tracking time with MobileOrg

[Erik Iverson]

Jeff Kowalczyk wrote:

Can the current version of MobileOrg be used for a simple time tracking
workflow? (i.e. does it have an easy clock in and clock out?)


I do not believe so, but I will put in my vote for this being a really,
really good idea.



My wife has a need for a simple time tracking application on the iPhone. The
only number needed is total hours spent per period (e.g. month) on one task, the
full-time job.

I use Org Mode for my own worklogs, and would do any necessary pre-templating
and post-processing on the resultant Org file, if a rapid-capture strategy can
be worked out for MobileOrg.

Given how much I use and like Org Mode myself, I'd be really pleased if we can
work with Org as a file format for this application, rather than some
closed-source app.

Thanks,
Jeff



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Re: [Orgmode] [babel] Writing R-packages the org way?

[Erik Iverson]

Rainer M Krug wrote:

Hi

I am about to write an R package, and as I am an org-mode and org-babel 
user, I would (obviously) like to use org-mode for that.


Is there a recommended way of writing an R package in org-babel, or do I 
have effectively wrap the R code for the documentation etc. into source 
blocks in babel?


That's what I do.  I've looked into converting an org-file to
Roxygen or Rd markup, but never got very far.  My idea at the time
was to do something like:

* function1
** Help
*** Title
this is function 1 title
*** Description
function1 does this...
*** Usage
function1(arg1, arg2, ...)
*** Arguments
arg1: the first argument
*** Examples
function1(arg1 = x, arg2 = y)
**Definition
begin_src R :tangle R/package.R
function1 <- function(arg1, arg2) {

}




Any suggestions how to best proceed?

Dream: I would like to have one org file which contains everything 
(documentation, code, other relevant files) and if I export or tangle 
the file, I have the package ready.


Well, that functionality is essentially present with code blocks
and tangling, except the documentation part.



Is there anything like that?

Rainer

--
NEW GERMAN FAX NUMBER!!!

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


Centre of Excellence for Invasion Biology
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Skype:  RMkrug
Google: r.m.k...@gmail.com 




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[Orgmode] Re: [babel] Writing R-packages the org way?

[Erik Iverson]

Dan Davison wrote:

Erik Iverson  writes:


Rainer M Krug wrote:

Hi

I am about to write an R package, and as I am an org-mode and
org-babel user, I would (obviously) like to use org-mode for that.

Is there a recommended way of writing an R package in org-babel, or
do I have effectively wrap the R code for the documentation
etc. into source blocks in babel?

That's what I do.  I've looked into converting an org-file to
Roxygen or Rd markup, but never got very far.  My idea at the time
was to do something like:

* function1
** Help
*** Title
this is function 1 title
*** Description
function1 does this...
*** Usage
function1(arg1, arg2, ...)
*** Arguments
arg1: the first argument
*** Examples
function1(arg1 = x, arg2 = y)
**Definition
begin_src R :tangle R/package.R
function1 <- function(arg1, arg2) {

}



Any suggestions how to best proceed?

Dream: I would like to have one org file which contains everything
(documentation, code, other relevant files) and if I export or
tangle the file, I have the package ready.

Well, that functionality is essentially present with code blocks
and tangling, except the documentation part.


Hi Erik,

Would you mind expanding on that -- what are we missing for the
documentation part?



Dan, by "except for the documentation part", I meant generating
.Rd files (the LaTeX-like syntax) automatically from some org-syntax
that does *not* depend on code blocks.  I.e., it would be cool to
specify syntax like I have above for documentation.  Using org-mode
headlines for each section like Description, Usage, Arguments, etc.

Just like exporting to LaTeX generates sections, some process would
use these headlines to generate the .Rd sections.

That way, you don't have to use the .Rd syntax yourself.  No big deal,
just a convenience feature.  I don't know how you'd specify to org-mode
that a particular subtree was to generate .Rd syntax, and I don't know
if it would be on export or tangling.

An alternative is simply just to use code blocks of type Rd within
org-mode and then tangle to .Rd files.  That's what I currently do.

Hope that explains it,
Erik



Dan


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Re: [Orgmode] Re: mobileorg app can't sync

[Erik Iverson]

I have same same error. The steps I took are as follows;

- Downloaded MobilOrg app for iPhone.
- Created an account on Dropbox.
- Linked Mobilorg to Dropbox account.
- Created test entry in Mobilorg.
- Attempted to sync.

Error returned "Error syncing changes. An error was encountered while attempting 
to fetch mobileorg.org from the server. The error was: Unexpected error"


On my Dropbox account, I see:

MobileOrg\.dropbox



But you need to run org-mobile-push from Emacs, and set any
variables it relies on.  I forget which, but they are in the
manual.

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Re: RE [Orgmode] Re: Issues with org-mode and LaTeX export.

[Erik Iverson]

For the time being I am stuck with this version.  I am sending a request to
our IT group to upgrade Emacs to the most recent version for the version of
RedHat we have, this should have a more recent version of org-mode, if I am
lucky that should be done in a couple weeks.  In the mean time I will
manually add, or exclude, what I want from the exported "*.tex" file.


Do you have write access to your home directory?  That's all you need
to install the latest and greatest. Although I do not know how org 7
works with your version of Emacs.  Probably smart to have them
upgrade since there are tons of improvements in Emacs, and it's,
you know, free.


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Re: [Orgmode] Re: mobileorg app can't sync

[Erik Iverson]

Luke Crook wrote:



On Thu, Oct 21, 2010 at 11:17 AM, Erik Iverson <mailto:er...@ccbr.umn.edu>> wrote:




I have same same error. The steps I took are as follows;

- Downloaded MobilOrg app for iPhone.
- Created an account on Dropbox.
- Linked Mobilorg to Dropbox account.
- Created test entry in Mobilorg.
- Attempted to sync.

Error returned "Error syncing changes. An error was encountered
while attempting to fetch mobileorg.org <http://mobileorg.org>
from the server. The error was: Unexpected error"

On my Dropbox account, I see:

MobileOrg\.dropbox


But you need to run org-mobile-push from Emacs, and set any
variables it relies on.  I forget which, but they are in the
manual.


Ah, so I have to have an existing org-mobile-push'ified ".org" file in 
Dropbox prior to syncing? I don't think this is really made clear in the 
instructions. I didn't know that there was an org-mobile-push dependency 
between Emacs and Mobileorg. I had the impression that Mobilorg could be 
used stand-alone.


No, I don't think so.  That's why the instructions talk about the
'staging area'.

So my system is: I have my 'real' orgmode files in Dropbox, but
not in my MobileOrg directory.  I then have a command in Emacs
that when I press C-c g, my .org files are committed to git, and
org-mobile-push is called to copy them to the dropbox/MobileOrg
directory.  I then can sync from the ipod and have them there.

I can make changes on the device, marking items as done and taking
notes.

When I come back to my desk, I use a command bound to C-c p to
call org-mobile-pull.  I also have auto-revert-mode enabled for
org files, so all changes simply appear on screen in my org
files.

 
I'll try this and report back.


-Luke


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Re: [Orgmode] TikZ to separate file (babel?) possible?

[Erik Iverson]

John,

Does
http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.php#sec-4_2
help?  There is a tikz example there.  The :file argument may be all
you're missing, and putting your code in a latex source block.

Here is what I do when I have an R code block that generates
LaTeX code.  Hopefully this can be adapted to your case.

#+srcname: R-latex
#+begin_src R :results silent :exports code
  lf <- function() {
  "\\LaTeX"
  }

  lf()
#+end_src

#+begin_src latex :noweb yes :file (if (and (boundp 'htmlp) htmlp) 
"latex-logo-html.png" "latex-logo.png") :buffer (if (and (boundp 'htmlp) 
htmlp) "no" t)

<>~is a high-quality typesetting system; it includes
features designed for the production of technical and scientific
documentation. <>~is the de facto standard for the
communication and publication of scientific
documents. <>~is available as free software.
#+end_src

That messy :file and :buffer arguments needs some explanation.

They are there so that when I eval the code block *in* an org-mode
buffer, with C-c C-c, that an image will be generated to be
inserted into the buffer.  However, this uses my background color
in emacs, which I don't actually want when exported to HTML, that's
what the :buffer argument controls.  Essentially, it's just
what arguments get passed to dvipng (if I recall correctly).

On Latex export, the actual latex code should be included in the
document, so I think all of my use cases are covered.

The only issue is that org-mode doesn't display PDFs generated
from a :file argument in buffer, but you might not care about
that.

If you're an R user, you might also check out the tikzDevice package:
http://r-forge.r-project.org/projects/tikzdevice/

HTH,
--Erik


John Hendy wrote:

Hi,


I've recently gotten into TikZ and love it. It is simply fantastic for 
creating neat diagrams and other thingies.


One question... I created an org file with a flow chart in it and simply 
put my TikZ code in between #+begin_latex and #+end_latex. This is fine 
when the picture is in a document, but what if I want just a 
.png/jpg/eps/pdf output? Is it possible to use babel or something else 
so that I can simply generate a picture vs. needing it to be "in" the 
PDF output?


I can ask the PGF list as well, but this one is far more active and I 
know some use TikZ here. I ask because sometimes in my notes I'd like to 
have the code present but also be able to reuse my work elsewhere, like 
when I have to present using powerpoint. It'd be nice to just grab the 
picture (like what I do with gnuplot output) rather than generating a 
pdf just for the TikZ pic, screenshot or gimp it down to size, and then 
be able to use it.


Does that make sense? It seems like babel would be perfect for this. It 
already allows all the typical handles -- file output, what to export, etc.


Or does this already exist and I'm ignorant?


Thoughts?
John




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Re: [Orgmode] Release 7.02

[Erik Iverson]

Jeff Horn wrote:

On Fri, Oct 29, 2010 at 2:49 AM, Carsten Dominik
 wrote:

Implement MathJax support
==

Org-mode now uses MathJax to display math on web pages.  We serve
MathJax from the orgmode.org server, at least for the time being
(thanks Bastien!).  If you are going to use this for pages which
are viewd often, please install MathJax on your own webserver.


I use this, and forty page views a week may be too much (I don't
know). I didn't know how MathJax worked, and I thought it was always
served from MathJax servers (I didn't give it much thought,
obviously).

What do I need to customize to get MathJax to load from my own server
instead of orgmode.org?



See the org-export-html-mathjax-options variable.

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Re: [Orgmode] Release 7.02

[Erik Iverson]

Jeff Horn wrote:

Thanks. That did the trick. I think it may be a bit faster too,
running on my server... but that could be my imagination.


It is very likely faster.

Also, note the following about using Firefox:

http://www.mathjax.org/resources/faqs/#image-fonts



On Fri, Oct 29, 2010 at 2:03 PM, Erik Iverson  wrote:


Jeff Horn wrote:

On Fri, Oct 29, 2010 at 2:49 AM, Carsten Dominik
 wrote:

Implement MathJax support
==

Org-mode now uses MathJax to display math on web pages.  We serve
MathJax from the orgmode.org server, at least for the time being
(thanks Bastien!).  If you are going to use this for pages which
are viewd often, please install MathJax on your own webserver.

I use this, and forty page views a week may be too much (I don't
know). I didn't know how MathJax worked, and I thought it was always
served from MathJax servers (I didn't give it much thought,
obviously).

What do I need to customize to get MathJax to load from my own server
instead of orgmode.org?


See the org-export-html-mathjax-options variable.







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Re: [Orgmode] Installing Orgmode through ELPA-tarball

[Erik Iverson]

I agree about the word 'easiest'.  Perhaps a more neutral
phrasing of the question, such as:

"How can I install Orgmode through Emacs' Package Manager?"

Tom Short wrote:

On Mon, Nov 1, 2010 at 8:05 AM, Jambunathan K  wrote:

** What is the easiest way to install latest version of Orgmode?



That's all good information to have, but I'm not sure it's the easiest
way to install the latest version. It may eventually be easy, but the
existing steps look relatively cumbersome.

Using git seems like the easiest way to get the latest version with
the advantage that you can pick the version you want (latest
up-to-the-minute, latest release, or some other release).

- Tom

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[Orgmode] org-mode completion tip

[Erik Iverson]

Hello,

I have always ignored in-buffer Completion
(http://orgmode.org/org.html#Completion) in org-mode
because it is bound to M-, which my window manager
(any many others) use to switch applications.

Many of you may have disabled your window manager's
special usage of that key, or re-bound the org-complete
command to another key chord in emacs.

However, just this morning I discovered you can use
C-M-i in as an alternative to M- in emacs, so that
completion also works with that key chord.

Hopefully someone else may find this useful.

--Erik

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Re: [Orgmode] Re: [babel] "tangle" results of source blocks?

[Erik Iverson]

Unfortunately I can't look this up at the moment, but
my guess is that the :results code option might help with
what you want?

Maurizio Vitale wrote:

"Sébastien" == Sébastien Vauban  writes:


Sébastien> Hello Maurizio,
Sébastien> Maurizio Vitale wrote:
>> Hi, I have procmail rules defined in a org table which is then
>> used as an argument for an elisp block which produces procmailrc
>> results.
>> 
>> Something like:
>> 
>> #+tblname: mailing-lists | to | emacs-users | emacs-users |

>> #+TBLFM:
>> 
>> #+srcname: procmail-rules(mailing-lists=mailing-lists)

>> #+begin_src emacs-lisp :exports results :results output :tangle
>> no ... elisp code that evaluates to procmail rules #+end_src
>> 
>> #+results: procmail-rules :tangle /tmp/YYY :0: *

>> ^to_emacs-us...@xxx.com
>> $MAILDIR/emacs-users/
>> 
>> I'd like to tangle the result section, not the code block. Is

>> that possible?

Sébastien> See the "exports" header argument.

Sébastien> http://orgmode.org/manual/exports.html#exports

That option controls what is exported, but I really need to tangle:
there're portions of the file, section headings and other documentation
that don't belong into the output file. So for instance given:

* Introduction
  This is a file that does blah
* Configuration
#+tblname: config
|a | nice table|

*Details
#+srcname: procmail-rules(config=config)
#+begin_src emacs-lisp :exports results :results output :tangle ~/.procmailrc
 ... elisp code that evaluates to procmail rules  
#+end_src


Of this entire file, noting should end up in ~/.procmailrc except for the
result of the evaluation of procmail-rules, which is what I hoped to
achieve with ':tangle ~/.procmailrc' and ':exports results' combined.

Thanks,

Maurizio







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Re: [Orgmode] Inserting text into the part of an HTML document?

[Erik Iverson]

Stephen,

There may be a better answer, but I see in the
doc-string for org-export-html-style, that:

As the value of this option simply gets inserted into the HTML 
header, you can \"misuse\" it to add arbitrary text to the header.
See also the variable `org-export-html-style-extra'.

However, I doubt you want to use the 'org-export-html-style' variable,
since it looks like you have to specify the entire header, but
perhaps the 'style-extra' version will do what you want?

--Erik

Stephen Eglen wrote:

I'm using org-mode to export an html file of my org file.  I'd like to
add the following line to the   ...  section of the
document:

#+HTML: 

[This line tells search indexes not to index the file.
http://www.google.com/support/webmasters/bin/answer.py?hl=en&answer=93710
]

but the HTML directive puts it in the body, rather than the head.
Any ideas how I'd get it into the head?  I tried +HTML_HEADER as an
analogy to LATEX_HEADER, but that doesn't seem to be defined.

Thanks, Stephen

org-version
"7.02trans"


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Re: [Orgmode] Re: Clock report (R from the agenda)

[Erik Iverson]

I don't know what this thread is about, but it seems related.
Aapologies if I'm
hijacking it, but as of my latest pull just this morning,
my agenda has no clocktable in it, where as it previously
did.  I have not changed anything as far as I know.

Thanks!

--Erik

Sébastien Vauban wrote:

Hi Carsten,

Carsten Dominik wrote:

On Nov 4, 2010, at 11:39 AM, Sébastien Vauban wrote:

Carsten Dominik wrote:

you should now be able to use `C-u R' to achieve this.

OK.



The lighter in the mode line will then switch from "Clock" to "Clock{}",

A detail: I'd eventually would have written "Clock/" to remind the "/" used
for applying the filters.

I did use {} because the current filter is actually listed in the mode line,
surrounded by {}.


Another: could we append, in the modeline, the tags (or their abbrev, such
as "w" for "work") used in the filtered view?

The filter *is* shown in the mode line.  Just not as part of the Clock
lighter.


I wanted to (re-)test these, but now, when doing R, nothing is appended into
my buffer with logged times. Did I do something wrong?

Same with C-u R.



and the current tags filtering should apply to the clock table in the
agenda.

Please test this and report back.

Only minor thing: while the logged lines are correctly shown or made
invisible in the grid time, you need to refresh the table with "g" for it
to display the correct values.

Until that, what's above is not in sync' with what's in the table. Isn't
there a way to make this refresh happen automatically?

That would be possible. However, the whole idea of filtering is to be *very*
fast, it works by hiding lines that are already in the buffer. Doing a
refresh for each change in filter would be time consuming. So I'd say having
to refresh by hand if the clock is showing filtered stuff is the smaller
evil.


I would privilege coherency of sums above small delay in table appearance. You
know, when we look at tables for chasing time, we really need trustable
figures.

In fact, I don't really understand your argument: if I want quick reports, I
would just choose for the unfiltered view. If I need detailed sums of clocked
times, I would go for the "filtrable" view (by C-u R) and would accept a
little delay.

If you really don't share this vision, could you at least make this
customizable?  TIA.



: | File | L | Headline | Time|  |
: |--+---+--+-+--|
: |  |   | *Total time* | *10:15* |  |
: |--+---+--+-+--|
: | Clock-Report.org |   | *File time*  | *10:15* |  |
: | Clock-Report.org | 1 | Work | 8:09|  |
: | Clock-Report.org | 2 | Client A | | 3:23 |
: | Clock-Report.org | 2 | Client B | | 4:46 |
: | Clock-Report.org | 1 | Personal | 2:06|  |
: | Clock-Report.org | 2 | DONE Lunch with Mary | | 2:06 |

Nice new layout. Much clearer for the levels...

Yes, I think so to.  Try :compact t, that is also nice, I think.


I'll have a look -- when reports will come back to life.



| File | Headline | Time|  |
|--+--+-+--|
|  | ALL *Total time* | *10:15* |  |
|--+--+-+--|
| Clock-Report.org | *File time*  | *10:15* |  |
|  | Work | 8:09|  |
|  | \__ Client A | | 3:23 |
|  | \__ Client B | | 4:46 |
|  | Personal | 2:06|  |
|  | \__ DONE Lunch with Mary | | 2:06 |


A couple of days ago, when it still worked, I've just seen something really
painful: all the Org buffers were referenced in that table, even those which
should not participate -- because I did not clock any time in them (for that
or those days).

Plus, having many Org files, in fact, I did not see anymore the lines with the
real time, as there were many lines with 0:00 time before them...

Best regards,
  Seb



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Re: [Orgmode] org-latex-to-pdf-process missing?

[Erik Iverson]

I'm guessing you just need to

(require 'org-latex)

--Erik

Jeff Horn wrote:

Dear orgsters,

Sorry for the noise, but it isn't immediately clear to me from the
docs. `C-h v org-latex-to-pdf-process` indicates that the variable
doesn't exist in my org-mode installation. I'm using org-mode 7.3 in
emacs 23.2 (Aquamacs 2.1).

I remember a discussion a few weeks ago centered on how to get org to
export to PDF using the appropriate compilation sequence. Is this
variable missing because org now uses texi2dvi or another shell
program that automagically figures this stuff out?

If so, someone who knows how might wish to update the latex export
page at worg.[1]

Thanks for the info,
Jeff

Footnotes:
[1] http://orgmode.org/worg/org-tutorials/org-latex-export.php



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Re: [Orgmode] Re: Clock report (R from the agenda)

[Erik Iverson]

Carsten, yes, fixed, thank you!

Carsten Dominik wrote:

Hi Erik,

please pull and see if the error persists.
What is the value of org-agenda-start-with-clockreport-mode

?

- Carsten

On Nov 19, 2010, at 7:38 PM, Erik Iverson wrote:


I don't know what this thread is about, but it seems related.
Aapologies if I'm
hijacking it, but as of my latest pull just this morning,
my agenda has no clocktable in it, where as it previously
did.  I have not changed anything as far as I know.

Thanks!

--Erik

Sébastien Vauban wrote:

Hi Carsten,
Carsten Dominik wrote:

On Nov 4, 2010, at 11:39 AM, Sébastien Vauban wrote:

Carsten Dominik wrote:

you should now be able to use `C-u R' to achieve this.

OK.


The lighter in the mode line will then switch from "Clock" to 
"Clock{}",
A detail: I'd eventually would have written "Clock/" to remind the 
"/" used

for applying the filters.
I did use {} because the current filter is actually listed in the 
mode line,

surrounded by {}.

Another: could we append, in the modeline, the tags (or their 
abbrev, such

as "w" for "work") used in the filtered view?

The filter *is* shown in the mode line.  Just not as part of the Clock
lighter.
I wanted to (re-)test these, but now, when doing R, nothing is 
appended into

my buffer with logged times. Did I do something wrong?
Same with C-u R.

and the current tags filtering should apply to the clock table in the
agenda.

Please test this and report back.

Only minor thing: while the logged lines are correctly shown or made
invisible in the grid time, you need to refresh the table with "g" 
for it

to display the correct values.

Until that, what's above is not in sync' with what's in the table. 
Isn't

there a way to make this refresh happen automatically?
That would be possible. However, the whole idea of filtering is to 
be *very*

fast, it works by hiding lines that are already in the buffer. Doing a
refresh for each change in filter would be time consuming. So I'd 
say having
to refresh by hand if the clock is showing filtered stuff is the 
smaller

evil.
I would privilege coherency of sums above small delay in table 
appearance. You

know, when we look at tables for chasing time, we really need trustable
figures.
In fact, I don't really understand your argument: if I want quick 
reports, I
would just choose for the unfiltered view. If I need detailed sums of 
clocked

times, I would go for the "filtrable" view (by C-u R) and would accept a
little delay.
If you really don't share this vision, could you at least make this
customizable?  TIA.

: | File | L | Headline | Time|  |
: |--+---+--+-+--|
: |  |   | *Total time* | *10:15* |  |
: |--+---+--+-+--|
: | Clock-Report.org |   | *File time*  | *10:15* |  |
: | Clock-Report.org | 1 | Work | 8:09|  |
: | Clock-Report.org | 2 | Client A | | 3:23 |
: | Clock-Report.org | 2 | Client B | | 4:46 |
: | Clock-Report.org | 1 | Personal | 2:06|  |
: | Clock-Report.org | 2 | DONE Lunch with Mary | | 2:06 |

Nice new layout. Much clearer for the levels...

Yes, I think so to.  Try :compact t, that is also nice, I think.

I'll have a look -- when reports will come back to life.

| File | Headline | Time|  |
|--+--+-+--|
|  | ALL *Total time* | *10:15* |  |
|--+--+-+--|
| Clock-Report.org | *File time*  | *10:15* |  |
|  | Work | 8:09|  |
|  | \__ Client A | | 3:23 |
|  | \__ Client B | | 4:46 |
|  | Personal | 2:06|  |
|  | \__ DONE Lunch with Mary | | 2:06 |
A couple of days ago, when it still worked, I've just seen something 
really
painful: all the Org buffers were referenced in that table, even 
those which
should not participate -- because I did not clock any time in them 
(for that

or those days).
Plus, having many Org files, in fact, I did not see anymore the lines 
with the

real time, as there were many lines with 0:00 time before them...
Best regards,
 Seb


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Re: [Orgmode] inconsistent export of R results in orgmode 7.3,

[Erik Iverson]

Ian,

What does your *R* session buffer look like
when this does and does not work?  The same?

Perhaps the prompt is getting confused at some point?

Your example has worked 4 times in a row for me...

--Erik

Ian Kennedy wrote:

Since upgrading to org-mode 7.3 I have had inconsistent export of R code
block results. Sometimes the results appear in the exported document,
sometimes they don't. I've included the simplest example I've been able to
come up with below. When I export this file the data frame is exported
about half the time. The example below is about the shortest I've come up
with that shows inconsistent export. I usually have the problem with more
complex documents, which use R only, and  which have R read in data from
external files.

I do not have the problem if I use org-mode 7.01h. I am running emacs 23.2
on Windows XP with R 2.12.0. My apologies if this has already been
discussed (if it has, maybe somebody can point me to the discussion I
missed).

Here's the example:
* Ditaa Example
  #+BEGIN_SRC ditaa :file dit.png :width 300 :height 300  :exports results
+---+
|   |
|Block 1|
|   |
+---+---+
|
|
v
+---+
|   |
|Block 2|
|   |
+---+

  #+END_SRC
* R example
** Something  in R

   #+BEGIN_SRC R :session *R* :exports none
 x <- 1:5
 y <- data.frame(A=x, B=round(sin(x/3.3),3))
   #+END_SRC

** A table which is often not exported
   #+BEGIN_SRC R :session *R* :exports results :colnames yes
 y
   #+END_SRC


Thanks,
Ian


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[Orgmode] org-indent mode not indenting free text?

[Erik Iverson]

Hello,

I just pulled the latest org from git, and org-indent
mode does not seem to be fully working anymore.

I still see the additional stars added to headlines, and
they are shadowed properly.  But the free text lines under
each headline are not shown indented as they previously
were.

I cannot be sure when this change happened, but I think
within the last week or so.  Can anyone else reproduce
this?

It wasn't clear from looking at the git logs for
org-indent.el that anything has recently changed that
would affect this, so I'm currently stumped.

--Erik

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Re: [Orgmode] Synchronize files among computers via MobileOrg, and create tasks from iPhones?

[Erik Iverson]

Jing Su wrote:

Dear all,

Just curious that if we could push to the MobileOrg server, e.g., 
DropBox, from a computer, and pull it down from another computer, so 
that we can synchronize org files on different computers via MobileOrg. 


I store all my *actual* org files on Dropbox, along with the Mobile Org
versions.  This gives me sync'ing between all my computers with Dropbox
installed.

I used to use CVS for synchronizing, but now SSHing in and out are 
blocked at my working places, so I can no longer synchronize files 
between home computers and work computers via ssh+cvs. Could someone 
kindly suggest some methods to securely synchronize files without ssh 
please?


This I am not sure about, although some people use org-crypt for this
I think.  There is also something called "mobile org crypt" also which
lets you store encrypted org files on Dropbox for viewing on the iphone.

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg32149.html



It would also be great if more functions of the org-mode (e.g., creating 
new tasks) can be accessed from an iPhone. I am struggling to decide if 
I should stay with Org-mode (I love Emacs) or switch to outlook. 


!!!

I can 
access all functions of my online calendars from my iPhone or from 
Outlook or a web browser on any computer; but for MobileOrg, I have to 
put things as notes on my iPhone, then do the copy/paste later when I 
can access my MAIN desktop -- synchronizing org files among computers is 
painful, as I just explained, so I have to set one as the MAIN desktop 
for using the org-mode.


Not if you just use Dropbox for storing your actual org files. Also,
there is org-mobile-pull that should pull in any notes captured on
the iPhone and place them in an org file of your choosing for
refiling.

As for calendar, there are tools on the list for synching with
Google calendar, although not from mobile org as far as I know.


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Re: [Orgmode] org-indent mode not indenting free text?

[Erik Iverson]

Carsten,

Not as far as I can tell, it seemed fixed to me
after David's message:

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg33781.html

I haven't had any problems since then, and I just did
a pull just now, reloaded and all appears well.

If there's anything else I can do to help, please let me
know, but I can say that my original issue was fixed, so
I'm not sure if anyone else is still having the problem,
why it would be? Did they org-reload or restart emacs?
I thought maybe with that problem, I actually had to
restart emacs to get it to work again, but could be
mis-remembering.

--Erik

Carsten Dominik wrote:

Hi Erik,

are you still having this problem?

- Carsten

On Nov 23, 2010, at 5:47 PM, Erik Iverson wrote:


Hello,

I just pulled the latest org from git, and org-indent
mode does not seem to be fully working anymore.

I still see the additional stars added to headlines, and
they are shadowed properly.  But the free text lines under
each headline are not shown indented as they previously
were.

I cannot be sure when this change happened, but I think
within the last week or so.  Can anyone else reproduce
this?

It wasn't clear from looking at the git logs for
org-indent.el that anything has recently changed that
would affect this, so I'm currently stumped.

--Erik

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Re: [Orgmode] org-indent mode not indenting free text?

[Erik Iverson]

I also don't understand the following part of
Antti's message:

"Free text is still not indented and indents are only one space."

That seems contradictory to me?

--Erik


Erik Iverson wrote:

Carsten,

Not as far as I can tell, it seemed fixed to me
after David's message:

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg33781.html

I haven't had any problems since then, and I just did
a pull just now, reloaded and all appears well.

If there's anything else I can do to help, please let me
know, but I can say that my original issue was fixed, so
I'm not sure if anyone else is still having the problem,
why it would be? Did they org-reload or restart emacs?
I thought maybe with that problem, I actually had to
restart emacs to get it to work again, but could be
mis-remembering.

--Erik

Carsten Dominik wrote:

Hi Erik,

are you still having this problem?

- Carsten

On Nov 23, 2010, at 5:47 PM, Erik Iverson wrote:


Hello,

I just pulled the latest org from git, and org-indent
mode does not seem to be fully working anymore.

I still see the additional stars added to headlines, and
they are shadowed properly.  But the free text lines under
each headline are not shown indented as they previously
were.

I cannot be sure when this change happened, but I think
within the last week or so.  Can anyone else reproduce
this?

It wasn't clear from looking at the git logs for
org-indent.el that anything has recently changed that
would affect this, so I'm currently stumped.

--Erik

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Re: [Orgmode] Re: org-indent mode not indenting free text?

[Erik Iverson]

Just a guess here: This may be some weirdness
because the check in org-indent *will* allow
people using GNU Emacs 23.1.50 to turn on
org-indent, as far as I can tell.

The message "org-indent-mode can crash Emacs 23.1"
does not fully explain if it can also crash 23.1.50.

If indeed you should be having to run Emacs 23.2 or
greater to get org-indent-mode, I don't believe that
is what is currently happening.

Perhaps that check should require 23.2 or
greater? I don't know the details here, but
it's a starting place to look.

Antti Kaihola wrote:

2010/12/2 Achim Gratz :

What version of Emacs are you running?


This is:
GNU Emacs 23.1.50.1 (i486-pc-linux-gnu, GTK+ Version 2.18.0) of
2009-09-27 on palmer, modified by Debian


 What does C-h f with-silent-modifications result in?


with-silent-modifications is a Lisp macro in `org-macs.el'.

(with-silent-modifications ORG-UNMODIFIED)

Not documented.


 Could you back out the change
(most likely the defmacro for with-silent-modifications in org-macs.el,
even though I have no clue why this would interact with org-indent-mode
as it should not be defined for versions >23.1) and tell us if that
solves your problem (which I can't test because org-indent-mode doesn't
even start on Emacs 23.1)?


Yes it does! I commented out:

;;(if (or (< emacs-major-version 23)
;;  (and (<= emacs-major-version 23)
;;   (< emacs-minor-version 2)))
;;(defmacro with-silent-modifications
;;  (org-unmodified)))

and it now works correctly. Thanks a lot!

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Re: [Orgmode] Re: org-indent mode not indenting free text?

[Erik Iverson]

Carsten Dominik wrote:

Hi Erik,

On Dec 3, 2010, at 5:18 PM, Erik Iverson wrote:


Just a guess here: This may be some weirdness
because the check in org-indent *will* allow
people using GNU Emacs 23.1.50 to turn on
org-indent, as far as I can tell.


org-indent-mode should work in 23.1.50, this is the
release where the fix was made.



The message "org-indent-mode can crash Emacs 23.1"
does not fully explain if it can also crash 23.1.50.


Yes, may be this is not so clear.  The current setup forbids it
before 23.1.50, and allows it from 23.1.50.  At least that is
what I meant.  Is there a bug?


No, I did not realize that this is what was indeed meant.
More below...




Could you back out the change
(most likely the defmacro for with-silent-modifications in org-macs.el,
even though I have no clue why this would interact with org-indent-mode
as it should not be defined for versions >23.1) and tell us if that
solves your problem (which I can't test because org-indent-mode doesn't
even start on Emacs 23.1)?

Yes it does! I commented out:
;;(if (or (< emacs-major-version 23)
;;(and (<= emacs-major-version 23)
;; (< emacs-minor-version 2)))
;;(defmacro with-silent-modifications
;;  (org-unmodified)))
and it now works correctly. Thanks a lot!



I have now changed the definition like this:

(if (and (not (fboundp 'with-silent-modifications))
 (or (< emacs-major-version 23)
 (and (= emacs-major-version 23)
  (< emacs-minor-version 2
(defmacro with-silent-modifications (&rest body)
  `(org-unmodified ,@body)))


I must admit I don't understand the above macro,
but what I was getting at before was:

It only appears defined for Emacs < 23.2,
So in particular, 23.1.50 is 'stuck' in
between these two version checks, and maybe
that's causing Antti's issue?


May I ask you to pull and check if this is
working for you out of the box?


Works for me fine on Emacs 23.2, we will see
if it does for Antti also.



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Re: [Orgmode] Elsevier's "Executable Paper Grand Challenge"

[Erik Iverson]

  The purpose of the Executable Paper Challenge is to invite scientists
  to put forth their ideas pertaining to these pressing and unsolved
  questions.


I come up with the same answer to all four questions --- Org-mode!


Yes, these are only unsolved questions to those who haven't
discovered the answer yet.

It does seem like an interesting challenge though, it will be
good to see what the entries look like.

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Re: [Orgmode] [RFC] Self-configuring Org-mode files

[Erik Iverson]

Jeff Horn wrote:

On Fri, Dec 10, 2010 at 2:09 AM, Thomas S. Dye  wrote:

4) A super-function in the Library of Babel would set the buffer-local
instance of every relevant Org-mode variable to its default state:
#+source: lob-set-local-defaults
#+begin_src emacs-lisp
...
#+end_src


Would this function save the current state of each variable it changes
for restoration after the user exits the buffer?


Perhaps I'm mis-understanding, but Thomas' suggestion is to set the
variables *buffer-local*, not global, so once the buffer is killed,
so are the buffer-local versions of the variables.


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Re: [Orgmode] How can i share a single org-default-notes-file between multiple instances of emacs?

[Erik Iverson]

Note a direct answer, but I would just open up all the
buffers you use, and then either save window configurations
in registers to recall them when you switch contexts, or use
a package like Elscreen:

http://www.emacswiki.org/emacs/EmacsLispScreen

Eric Holbrook wrote:

At work i typically need to have at least 2 emacs running: 1 for the
project i'm working on at the moment; 1 for notes, email, ~/.bashrc,
~/.alias, etc.

I often have more than 1 project going at a time, so i end up with 3
or 4 emacs running, sometimes more.

I'd like to be able to do 'org-capture from any emacs, and have them
all dump into the same org-default-notes-file, which i have creatively
named notes.org.

How can i do this? I thought of possibly setting a defadvice tied to
notes.org that tells all running emacs to unceremoniously revert that
buffer before doing anything else to it, and to save it when done with
it.

Has anybody already solved this problem?

tia,
Eric

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Re: [Orgmode] [OT] Emacs for Windows 7

[Erik Iverson]

Markus Heller wrote:

Hello all,

I know this is OT, but I'm going to have to have my work computer
upgraded to 


Apparently that's a good idea! :)


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Re: [Orgmode] [babel] ob-web

[Erik Iverson]

Sebastien,

This is probably pretty simple to do with a number of org-mode
supported languages.  Since I know R best, I can recommend the
RCurl package (http://www.omegahat.org/RCurl/) for doing exactly
as you describe.

I'll look into an R implementation of this when I get some
time over break in the next couple weeks.

There are doubtless other solutions!

--Erik

Sébastien Vauban wrote:

Hi Eric, Dan & Co,

A dream here: would we have an ob-web package, we could have easy block codes
for fetching some info from Web pages, possibly by giving as parameters 2
delimiters (strings or regexps), and re-arranging it into tables when it fits.

Use cases: statistics from Google Analytics, prices for flights, etc.

A potentiel show-stopper is, I guess, the fact that some (more and more) pages
are accessible via HTTPS, like the Google Analytics ones.

Is all of this do-able somehow: already, nearly, could be or never ever?

Best regards,
  Seb



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Re: [Orgmode] MobileOrg Android 0.5.0 - Now with native Dropbox support!

[Erik Iverson]

On 12/21/2010 06:25 PM, Matthew Jones wrote:

Merry Christmas to all MobileOrg Android users... I am pleased to announce the
0.5.0 release of MobileOrg for Android.


Great, looking forward to trying it out!



This release includes support for Dropbox which is the single most requested
feature.  I actually finished writing the code for this a few weeks ago, but it
has taken a little while for the Dropbox folks to approve it for release.


Can you briefly describe what this approval process it about?  As in, what
exactly are they approving of?  That you use their trademarked name in the
app perhaps?


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Re: [Orgmode] Babel and R issue when exporting to PDF via LaTeX in Windows 7

[Erik Iverson]

Ben Ward wrote:

Hi, all, I hope someone can help with this issue,

Unfortunately I'm having a work PC upgrade, and it means Windows 7 and 
the order not to install any other system on it for compatibility and 
for the IT experts - I use the term loosely, to only need to know how to 
use one system.


Im trying to get org-mode set up with emacs so I can icorporate R code 
in my documents - like Sweave functionality. I have this achieved in 
Arch Linux. Howeer when I export to PDF in Windows 7 I'm just getting a 
PDF with Titl, Author, Date, and Contents and then no R stuff.


Is R in your path?  ESS uses its own tricks to find a valid version
of R on your system, but I think org-mode will just use your system
path, if I recall correctly.


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Re: [Orgmode] Images from R in LaTeX and PDF

[Erik Iverson]

And what version of org are you using?

Ben Ward wrote:


#+begin_src R :exports both
 full <- read.csv(file="~/Documents/BSc Biology/Third Year/BY6001-40 - 
Dissertation/Data and Analysis/Evolution Results.csv", head=T)

 library("lattice")
 ecoli = subset(full, Bacterium=="E.coli")
 edett = subset(ecoli, Cleaner=="Dettol")
 egarl = subset(ecoli, Cleaner=="Garlic")
MIC.mod = lm(MIC. ~ 1+Challenge*Cleaner*Replicate, data=ecoli)
#+end_src

#+begin_src R :file fig1.pdf
 xyplot( MIC.+fitted(MIC.mod) ~ Challenge, data=ecoli, xlab="Challenge", 
ylab="MIC %", auto.key=TRUE)

#+end_src

#+attr_latex: width=0.6\textwidth wrap placement={h}{0.4\textwidth}
#+label: fig:one
#+caption: Linar Plot of real data and fitted model values
#+results: fig1
[[file:fig1.pdf]]

In the case of this code, actually altering size works, but it keeps 
putting the image at the end of my document. Then other images, placed 
with pretty much the same code, give or take for filenames and such, 
won't increace in size, but will alter their movement.
I'm wondering if using pure latex for my images would be an easier 
solution.


Cheers,
Ben.


On 07/01/2011 18:30, Thomas S. Dye wrote:

Aloha Ben,

Can you share an example that doesn't work for you?

All the best,
Tom

On Jan 7, 2011, at 7:23 AM, Ben Ward wrote:


Hi All,

I've been doing some work with babel and R to generate graphs that 
I've then been including useing attr latex.


But when I include images the always appear very very small, even 
when I mess about with the width settings of the attr latex line and 
remove the options for wrap and such.


Does anybody else use R with images and org, and could tell me how 
they handle including R graphics in their documents?


Thanks,
Ben. W

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Re: [Orgmode] Help with migrating blog to org-mode format

[Erik Iverson]

Myriam,

I write my content in Org-mode, and use weblogger.el to post my content. 
Just search for weblogger on Emacs wiki, and perhaps this will help a 
bit too:


http://www.randomsample.de/dru5/node/77

This is about Drupal, but the ideas should work for posting to anything 
that supports xmlrpc.


--Erik

Myriam Abramson wrote:

Hello,

After Google dropped the ftp option to blogger, I dumped my blog to an
xml file with the hope of ressucitate it to a more friendly
environment for me. I've found this environment with a combination of
org-mode, blorg, and ... dropbox. Dropbox just provides me a link to
publish my blog wherever I want to. Blorg isn't being maintained I
believe and it has lots of error but it works in converting org-mode
to blog formatting for now and I can work on it later. 


Each topic in a blog is a TODO task and the date is inserted when the
task is DONE. I'm planning to read from my xml blog and write topics
simply as "* DONE mytopic ... " but how can I get the publication date
in org to get "CLOSED: " on the next line? 

The xml of my blog is something like that: 


 my title
 my content
2003-10-22T18:27:00.000-04:00

TIA,

myriam




From the cat's little instruction handbook:

Treat yourself to a nap in the sock drawer once in awhile.

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Re: [Orgmode] org-babel, R, and org-babel-open-src-block-result

[Erik Iverson]

On 01/11/2011 04:22 AM, Leo Alekseyev wrote:

I recently started using org-babel with R, and so far I think it's
pretty great!  I'm still getting accustomed to org-babel workflow and
am playing with available options.  I have a couple of questions:

I noticed that C-c C-o (org-babel-open-src-block-result) always gives
me an empty *Org-Babel Results* buffer, even if there's output printed
to #+results section.  Is this a bug?  Am I doing something wrong?

On a similar note, is there an option for the #+ results session to be
completely suppressed?..  I can see situations where I might simply
want to send the code to the inferior process and examine the results
there using :results output :session, or perhaps I'm running the code
just for the side effects.  It would be nice if I could say e.g.
:results none.


From the manual:

The following results options indicate what happens with the results once they 
are collected.


* silent
The results will be echoed in the minibuffer but will not be inserted into the 
Org-mode buffer. E.g., :results output silent.


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[Orgmode] Question on org-beamer markup

[Erik Iverson]

Hello,

According to http://orgmode.org/worg/org-tutorials/org-beamer/tutorial.html

the following markup should work when exporting to PDF from an 
org-beamer document.


- the first, very @important@, point!
- the previous point shows the use of the special markup which
  translates to the Beamer specific /alert/ command for highlighting
  text.

However, upon export the resulting .tex file does not actually contain 
this translation from @important@ to the alert command, but rather sill 
has @important@ in the output.


Am I missing some part of the setup process?

I am using the latest org pulled from git.

Thanks!
--Erik

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Re: [Orgmode] Basic organization question

[Erik Iverson]

On 01/14/2011 09:35 PM, Tommy Kelly wrote:

I can see that TODOs can be organized using tags, or categories, or
files, or simply subtrees (or several of those). Is there an obvious
choice?


My vote is "NO", org is really about finding what works best for you,
and the plethora of choices reflects that different people work in
different ways!  Try out a few until something feels natural.



All I'm really looking for is a basic organization, to let me "group"
tasks of different broad functional areas -- accounting, recruitment,
IT, and so on.

And I like the idea discussed in http://orgmode.org/org.html, where
tasks get captured into a single refile.org file and then later moved
about into their classification homes.

But of those various ways of classifying, is there one to be preferred?

thanks,
Tommy


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Re: [Orgmode] Blogging from org-mode

[Erik Iverson]

On 01/17/2011 01:13 PM, Juan Reyero wrote:

On Sun, Jan 16, 2011 at 9:57 PM, Tom Breton (Tehom) mailto:te...@panix.com>> wrote:

Some months back I contributed improvements to org-html.  My intent was to
make it easy to post org files as blog posts.

So this is a sort of delayed announcement.  There are two packages that
post to blogs from org-mode: My org2blog/atom and Puneesh's (punchagan's)
org2blog/wp.  I know there are also blog hosts based on org-mode, but
that's different.  This is pushing org files to a "normal" blog host such
as Blogger (for org2blog/atom) or Wordpress (org2blog/wp)

org2blog/atom lives in the git repo http://repo.or.cz/r/org2blog.git and
org2blog/wp lives in https://github.com/punchagan/org2blog.git

Both respect the normal export options (#+TITLE: etc) but other than that
the approaches are fairly different.

Please tell me if I've missed any other org-based blogging software (other
than the blog hosting software which is a different category).


I wrote org-jekyll a while back to export a blog to jekyll,

http://juanreyero.com/open/org-jekyll/index.html



I also simply use weblogger.el (http://www.emacswiki.org/emacs/WebloggerMode) 
combined with a really easy function defined at 
http://www.randomsample.de/dru5/node/77 to post to blogs including Drupal. 
Weblogger.el is really nice because it lets you also edit existing entries in 
Emacs.  Don't know if all the solutions above do the same.  This method also 
allows you to use different blog systems than Drupal, I believe any that support 
XMLRPC updates, including Blogger, Drupal, Wordpress, ...


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Re: [Orgmode] Blogging from org-mode

[Erik Iverson]

Hello,

On 01/17/2011 03:02 PM, Samuel Wales wrote:

On 2011-01-17, Erik Iverson  wrote:

I also simply use weblogger.el
(http://www.emacswiki.org/emacs/WebloggerMode)


I made the mistake of trying this, thinking it had no dependencies
other than the other .el file so would be easier.  It looks
potentially useful.

I looked at 2 versions of this, and both had the same version number,
but the code was different.  That's a slightly bad sign.

   http://launchpadlibrarian.net/40758914/weblogger.el
   
http://windows-config.googlecode.com/svn/trunk/.emacs_d/weblogger/weblogger.el

Also, there is a compiler warning for obsolete variable, so the code
might be old?

Finally, I couldn't figure out the basics.  Just to confirm, this
takes HTML and posts it?  It does not make this clear.


Yes, you can set up a blog by first doing:

M-x weblogger-setup-weblog RET

But there were some quirks when I tried this with Drupal 6. I think I had to 
have at least one post already in the blog before it worked. But after that, I 
was able to weblogger with the function defined in the link below to post to 
Drupal.




combined with a really easy function defined at
http://www.randomsample.de/dru5/node/77 to post to blogs including Drupal.


What does your really easy function do that weblogger.el does not do?


Weblogger just sends the HTML to the blog, and lets you edit existing entries. 
It does not produce the actual HTML.


The function from randomsample.de exports an Org-mode buffer to HTML and 
"massages" the HTML output to be of a form that blogs like. I.e., gets rid of 
the headers.  Weblogger has nothing to do with org-mode per se, it just lets you 
post content to blogs that support XMLRPC.


That's about as far as my knowledge goes, so I hope it helps. This method isn't 
completely clean, but it did work for me with Drupal 6 (but haven't gotten it to 
work yet in Drupal 7...)


As usual, there's more than a few ways to do things, so the more options the 
better in my opinion.


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Re: [Orgmode] Re: Worg needs some reorganizing

[Erik Iverson]

Jeff Horn wrote:

On Thu, Jan 20, 2011 at 6:22 AM, Dan Davison  wrote:

I strongly second this. In fact I'll stick my neck out more: Worg is
great, but for tutorials on org-mode, HTML export is often the wrong
format for obvious reasons (i.e. unless you go to some trouble, it
conceals a lot of the org syntax). I'm tempted to suggest that htmlized
output should be the default format for many org tutorials on Worg.


I respectfully disagree with your assertion. When someone writes a
document "properly", i.e. in a literate fashion, i.e. using org source
blocks, the right syntax is shown at the right time. Please see the
manual as an example.


I must admit I ran into this exact problem when writing an org-babel/R
tutorial.  The problem came down to the following: I was writing an
interactive org-mode document showing mainly how code blocks work within
org.  This of course necessitates that I describe code block arguments.
But these aren't shown in export. I believe the solution would be
to export an "example block" to HTML, but then *also* include a source
code block for interactive org-mode use.

So my tutorial makes perfect sense when you're following along in org
mode.  But the HTML export seems a little odd since only the content
of the code blocks are shown, and not the full code blocks, which is
the point of the tutorial.

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Re: [Orgmode] Need help on org-exp-blocks and dot

[Erik Iverson]

Bryan Emrys wrote:

Hi,

Now getting an error message: /bin/bash: dot: command not found

Hmm. Pathname issue?


Absolutely.



On the mac, dot is in /opt/local/bin/dot
My .emacs file has: (setq load-path (cons "/opt/local/bin" load-path))



That won't add anything to your shell's path, it's just where Emacs
looks for code to load.

I can certainly just open a terminal window and run dot from the command 
line.


Can you grep your shell startup files and find out which one adds
/opt/local/bin to the path?


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Re: [Orgmode] Need help on org-exp-blocks and dot

[Erik Iverson]

Bryan Emrys wrote:

/usr/local/bin is also in /etc/paths

if I echo $PATH, I get

/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin


How are you echoing path, starting up a terminal, or within
Emacs M-x shell?

What if you try M-x getenv  PATH  in Emacs?




Thanks,

Bryan

On Thu, Jan 20, 2011 at 1:33 PM, Bryan Emrys <mailto:bryan.em...@gmail.com>> wrote:


Eric,

.profile has:
# MacPorts Installer addition on 2009-04-08_at_20:48:37: adding an
appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
# Finished adapting your PATH environment variable for use with
MacPorts.



On Thu, Jan 20, 2011 at 1:28 PM, Erik Iverson mailto:er...@ccbr.umn.edu>> wrote:



Bryan Emrys wrote:

Hi,

Now getting an error message: /bin/bash: dot: command not found

Hmm. Pathname issue?


Absolutely.



On the mac, dot is in /opt/local/bin/dot
My .emacs file has: (setq load-path (cons "/opt/local/bin"
load-path))


That won't add anything to your shell's path, it's just where Emacs
looks for code to load.


I can certainly just open a terminal window and run dot from
the command line.


Can you grep your shell startup files and find out which one adds
/opt/local/bin to the path?





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Re: [Orgmode] C-c a t shows empty list

[Erik Iverson]

Which version of Emacs / org-mode?

Микола Стрєбков wrote:

Hi orgsters,
 
I started to use org-mode together with MobileOrg and everything was fine. But two days ago I realized that I'm unable to build neither agenda nor todo lists from my org files. Problem occurred on both Emacs and my iPhone even on the simplest files like:


* test
** TODO test2
** TODO test3
* test4

I found similar issue in google cache (osdir.com gives 403) but it was resolved 
by just Emacs restarting. I'm not so happy.

Please help.



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Re: [Orgmode] C-c a t shows empty list

[Erik Iverson]

Микола Стрєбков wrote:

Hi

On 20 січ. 2011, at 23:43, Erik Iverson wrote:


Which version of Emacs / org-mode?


Hmm...
Emacs 23.2 OS X,
"M-x org-info" shows docs for 6.33 but I have installed version 7.4...


Does M-x org-version report the correct version?



The latest org-mode installed in:
(setq load-path (cons "~/.emacs.d/org" load-path))

Here is org part of my .emacs:

;;;
;;; Org mode
;;;
(require 'org-install)
(transient-mark-mode 1)
(setq org-log-done 'time)
(setq org-directory "~/Org")
(setq org-footnote-auto-adjust t)
(setq org-mobile-files (quote ("~/Org/main.org")))
(setq org-mobile-directory "~/Dropbox/MobileOrg")
(setq org-mobile-inbox-for-pull "~/Org/inbox.org")
(setq org-todo-keywords
  '(
(type "TODO" "|" "DONE")
(sequence "PROJ" "|" "FINISHED")
(sequence "PROG" "|" "CANCELLED" "DONE")
)
  )
(setq org-default-notes-file (concat org-directory "/notes.org"))
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))



Микола Стрєбков wrote:

Hi orgsters,
I started to use org-mode together with MobileOrg and everything was fine. But 
two days ago I realized that I'm unable to build neither agenda nor todo lists 
from my org files. Problem occurred on both Emacs and my iPhone even on the 
simplest files like:
* test
** TODO test2
** TODO test3
* test4
I found similar issue in google cache (osdir.com gives 403) but it was resolved 
by just Emacs restarting. I'm not so happy.
Please help.




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Re: [Orgmode] [OT] emacsclient -t (was Re: [OT] Have you also got hooked by Vim?)

[Erik Iverson]

Jeff Horn wrote:

On Thu, Jan 20, 2011 at 11:00 AM, Eric S Fraga  wrote:

Matt Lundin  writes:


Jeff Horn  writes:


On Wed, Jan 19, 2011 at 9:51 PM, Matt Lundin  wrote:

alias emacs="emacsclient -t -a /usr/bin/emacs"

Thanks for sharing this. My manual doesn't mention the -t flag. What
does it do? (I didn't know about -a, but it looks nifty)


Now that I consider this further (and read the emacs man page), I'm not
sure if the -t flag is correct here. (It may be new to emacs 24).

In any case, "-nw" is the tried and true flag for doing this.

IIRC, -t is the same as -nw and is present from emacs 23.1 (maybe
earlier) onwards.  Very useful when connecting from a non-graphical
terminal (e.g. a mobile phone) to an existing Emacs running on
X... something I do frequently via =screen= for emulating a persistent
connection.


So IIUC, I have a windowed Emacsen running on a box where I work. If I
run `emacsclient -t somefile.txt` from an SSH connection to that box,
it uses the server that was started by the windowed emacs, but instead
of opening the file in the windowed emacs, it re-routes it to my SSH
session?


Even possibly better, if you've got X-forwarding enabled on your
SSH connection, you can start a windowed emacs instance on your
local machine that exactly matches the one on the server, even
with all the same buffers open, processes running, etc.

I use this type of setup at home.  You need to start emacs in
'daemon' mode, see 
http://emacs-fu.blogspot.com/2009/02/emacs-daemon.html , for

example.  That site has examples of how to use it.

One caveat. I use Ubuntu, and I think I had to do something
special with my Xauth file for this to work, please follow
up if you run into trouble and use Ubuntu, and I'll be glad
to look into what I did.

--Erik


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[Orgmode] changing the time of one instance of a recurring appointment

[Erik Iverson]

Hello,

I did not see this addressed in the manual or FAQ.

Say I have a recurring appointment, every third Monday of the month, at 
11:30 AM, no problem:


** Monthly meeting with Boss <%%(diary-float t 1 3)>11:30

Now, my boss emails me and says, let's change next week's meeting to 
10:30.  How would you handle that?  Just simply change the 11:30 to 
10:30 and remember to change it back next week?  Add a new one-off 
appointment for 10:30 that day and ignore the 11:30 one on your agenda? 
 Or is there some way to do this built into org-mode already?


Thanks a lot!
Erik Iverson



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[Orgmode] org-babel with R, scrolling an inferior ESS process

[Erik Iverson]

Hello,

I have been a happy user of ESS with R for years.  Recently, I've begun 
to use org-mode for a lot of things, so of course I am interested in 
org-babel. I checked out a version of org-mode yesterday (2-15-2010) 
from git.


Using just ESS,  I would write a source file, test.R, and define a 
function in it, say


#identity function
test <- function(x) {
x
}
test(3)

I could then type C-c C-c (coincidentally, and happily, this is the ESS 
keybinding used to send a block of code to the inferior *R* process) to 
send the above lines to the running *R* process, and the output would 
show up in the *R* buffer, and scroll to the bottom of the *R* buffer 
since I have set


(setq comint-scroll-to-bottom-on-output t)

in my .emacs.

However, now I hope to write a file, test.org, and write something like:

* Identity function
#+begin_src R :session :results output silent
  test <- function(x) {
x
  }
  test(3)
#+end_src

If I use C-c ' to open an R code buffer and C-c C-c, I see the same 
behavior as in ESS. However, when I do C-c C-c on the code block *in the 
test.org buffer*, the code is sent to the *R* buffer, but it does not 
scroll.  In the *R* buffer, once I do scroll to the bottom, I see the 
following:


>
test <- function(x) {
  x
}
test(3)
'org_babel_R_eoe'

> test <- function(x) {
+   x
+ }
> test(3)
[1] 3
> 'org_babel_R_eoe'
[1] "org_babel_R_eoe"

Can anyone
1) replicate that you don't see the scrolling, even with the 
comint-scroll-to-bottom-on-output variable set to 't'?
2) suggest a way to get the *R* buffer to scroll to the bottom when I 
execute a source block from an org-mode file to a running *R* session?


I am surprised by this behavior since I just assumed comint-mode should 
do the right thing, so I'm not sure where the issue is! Even if this 
can't be changed, I think org-babel is going to be a great use to me, 
thank you!


Best Regards,
Erik Iverson


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Re: [Orgmode] org-babel with R, scrolling an inferior ESS process

[Erik Iverson]

Hello,




Can anyone
1) replicate that you don't see the scrolling, even with the
comint-scroll-to-bottom-on-output variable set to 't'?


Yes, this has been on my todo list for a while! Definitely time to fix it.


Great, I'd be happy to test out the code when it's ready!




2) suggest a way to get the *R* buffer to scroll to the bottom when I
execute a source block from an org-mode file to a running *R* session?


It seems to be fixable by changing a couple of save-window-excursions
into save-excursions (patch below). I haven't thought of anything that
this will break, but in any case I suspect that Eric S. will apply the
correct fix to the main git repo soon.

As for the 'org_babel_R_eoe' stuff, that is org-babel internals that
ideally would not be exposed to the user. I suspect that it is possible
to remove it from the comint buffer -- Eric S. is definitely best placed
to comment on the best way of doing that.



That would be great, too!



Please do let us know of any other improvements we can make to using
org-babel with ESS. Good integration with ESS has been one of our aims
from the beginning.


I will let you know as I continue using it.  The ultimate improvement 
IMO would be some sort of good multi-mode support, so that things 
between #+begin_src/#+end_src would be fontified according to their 
mode. And when I, for example, move into an R source section in my 
org-mode buffer, all ESS key bindings would work.


I have read a couple recent threads about getting functionality like 
this via two-mode-mode for instance, but they have some quirks that make 
it unusable for me.  Are you and Eric working on anything like this?  I 
have been investigating different options and will let you know if I 
find anything promising!


Thanks!
Erik


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Re: [Orgmode] [babel] multiple result outputs from function

[Erik Iverson]

Graham -

Graham Smith wrote:

Below is a function that I am trying to run in orgmode/babel.

It seems to run OK, but instead of printing out three values, its only
printing the final result.

Once again, i would appreciate some help with what I am missing.

Thanks,

Graham


#+srcname: CI_function
#+begin_src R :session daf
summary.ci<-function(x){
xbar<-mean(x)
sigma<-sd(x)
n<-length(x)
sem<-sigma/sqrt(n)
lower.ci<-xbar+sem*qnorm(0.025)
upper.ci<-xbar+sem*qnorm(0.975)
print (xbar)
print  (lower.ci)
print  (upper.ci)
}
#+end_src

#+srcname: SumFlowering2005
#+begin_src R :session daf
summary.ci(daf$Flower[daf$YEAR=="2005"])
#+end_src

#+results: SumFlowering2005
: 1.97860201016947



From org-babel docs...

The following options are mutually exclusive, and specify how the 
results should be collected from the source code block.


--
value
This is the default. The result is the value of the last statement 
in the source code block. This header argument places Org-babel in 
functional mode. Note that in some languages, e.g., python, use of this 
result type requires that a return statement be included in the body of 
the source code block. E.g., :results value.


output
The result is the collection of everything printed to stdout during 
the execution of the source code block. This header argument places 
Org-babel in scripting mode. E.g., :results output.

---

So, add ":results output" to your source header block.

Or, you might want to define your R function to return a list of the 
three components you're after for further processing, and then not have 
to include ":results output"


Instead of the 3 print statements, which don't create objects, you could 
substitute


list(xbar, lower.ci, upper.ci)

--Erik



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Re: [Orgmode] hyperlink to IMAP email

[Erik Iverson]

I presently use thunderbird as my email client and it doesn't support this, I've
looked at several other linux email clients and they do not support this either.

Does anyone know of an email client that can be invoked from the command line to
open up at a specific IMAP email?   How do the org-mode  users link to their
IMAP mail?


I haven't looked at this in a while, but years ago I wanted the exact 
same thing for Thunderbird, but could not find out how to do it.  I did 
put together something that did this very smoothly with Outlook, but 
that is not going to help you.


I will be watching this thread to see if anyone has any good idea.

Does any of this change with Thunderbird 3, I wonder?

--Erik


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Re: [Orgmode] Turn off "pushed to kill ring and clipboard" exporting HTML

[Erik Iverson]

Dan Davison wrote:

Xin Shi  writes:


Hello,

When exporting to HTML, the default behavior is to "pushed to kill ring and
clipboard". As shown in the message:

HTML export done, pushed to kill ring and clipboard

Are there any way to turn off this push?


(setq org-export-copy-to-kill-ring nil)

Or use customize to do the same.

I'd be interested to know how people make use of this feature (i.e. why
it is on by default.)



I use org-mode to write blog posts (including R code) and post the 
resulting HTML to Wordpress, so it works for me.


I run the org-file through a custom Sweave first to generate output, 
then export that.  I've been meaning to look at org-babel as a 
substitute to this in the future.




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Re: [Orgmode] [org-babel] suggestions for using tikz() graphic device with org-babel-R

[Erik Iverson]

But, back to your question.  What does the R block return?

- if it returns the path to a file, then you can use :results file to
  insert a link to that file in your org-mode buffer, or you can wrap
  the path to that file in an include with something like the following

  #+source: graph-generator
  #+begin_src R :results file
...
  #+end_src
  
  #+begin_src emacs-lisp :var path=graph-generator :results latex

(format "input{%s}" path)
  #+end_src

- if it returns raw LaTeX then you can use the :results latex header as
  used in the elisp block above


I just started looking at tikzDevice in R about two days ago.  It is 
indeed a graphical device, just like X11, pdf, or postscript, so it 
doesn't return anything.  It writes out a .tex file though, so you 
should be able to write a wrapper function that does return something 
useful for you.


--Erik




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Re: [Orgmode] Re: [Babel] Macro for begin_src?

[Erik Iverson]

http://doc.norang.ca/org-mode.html#Yasnippets

If anyone else has a different macro set up, I'm still interested in 
hearing your solutions.




Nope, yasnippet is the way to go I think!


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Re: [Orgmode] Re: [Babel] Macro for begin_src?

[Erik Iverson]

I'm guessing what you really want there is

(set (make-local-variable 'yas/trigger-key) [tab])

instead of

 >   (make-variable-buffer-local 'yas/trigger-key)
 >   (setq yas/trigger-key [tab])


Hmmm.

Do you guys un-map your TAB key so that it doesn't run org-cycle?
My TAB key will correctly trigger yas/insert-snippet in emacs-lisp mode.
However, in org-mode my TAB key is still mapped to org-cycle, even if I 
add the org-mode hook using the code above.


Thanks,
--Nate



The order you do it might matter?


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Re: [Orgmode] A shorter manual

[Erik Iverson]

Carsten Dominik wrote:

Dear all,

with the Org-mode manual moving toward 200 pages,  I am
starting to worry that people with stop in their tracks
when considering Org-mode, just because of the sheer size
of the manual.

So I did a little experiment.  I took the manual and stripped
everything which could be considered advanced material, but
keeping all features and all basic commands and customizations.

What remains are about 50 pages.  A document with the same
structure (even the same chapter numbers) as the manual.
I am wondering if it would be useful to have this as a beginners
document - or if the existence of this document would lead
to more confusion than relief.

http://orgmode.org/orgguide.pdf

I don't see this a an alternative for the manual - just
as an additional, rather static document, with little need for
updates.  The manual would continue to be the comprehensive
and constantly updated document.

Comments are welcome.


I think it's a great idea.  The R project has something called "An 
Introduction to R" for beginners, separate from the complete manual.  I 
think that as a beginner, and wondering how to break into learning a new 
package, that "reading the manual" has certain negative psychological 
connotations that "reading the intro document" does not, not the least 
of which is the length of full manual.


And since knowing just the basics of org can be immensely beneficial, I 
think it's even more reason to have a basic intro document.


--Erik


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Re: [Orgmode] [babel] Future of Org-babel?

[Erik Iverson]

My pie-in-the-sky extension of this dream would be to have Org-babel
firmly ground in some virtual machine (maybe Guile's if Emacs is ported
to Guile), in such a way that the byte-code of the VM becomes the lowest
common denominator of all Org-babel languages.  This would allow for
seamless integration of languages which compile to run on the VM, and
for all other languages this would provide a great speed/efficiency
boost over Emacs Lisp.  I should disclaim that without having given this
much serious though I could be missing some critical road blocks.


Regardless, the technology will have to be called ".ORG". :)


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[Orgmode] [babel] showing image of latex code results produced from an R code block

[Erik Iverson]

Hello, consider the following org-mode file:

=

* R returning LaTeX for display

I have an R function that generates LaTeX code.  I would like the 
resulting LaTeX to be displayed in an inline image in the org-buffer



#+begin_src R
lf <- function() {
"\\LaTeX"
  }

lf()
#+end_src

#+results:
: \LaTeX

I want the above results to actually be just like below, i.e., process 
the results as LaTeX and include an image of the results.  I think 
org-babel can do this sort of thing, it's just escaping me how!


* If I just specify LaTeX as the input language, all works as I hope

#+begin_src latex :file latex-logo.png
  \LaTeX
#+end_src[$]

The LaTeX logo is displayed properly below on my screen with the latest 
inline image functions.


#+results:
[[file:latex-logo.png]]

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Re: [Orgmode] [babel] showing image of latex code results produced from an R code block

[Erik Iverson]

Solution below!

Erik Iverson wrote:

Hello, consider the following org-mode file:

=

* R returning LaTeX for display

I have an R function that generates LaTeX code.  I would like the 
resulting LaTeX to be displayed in an inline image in the org-buffer



#+begin_src R
lf <- function() {
"\\LaTeX"
  }

lf()
#+end_src

#+results:
: \LaTeX

I want the above results to actually be just like below, i.e., process 
the results as LaTeX and include an image of the results.  I think 
org-babel can do this sort of thing, it's just escaping me how!


* If I just specify LaTeX as the input language, all works as I hope

#+begin_src latex :file latex-logo.png
  \LaTeX
#+end_src[$]

The LaTeX logo is displayed properly below on my screen with the latest 
inline image functions.


#+results:
[[file:latex-logo.png]]



The solution is simply to give the R src block a name, then create a new 
src block of LaTeX code which calls the R src block using the noweb 
syntax.  Note that in my actual application the LaTeX returned is *not* 
an R object like in my example, it is actually just text written to 
stdout, so in my R source block I use :results output.


#+srcname: R-latex
#+begin_src R
lf <- function() {
"\\LaTeX"
  }

lf()
#+end_src

#+begin_src latex :noweb yes :file latex-logo.png
<>
#+end_src

Now I can preview tables produced by Hmisc's latex function in my 
org-mode buffer, very nice!



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Re: [Orgmode] Latex export bug? Odd behavior with figures...

[Erik Iverson]

### latex order ##

I've inspected the generated .tex file and this shows up where expected 
in both picture instances:


\begin{figure}[htb]
\centering
\includegraphics[width=12cm]{/home/jwhendy/Desktop/file[1/2].pdf}
\caption{text here}
\end{figure}

I have generated a pdf from the .tex file and the same happens -- I 
can't figure out why it's sticking them in places where they are not 
called for.


Not at all an expert on this, but what if you substitute [!htb] instead of [htb] 
in the LaTeX and generate a PDF?  Obviously, not an org-mode solution, but does 
that do what you want?


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[Orgmode] [babel] possible bug in org-babel-execute-buffer?

[Erik Iverson]

Hello,

I am using Emacs 23.1, orgmode pulled from git just an hour ago, but I noticed 
the following issue on a version pulled about a week ago, too.  I don't know if 
it ever worked as I expect.  These development versions have C-c C-v as the 
babel prefix keys, so if you are using a stable version, the following may be 
different.  Also, all my examples use R.


I'm trying to use C-c C-v C-b to call org-babel-execute-buffer, which is 
documented as:


Call `org-babel-execute-src-block' on every source block in
the current buffer.

However, what happens when this is called seems to depend on which trees are 
visible in the buffer when it's called!


Paste the following orgmode file into an org buffer, and make sure all trees are 
fully collapsed, i.e., you just see the headlines "Big Block 1" and "Big Block 
2", and try C-c C-v C-b.


After it's done executing, notice that only the *last* source blocks of each 
tree were run.  Now collapse everything again, and call org-babel-execute-buffer 
again.  The same thing happens, except now there are *two* results present for 
those last code blocks.


Now start all over again with the below code, so no results are present.  Expand 
all subtrees so everything is visible.  Do C-c C-v C-b, and all results are 
inserted as expected.  Run the blocks a second time with everything open, and 
every block still only has 1 results section, as expected.  This is how I would 
expect/hope the function to work regardless of the hide/show states of the trees.


So I think there are two possibly related problems when trees aren't fully 
expanded:


1) Only the last source code block per hidden tree is getting run
2) That last block will insert results multiple times if 
org-babel-execute-buffer is called multiple times


Thanks!
Erik

=== orgmode code follows below ==


* Big Block 1
** my first bit of code!
#+begin_src R
 "from the first nested code block in Big Block 1"
#+end_src
** and some more code!
#+begin_src R
  "from the middle nested code block in Big Block 1"
#+end_src
** and final code!
#+begin_src R
  "from the final nested code block in Big Block 1"
#+end_src
* Big Block 2
#+begin_src R
  "from the only code block in Big Block 2"
#+end_src



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Re: [Orgmode] [babel] possible bug in org-babel-execute-buffer?

[Erik Iverson]

Eric Schulte wrote:

Hi Erik,

Thanks for the report, this should now be fixed in the latest git HEAD,
please let me know if the problem persists.

Best -- Eric


Looks good on the test file I had included in my initial report, thank you very 
much.  When I get back to work tomorrow, I will try it on the actual file that 
was giving me trouble.  Thank you, Eric.



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[Orgmode] [babel] buffer-wide settings for R graphical header arguments

[Erik Iverson]

Hello,

You can specify graphical header args in source blocks for R blocks that 
produce graphical output, e.g.:


#+BEGIN_SRC R  :file output.png :width 720

You can also set buffer-wide options with the following syntax, for 
example, with the tangle header argument.


#+PROPERTY: tangle yes

However, this doesn't appear to be working for me if I use, say `width`, 
in the following fashion.


#+PROPERTY: width 720

Are R graphical header arguments supposed to be able to be set buffer-wide?

Thanks!
Erik

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Re: [Orgmode] [babel] `org-babel-tangle-w-comments' controls comment insertion in tangled code

[Erik Iverson]

Eric Schulte wrote:

Hi,

The insertion of automatically generated comments in tangled source code
is now controlled by the new `org-babel-tangle-w-comments' variable.
Setting this variable to non-nil will allow org-babel to insert comments
for those languages with comment support.


Can you briefly elaborate on what this means?  I'm used to seeing, when 
I tangle an R file, something like:


## 
[[file:~/private/R-org-babel/test.org::*cube%20lets%20go%20to%20the][block-2]]


cube <- function(x) {
  # a test comment
  x * x * x * x
}
## block-2 ends here

So, you mean that all three of the comments would no longer appear by 
default?  Or you mean that only my inline function comment would not 
appear?


One more idea I had was that it might be interesting to be able to 
maintain properties for headlines that indicate the headline/body should 
be included as a comment in a specific source file.  The reason I say 
this is that even if I write my code in org-mode, and in effect comment 
the code using org-mode constructs like headlines and free text, someone 
who just wants the tangled file might want to see comments, for example, 
function headers or something like that.


Any thoughts on that?

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Re: [Orgmode] [babel] `org-babel-tangle-w-comments' controls comment insertion in tangled code

[Erik Iverson]

## 
[[file:~/private/R-org-babel/test.org::*cube%20lets%20go%20to%20the][block-2]] 



cube <- function(x) {
  # a test comment
  x * x * x * x
}
## block-2 ends here

So, you mean that all three of the comments would no longer appear by 
default?  Or you mean that only my inline function comment would not 
appear?


Re-reading your post, I think maybe perhaps only my inline comment would 
*appear*.  If this is true, I like the idea.


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Re: [Orgmode] [babel] `org-babel-tangle-w-comments' controls comment insertion in tangled code

[Erik Iverson]

One more idea I had was that it might be interesting to be able to
maintain properties for headlines that indicate the headline/body
should be included as a comment in a specific source file.  The reason
I say this is that even if I write my code in org-mode, and in effect
comment the code using org-mode constructs like headlines and free
text, someone who just wants the tangled file might want to see
comments, for example, function headers or something like that.




Maybe we should allow either exporting just the headlines of the
org-mode file or exporting the entire org-mode file -- possibly after an
ASCII export -- this would have the effect of prefixing every line in
the org-mode file behind a comment *except* for the tangled source-code
blocks.

Implementation wise I'm not sure how easy/difficult this would be, but I
definitely think it's worth looking into.

Have I understood your suggestion?


Yes, your idea about prefixing every line in the org file behind a 
comment except for the tangled code was the initial idea in my head.  I 
then thought that there may be several different languages of code in an 
org-mode file, and even if there is only one language, the tangling of 
that file could be generating multiple source files, for example, one 
per function.  In addition, some of the org-mode material I have in my 
file might not relate to a commented source file, per se.  For example, 
the org-mode file where I maintain my source for a function might have 
links to emails discussing the implementation, or internal dialogs 
relating to alternative approaches that were abandoned.


So, I thought it might be neat to have some way of specifying which 
subtrees would be a part of the comments for a source file, and for 
which tangled file.  My guess as the easiest way to do that would be 
through properties.  That is, you'd set a property for (sub)tree like, 
for example:


:PROPERTIES:
:SrcComment: Yes
:SrcCommentTangleFile: cube.R
:SrcCommentCharacter: ##
:END:

These (sub)trees would then appear as comments in their respective 
tangled source files in whatever order they appear in the org-mode file.


Why am I suggesting this?

People obviously like commented code.  Writing a function in org-babel, 
I am in effect using org-mode as the commenting system.  Giving someone 
who does not use Emacs an org-mode file to see how something was 
implemented is not going to fly, to say the least :).  Giving them the 
tangled version of the code along with, say, an HTML export of the 
org-mode buffer is a good start.  But if they're used to reviewing code 
in the typical, "just send me the source file" manner, they would 
appreciate comments in the code. This is one way they could be 
automatically generated from org-mode/org-babel, which is, in my mind, 
the ideal.


As I'm sure you have plenty to do, I would be happy to take a look at 
this.  I'll give the requisite "I'm just getting started with elisp ..." 
warning though. :)


Thanks!
Erik


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Re: [Orgmode] [babel] `org-babel-tangle-w-comments' controls comment insertion in tangled code

[Erik Iverson]

Thomas S. Dye wrote:

Hi Erik,

If the proposed functionality places comments in the source code in 
whatever order they appear in the org-mode file, then the result will 
likely frustrate literate programming efforts that rearrange code blocks 
on tangling.


Yes, thank you for pointing that out.



Another way to get pieces of the org-mode file into the source file as 
comments might be with a little helper function, 
org-babel-copy-subtree-to-commented-code.  The source blocks could be 
named so the literate programming facilities of org-babel could work 
with them.


I'm not following this; could you provide a minimal pseudo-example of 
how you see this working in practice?


Thanks!
Erik

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[Orgmode] [babel] writing my .Rprofile in orgmode, issue with emacsclient

[Erik Iverson]

Hello,

In the spirit of the examples of writing your .emacs file in orgmode, I wrote my 
.Rprofile (R's startup file) in orgmode.  I do have one issue where I have no 
idea what is going wrong, and would appreciate any information!


Basic setup, GNU Emacs 23.1, latest git org-mode, running on Linux.  I start 
emacs with emacs --daemon on startup, and always just use emacsclient to do 
everything.  So for my org-mode .Rprofile,


1) I create a ~/.Rprofile.org file that uses org-mode syntax and includes all R 
code in R source blocks that will be tangled into a .Rprofile.R file.


2) In my actual .Rprofile, I have the following, which actually works.  The 
basic idea was taken from 
http://orgmode.org/worg/org-contrib/babel/reference.php#sec-6 .  I simply want 
to tangle the .Rprofile.org file from (1) above into .Rprofile.R and source it. 
I know the lisp isn't as simple as it could be, since I adapted it from the more 
complex setup referenced, but this actually works for me.


#BEGIN .Rprofile
invisible(system("emacsclient -t --eval \"(progn
(add-to-list 'load-path (expand-file-name \\\"~/lisp/org-mode/lisp/\\\"))
(add-to-list 'load-path (expand-file-name 
\\\"~/lisp/org-mode/contrib/lisp/\\\"))
(require 'org)(require 'org-exp)(require 'org-babel)
(mapc (lambda (file)
   (find-file (expand-file-name file \\\"/home/erik\\\"))
   (org-babel-tangle)) '(\\\".Rprofile.org\\\")))\"", intern = TRUE, 
ignore.stderr = TRUE))


source("~/.Rprofile.R")
#END .Rprofile

Then I do 'M-x R' in emacs, and R tangles the org-mode file, sources the result, 
and everything works.  This even works without the '-t' option given above to 
emacsclient.


The problem is when I try to C-c C-c on an R source block in an org-mode file. 
My issue is, that *without* the '-t' option to emacsclient, (-t says it "opens a 
new emacs frame on the current terminal"), org-babel-execute-src-block hangs 
when I press C-c C-c in an R code block using the above setup.  It definitely 
relates to the emacsclient call in my .Rprofile,  because I can simply comment 
that system call out of my .Rprofile and all is well.  If I use :session, 
everything is fine.


The best lead I have is that if I change org-babel-R-evaluate in the following 
way, my setup also works without the -t option:


Give the R call in the following line

(point-min) (point-max) "R --no-save" nil 'replace (current-buffer)))

the --vanilla option.  Obviously this just doesn't run my problematic .Rprofile, 
but the point is that this is the exact location in the chain of calls where 
it's getting 'stuck'.  Emacs just hangs with the 'busy' mouse cursor until I C-g.


If I watch the system process list, the R process does get started, and a new 
(2nd) instance of emacsclient is also started, but it doesn't return.


Like I said, I have 'fixed' this with -t, but I really want to know why it 
wasn't working in the first place, and if this is really a fix.  Notice how I 
have to also ignore.stderr = TRUE in my 'system' R call, because if I don't, all 
my org-babel output contains


#+results:
: emacsclient: could not get terminal name
...further output...

if my source block has :results output as opposed to :results value.

I just don't get why my setup works with M-x R but not with 
org-babel-execute-src-block, there is some interaction between those two and I 
can't see what it is.


Sorry for the long post, I hope my question makes sense!

Best Regards,
Erik Iverson

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Re: [Orgmode] Re: org-babel-R export parameters

[Erik Iverson]

The idea is I want to be able to see the inline PNG image of my graph
while writing, and when I export I'll point the latex exporter to the
PDF. This provides a vector format for Latex, instead of a low
resolution bitmap. Yes you can use PDF's as includes, and they look
great because they are a vector format.


I have this exact same issue.  One idea I haven't explored, but that might be 
possible, is to generate PDFs in org-babel, and then display the pdf using emacs 
doc-view, which converts to png for display in an emacs buffer, if I understand 
correctly.


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Re: [Orgmode] Re: org-babel-R export parameters

[Erik Iverson]

#+begin_src R :results file :var basename="myplot"
  a <- 1:4
  pngfile <- sprintf("%s.png", basename)
  pdffile <- sprintf("%s.pdf", basename)
  
  png(pngfile)

  plot(a)
  dev.off()
  
  pdf(pdffile)

  plot(a)
  dev.off()
  
  pngfile

#+end_src


I like this better, and I can use dev.copy here too. The issue is a
plot is rarely one line. Most of my plots are a half page of code
between the data set, legend, etc.



You could just make your complex plots functions, and then call your 
function in in one line. Or if you're using lattice or ggplot2, create 
objects representing the plot, and then plot them in one line.





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Re: [Orgmode] Re: org-babel-R export parameters

[Erik Iverson]

I personally find this useful because it allows me to use code blocks to
generate results, and then when I'm content with the file I can set
":exports none" to avoid re-generating the file on every export -- while
retaining the existing link keeps the file included in my export.

I do see how this could be confusing, and maybe it would be appropriate
to begin stripping out the results of code blocks on export.


1 vote for that from me, for the exact same situation as this thread 
describes, i.e., I want to preview graphics in emacs, but have PDFs 
included in LaTeX upon export.


I have cobbled together something this afternoon that uses doc-view to 
overlay a png over a PDF results file.  There are a couple things to 
sort out, but I'll post that when I get home, it could possibly help 
here, at least with not having to generate both types of files from 
R/org-mode.



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[Orgmode] [babel] grid-based R graphical output with :results value

[Erik Iverson]

Hello,

This is an FYI for those using org-babel-R with grid-based graphical 
systems.


The documentation for org-babel-R says, "If a :file filename.ext header 
arg is provided to an R block, then graphical output from the source 
block is captured on disk, and the output of the source block is a link 
to the resulting file".


This is true for traditional R graphics, but needs a modifier for 
grid-based R graphics, e.g., the lattice and ggplot2 packages.


The graphics functions from lattice and ggplot2 return objects that must 
be explicitly printed to see them, using the print function.  This 
happens automatically when run interactively, e.g. :session, but when 
called inside another function, it does not.  The way :results value is 
defined to operate, my device and ggplot2 function calls are wrapped in 
a 'main' function, and unless I specifically print the object, no output 
is produced.


Another solution is to use :results output in those source headers that 
produce graphical output from these packages.


I believe the following org-mode file summarizes the different ways of 
getting this working.



= org-mode code begins ==

* Note that my .Rprofile loads the lattice package, i.e., library(lattice)

* does /not/ produce a file
#+begin_src R :file 1.png :results value
  xyplot(1:10 ~ 1:10)
#+end_src

* does produce a file, by printing object
#+begin_src R :file 2.png :results value
  print(xyplot(1:10 ~ 1:10))
#+end_src

* does produce a file, by using :results output
#+begin_src R :file 3.png :results output
  xyplot(1:10 ~ 1:10)
#+end_src

* does produce a file, by evaluating in :session
#+begin_src R :file 4.png :session
  xyplot(1:10 ~ 1:10)
#+end_src




= end org-mode code 

The following R code shows something potentially interesting


=== begin R code ==

## this produces a graphic when run with R CMD BATCH
myfun <- function() {
  xyplot(1:10 ~ 1:10)
}
png("with-function-wrapper-outside.png")
myfun()
dev.off()

## this does not produce a graphic with R CMD BATCH
myfun <- function() {
  png("with-function-wrapper-inside.png")
  xyplot(1:10 ~ 1:10)
  dev.off()
}
myfun()
== End R code =

In effect, :results value is doing the latter of the two things in the R 
code above.  If the process were reversed, i.e., the 'main' function 
call was wrapped in the graphics function, as in example 1 above, I 
believe it would work.  Of course, this isn't how it is currently 
implemented, and may introduce other complexities.  There are also 
solutions as I've posted above.


--Erik



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[Orgmode] simultaneous clocks?

[Erik Iverson]

Hello,

Is there any concept of being able to run multiple, simultaneous clocks 
in org-mode.  For example, I want one clock to track my total hours 
during the week at work, i.e., punch in and punch out.


Then, while that clock is running, I would use the normal clocking 
functionality to keep track of time on specific projects.


As it is, clocking into a new task clocks out of the current task.

There may not be a way, but thought I'd ask!

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[Orgmode] Re: simultaneous clocks?

[Erik Iverson]

Bernt Hansen wrote:

Erik Iverson  writes:


Hello,

Is there any concept of being able to run multiple, simultaneous
clocks in org-mode.  For example, I want one clock to track my total
hours during the week at work, i.e., punch in and punch out.


No.  Org-mode clocking clocks a single task at a time.  You can't do two
things at once :)


Then, while that clock is running, I would use the normal clocking
functionality to keep track of time on specific projects.


I punch in to a default task which starts my clocking day.  Everytime I
clock out the default task is clocked in to keep every minute clocked
from the moment I punch in until I punch out.


That will do!  That's all I really wanted, just wasn't aware of all the 
functionality.  Thanks, I've found your org-mode.html descriptions very helpful.




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Re: [Orgmode] a better way with babel

[Erik Iverson]

This does produce the figure and long/short contents BUT ALSO produces this:

#+results: r-nicedata
[[file:ndata.pdf]]

which upon export results in a link and consequently the plot appearing both 
in the figure and elsewhere. This second plot is unwelcome.




I believe in the latest git version, that #+results are no longer exported just 
because they appear in the buffer.


See:

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg25917.html

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Re: [Orgmode] Lifehacker votes on TODO list managers

[Erik Iverson]

Carsten Dominik wrote:

Hi everyone,

Put a comment on Lifehacker

http://lifehacker.com/5572129/best-to+do-list-manager

with the content

VOTE: Emacs Org-mode

if you want to see Org-mode in the top 5 competition about TODO managers


How can this even be called a 'competition' if org-mode is allowed?  :)

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Re: [Orgmode] [org-babel] Does org-babel needs some simplification?

[Erik Iverson]

Hello!




Whenever I come back to org-babel, it takes me a huge amount of time to
find myself back again in the syntax. Often I spend a day or two heavily
reading the website and manual again to figure out how to make it working.

There are so many options. tangle files, results, scripting mode,
sessions, noweb, lot, etc.

Just yesterday, I fighted again to make a simple python script running
as desired to generate an automatic report. I did this dozen of times
and even by using some old report as template I still struggle with it.
Comparing old reports I noticed that I did it in many different ways.
Tangeling all snipplets, using noweb syntax, with and without session
support, etc.




I have not used it for Python, but for R coding I've found it incredibly 
intuitive.  However, that might be because R has long supported literate 
programming through Sweave, complete with noweb syntax and code tangling.


I personally don't think it's too complex.  One thing that could help is a 
gentle introduction written by users of each language that babel supports.  I 
have started something like that with R already on my blog, see 
http://blogisticreflections.wordpress.com/2010/05/23/introduction-to-using-r-with-org-babel-part-1/ 



I think the best thing to do is to figure out a system that works for you, and 
document it (in org-mode of course!) so that there are notes the next time you 
come back to the file, or need to produce a new file.


Of course, the authors of babel might have plans to somehow simplify syntax, but 
I just wanted to point out that, like anything, with some repetition, you can 
commit the main ideas to memory and then consult the manual when needed.  I 
found that spending a couple hours running all the possible options in the 
manual with R while taking notes went a long way in helping me understand how it 
it all works.


Best Regards,
Erik

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Re: [Orgmode] [babel] Evaluating all source blocks in a document?

[Erik Iverson]

Hello,


On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
 > Hi
 >
 > I use Org-babel for literate programming in R, but the tangling
takes quite
 > long. Therefore my question: as it is possible to evaluate a
single code
 > block, is it possible to evaluate ALL code blocks i a document?
that would
 > make debugging much easier.

M-x org-babel-execute-buffer



C-c C-v C-b should be a shortcut for that in org-mode now, according to 
my reference card.


 
Thanks - that  seems to be what I am looking for, but after trying it 
out, I realized the following: for each block, e new R session is 
opened. This does not work for literate programming, as different blocks 
belong to each other, i.e. one block opens a function, the next one 
closes it. In addition, I want to evaluate the results, i.e. created 
objects, in R - therefore the session should stay open. So my guess: 
tangle and debug.


OTOH this may not make it easier to debug, the babel error window
doesn't list line numbers or blocks where the error occurred. 



Have you tried the :session argument?  It submits the code block to a 
running R session.  I use it for what you're doing with success.  You 
can set it per code block, or buffer-wide, try for example:


#+PROPERTY: session *R*



Perhaps that should be a feature request to log what src block or
org file
line number the errors occurred in.


That would be nice.


 > Also: is it possible, to get some kind of automatic headings for
the tangled
 > code blocks? That would make it easier to identify in which code
block the
 > source code in the tangled file comes from.


Try

(setq org-babel-tangle-w-comments t)

and see if that does what you're thinking.  It will give headings for 
the source block, but I don't recall  what information they contain.


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Re: [Orgmode] Good way to try new org-mode code?

[Erik Iverson]

Is there a way to have emacs read the org-mode source code "on the
fly" without having to run make, make install, etc?

Is there a way to run new code without restarting Emacs?


I think

M-x org-reload

is what you're after.

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Re: [Orgmode] hypermedia programming with babel

[Erik Iverson]

How can I help next?


Babel in general is in need of some language-specific introductory
tutorials, with the goal of laying out the basic usage plenty of
examples covering simple use case e.g.
- author a shell script which can be tangled out to an executable
- simple processing of data in tables, or execution of code blocks with
  the output captured in the buffer


What format do you have in mind for these? I'd be glad to work on R examples.

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Re: [Orgmode] Org-babel init

[Erik Iverson]

You need to see:

http://eschulte.github.com/babel-dev/DONE-document-configuration-changes-for-Babel-integration.html


Jordi Inglada wrote:

Hi all,

I am having the same problem as this user here:

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg17498.html

and the contrib/lisp directory is indeed in my load path.

I am using a git changeset cloned today (Org-mode version 6.34trans
(release_6.36.608.gc1ef)).

I have tried using "emacs -q" and then loading an .el file containing
only the following lines:

(setq load-path (cons "/home/inglada/local/src/org-mode/lisp" load-path))
(setq load-path (cons "/home/inglada/local/src/org-mode/contrib/lisp" 
load-path))

(require 'org-install)
(require 'org-babel-init)
(require 'org-babel-python)

and I get the same result.

Thank you very much for your help.

Jordi

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Re: [Orgmode] Help: Agenda not working anymore

[Erik Iverson]

Could be related:

I just pulled latest from git this morning:  my agenda seems to compile, 
but I get in the *Messages* buffer:


concat: Wrong type argument: listp, "* Letters"

Backtrace follows:

Debugger entered--Lisp error: (wrong-type-argument listp "* Letters")
  nth(0 "* Letters")
  (concat "(?\\(" (regexp-quote "\\") (nth 0 el) "[^[:alnum:]]" "\\)")
  (list (concat "(?\\(" (regexp-quote "\\") (nth 0 el) "[^[:alnum:]]" 
"\\)") (\` (0 ...)))
  (lambda (el) (list (concat "(?\\(" ... ... "[^[:alnum:]]" "\\)") (\` 
...)))("* Letters")
  mapcar((lambda (el) (list (concat "(?\\(" ... ... "[^[:alnum:]]" 
"\\)") (\` ...))) ("* Letters" "** Latin" ("Agrave" "\\`{A}" nil 
"À" "A" "À" "À") ("agrave" "\\`{a}" nil "à" "a" "à" "à") 
("Aacute" "\\'{A}" nil "Á" "A" "Á" "Á") ("aacute" "\\'{a}" nil 
"á" "a" "á" "á") ("Acirc" "\\^{A}" nil "Â" "A" "Â" "Â") 
("acirc" "\\^{a}" nil "â" "a" "â" "â") ("Atilde" "\\~{A}" nil 
"Ã" "A" "Ã" "Ã") ("atilde" "\\~{a}" nil "ã" "a" "ã" "ã") 
("Auml" "\\\"{A}" nil "Ä" "Ae" "Ä" "Ä") ("auml" "\\\"{a}" nil 
"ä" "ae" "ä" "ä") ("Aring" "\\AA{}" nil "Å" "A" "Å" "Å") 
("AA" "\\AA{}" nil "Å" "A" "Å" "Å") ("aring" "\\aa{}" nil 
"å" "a" "å" "å") ("AElig" "\\AE{}" nil "Æ" "AE" "Æ" "Æ") 
("aelig" "\\ae{}" nil "æ" "ae" "æ" "æ") ("Ccedil" "\\c{C}" nil 
"Ç" "C" "Ç" "Ç") ("ccedil" "\\c{c}" nil "ç" "c" "ç" "ç") 
("Egrave" "\\`{E}" nil "È" "E" "È" "È") ("egrave" "\\`{e}" nil 
"è" "e" "è" "è") ("Eacute" "\\'{E}" nil "É" "E" "É" "É") 
("eacute" "\\'{e}" nil "é" "e" "é" "é") ("Ecirc" "\\^{E}" nil 
"Ê" "E" "Ê" "Ê") ("ecirc" "\\^{e}" nil "ê" "e" "ê" "ê") 
("Euml" "\\\"{E}" nil "Ë" "E" "Ë" "Ë") ("euml" "\\\"{e}" nil 
"ë" "e" "ë" "ë") ("Igrave" "\\`{I}" nil "Ì" "I" "Ì" "Ì") 
("igrave" "\\`{i}" nil "ì" "i" "ì" "ì") ("Iacute" "\\'{I}" nil 
"Í" "I" "Í" "Í") ("iacute" "\\'{i}" nil "í" "i" "í" "í") 
("Icirc" "\\^{I}" nil "Î" "I" "Î" "Î") ("icirc" "\\^{i}" nil 
"î" "i" "î" "î") ("Iuml" "\\\"{I}" nil "Ï" "I" "Ï" "Ï") 
("iuml" "\\\"{i}" nil "ï" "i" "ï" "ï") ("Ntilde" "\\~{N}" nil 
"Ñ" "N" "Ñ" "Ñ") ("ntilde" "\\~{n}" nil "ñ" "n" "ñ" "ñ") 
("Ograve" "\\`{O}" nil "Ò" "O" "Ò" "Ò") ("ograve" "\\`{o}" nil 
"ò" "o" "ò" "ò") ("Oacute" "\\'{O}" nil "Ó" "O" "Ó" "Ó") 
("oacute" "\\'{o}" nil "ó" "o" "ó" "ó") ("Ocirc" "\\^{O}" nil 
"Ô" "O" "Ô" "Ô") ("ocirc" "\\^{o}" nil "ô" "o" "ô" "ô") 
("Otilde" "\\~{O}" nil "Õ" "O" "Õ" "Õ") ("otilde" "\\~{o}" nil 
"õ" "o" "õ" "õ") ("Ouml" "\\\"{O}" nil "Ö" "Oe" "Ö" "Ö") 
("ouml" "\\\"{o}" nil "ö" "oe" "ö" "ö") ("Oslash" "\\O" nil 
"Ø" "O" "Ø" "Ø") ("oslash" "\\o{}" nil "ø" "o" "ø" "ø") 
("OElig" "\\OE{}" nil "Œ" "OE" "OE" "Œ") ...))

  (font-lock-add-keywords nil (mapcar (lambda ... ...) org-entities))
  org-pretty-entities()
  run-hooks(text-mode-hook outline-mode-hook org-mode-hook)
  apply(run-hooks (text-mode-hook outline-mode-hook org-mode-hook))
  run-mode-hooks(org-mode-hook)
  org-mode()
  (progn (org-mode) (org-create-dblock props) (org-update-dblock) 
(font-lock-fontify-buffer) (forward-line 2) (buffer-substring (point) 
(progn ... ...)))
  (unwind-protect (progn (org-mode) (org-create-dblock props) 
(org-update-dblock) (font-lock-fontify-buffer) (forward-line 2) 
(buffer-substring ... ...)) (and (buffer-name temp-buffer) (kill-buffer 
temp-buffer)))
  (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn 
... ... ... ... ... ...) (and ... ...)))
  (with-current-buffer temp-buffer (unwind-protect (progn ... ... ... 
... ... ...) (and ... ...)))
  (let ((temp-buffer ...)) (with-current-buffer temp-buffer 
(unwind-protect ... ...)))
  (with-temp-buffer (org-mode) (org-create-dblock props) 
(org-update-dblock) (font-lock-fontify-buffer) (forward-line 2) 
(buffer-substring (point) (progn ... ...)))
  org-get-clocktable(:link t :maxlevel 2 :tstart 733965 :tend 733972 
:scope agenda)
  apply(org-get-clocktable (:link t :maxlevel 2 :tstart 733965 :tend 
733972 :scope agenda))

  (setq tbl (apply (quote org-get-clocktable) p))
  (let ((org-agenda-files ...) (p 
org-agenda-clockreport-parameter-plist) tbl) (setq p (org-plist-delete p 
:block)) (setq p (plist-put p :tstart clocktable-start)) (setq p 
(plist-put p :tend clocktable-end)) (setq p (plist-put p :scope ...)) 
(setq tbl (apply ... p)) (insert tbl))
  (progn (let (... ... tbl) (setq p ...) (setq p ...) (setq p ...) 
(setq p ...) (setq tbl ...) (insert tbl)))
  (if (and org-agenda-clockreport-mode clocktable-start) (progn (let 
... ... ... ... ... ... ...)))
  (when (and org-agenda-clockreport-mode clocktable-start) (let (... 
... tbl) (setq p ...) (setq p ...) (setq p ...) (setq p ...) (setq tbl 
...) (insert tbl)))
  (let* ((org-agenda-start-on-weekday ...) (thefiles ...) (files 
thefiles) (today ...) (sd ...) (start ...) (day-numbers ...) (day-cnt 0) 
(inhibit-redisplay ...) s e rtn rtnall file date d start-pos end-pos 
todayp nd wd clocktable-start clocktable-end) (setq 
org-agenda-redo-command (list ... ... start-day ndays)) (setq ndays (or 
ndays org-agenda-ndays) nd ndays) (while (> ndays 1) (push ... 
day-numbe

Re: [Orgmode] Wiki-like creating links on the fly for org

[Erik Iverson]

Perhaps I am confused, but have you tried radio targets?

http://orgmode.org/org.html#Radio-targets


Marcelo de Moraes Serpa wrote:

Hey all!

I used to be an avid user of WikiDPad, and I loved the way it
automatically (or manually, using [ ]) created links and files to
these links (CamelCase) for me. The way it provided a visual tree of
the wiki was also pretty cool.

This was awesome for reference kind of data, to build your own
knowledge base. I've been trying to test different approaches with
org, but none of them work as smoothly as it worked for me when using
wikidpad.

I divide reference data in two main categories: Dynamic and Static.
Static are the notes and stuff that youl want to keep somewhere and
that you'll eventually refer to later. Dynamic are the kind of that
you'll be editing often, but does not fit in any other category
GTD-wise. It is reference, you want to keep it somewhere, not take
action on it per se (other than editing it), but you want to expand
and modify it often.

How difficult would it be to implement a small system that would index
the files of directory, get the names (camel-case) and automatically
link to these names if written on an org buffer? My elisp skills are
very weak as of now.

I know some of you might list a number of points against implementing
this, but I really loved the way Wikdpad created links on the fly.

Thanks,

Marcelo

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[Orgmode] word wrap preferences in org-mode buffers

[Erik Iverson]

Hello,

As I use org-mode more and more for actually writing things, I'm 
wondering what your favorite Emacs word/line-wrapping mode is.


Basically, I see two main ways of doing this, auto-fill-mode and 
visual-line-mode.  Any others that you all use?  If you use 
auto-fill-mode or visual-line-mode, are there any obvious drawbacks, 
particularly regarding org-tables and source code blocks.


I'm sure I'll run into the main issues eventually, but thought I'd ask 
up front.


Thanks,
Erik

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[Orgmode] inline image display not working when org-indent-mode active

[Erik Iverson]

Hello!

Just pulled the latest org-mode from git.

I've upgraded to Emacs 23.2 so that org-indent-mode works properly.

However, when org-indent-mode is active, it seems that inline images (C-c C-x 
C-v) do not work properly.


They show up for a brief time (< 1 second) and then promptly return to showing 
just the file link.


Turning off org-indent-mode and re-toggling image display shows the image 
properly.

If it matters, these files were created in org-babel source blocks.

Can anyone reproduce this?

Thanks!
Erik

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Re: [Orgmode] inline image display not working when org-indent-mode active

[Erik Iverson]

On 07/17/2010 12:14 AM, Erik Iverson wrote:

Hello!

Just pulled the latest org-mode from git.

I've upgraded to Emacs 23.2 so that org-indent-mode works properly.

However, when org-indent-mode is active, it seems that inline images
(C-c C-x C-v) do not work properly.

They show up for a brief time (< 1 second) and then promptly return to
showing just the file link.

Turning off org-indent-mode and re-toggling image display shows the
image properly.

If it matters, these files were created in org-babel source blocks.


This also seems to happen if org-indent-mode is turned off, and the
source block that produces the image is re-run.  Then, the file link
is displayed, and I have to toggle inline image display to get it
to appear.

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Re: [Orgmode] Re: Org-mode release 7.01

[Erik Iverson]

I assumed I had to switch to the maint branch in order to get the 7.01
release.  How could I have done this while staying on the master branch?


Basically, as long as you're on master, you'll always have the latest 
and greatest, which may or may not be what you want.


At certain times, including in the past few days, 'master' is deemed 
release-worthy, and a stable release is produced.  However, development 
goes on in the master branch.


The maint branch was created so that small bugs in the latest release 
could be fixed and updated, without having to include whatever major 
developments might have happened on master in the mean time.



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Re: [Orgmode] Development setup (was: Org-mode release 7.01)

[Erik Iverson]

Suggestions:

1.) Could the original mail (the one including the actual patch, even if
 modified) be attached to the autogenerated email, please?
 This should be at the very bottom of the mail, because of length and
 priority.

2.) And how about the subject?  The OP's subject is what I read on the
 patchwork server.  Why can't that be (part of) the subject of the
 "Accepted" message? E.g.:

 [Orgmode] [ACCEPTED] org-capture with LISP function template

 Maybe something that works on gmane et al, too.

3.) If there are annotations to the patch,  would it be possible to
 include that comment in that automated message?  I don't now how the
 patch is switched to accepted on the patchwork server.  But a simple
 textarea field and appropriate POST variable would do, wouldn't it?


4) If traffic warrants it and as more users join this list generating more 
posts... perhaps a new list called emacs-orgmode-dev for development related work?


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Re: [Orgmode] babel versionitis?

[Erik Iverson]

Correct, about a month ago:

http://eschulte.github.com/babel-dev/DONE-document-configuration-changes-for-Babel-integration.html

On 08/03/2010 05:59 AM, Rustom Mody wrote:

In Bernt Hansen's Organize your life in plain text he has

(require  'org-babel-init)
(require  'org-babel-ditaa)
(org-babel-load-library-of-babel)

But with my 7.01trans org I get

Cannot open load file org-babel-init

I guess this has to change to

(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(ditaa . t)))

I am just guessing something about babel initialization has changed
recently??


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Re: [Orgmode] Re: [PATCH] Mode-specific fontification of babel source blocks

[Erik Iverson]

On 08/03/2010 06:14 PM, David O'Toole wrote:

I've placed a screenshot of the fontification here:

http://imagebin.ca/view/iRVK_as7.html



Wow, great job.  I once hacked something horrible together that involved several 
tricks to actually change the mode of the buffer when entering a source block 
(using indirect buffers) while keeping the indentation and syntax highlighting 
of the org content the same.


Can't wait to try this out.

victory.png, indeed!



On Tue, Aug 3, 2010 at 7:12 PM, David O'Toole  wrote:

I've got a preliminary patch that adds optional "native" fontification
for source blocks. It uses the block's declared mode to fontify the
block text. So now blocks look the way they should, and this opens the
way to further enhancements. Anyone up for an icons theme standard
discussion?



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