Re: [O] latest org from Elpa error: Invalid function: org-babel-header-args-safe-fn

[Mikhail Titov]

On Sat, Aug  8, 2015 at  8:54 AM, Ista Zahn  wrote:
> Unfortunately I now can't reproduce the problem, so I can't check if
> my suggestion to byte compile ob-R.el works or not.

For those still having this issue.

I do confirm this solves the problem that occurred upon upgrading Org
via ELPA on 64-bit MS Windows build of Emacs 24.5.1 maintained by Chris
Zheng.

I deleted and recompiled both ob-core.elc and ob-R.elc .

-- 
Mikhail

[O] [babel] #+INCLUDE does not account for relative paths to images

[Mikhail Titov]

I've noticed that if I include one Org file into another using
#+INCLUDE, then I'm not getting a proper path to babel-generated figures
at least while doing HTML export. I believe it is still an issue for
non-babel images.

I feel like it would be nice to export an updated relative path to
included image file with a different base when exporting master
document. Current implementation forces either to keep project Org files
in the same folder or use more sophisticated relative paths like
../sibling-project/foo.png . Though I did not try the latter.

-- 
Mikhail

Re: [O] [babel, ess] How can I make S-RET to be multi-session friendly?

[Mikhail Titov]

Another issue I've noticed is that if I save a buffer, that was
previously associated with R session, under different name in different
folder, then that association is not getting reset and/or overridden by
session property of Org buffer. Namely, I had dot R file that I saved in
different folder as dot org one while wrapping code in babel blocks and
adding session property. I did C-c C-c.

I believe there is somewhere a check whether a buffer is associated or
not but no check if it is associated with a proper buffer/session.

Eric Schulte writes on Fri Aug 17 2012 at 09:29 :


 The `org-src-in-org-buffer' macro may be used from an edit buffer to run
 elisp inside the code block, in the org-mode buffer of the edit buffer.
 e.g., the following 

 ;; -*- emacs-lisp -*-
 (org-src-in-org-buffer (message --%S (org-babel-get-src-block-info)))

 Where is org-src-in-org-buffer macro defined. Searching all dot el files
 in org folder does not show anything neither does C-h f show anything
 similar.

 (describe-function 'org-src-in-org-buffer) shows that
 org-src-in-org-buffer can be found in org-src.el (line 679 in my
 version).

I guess it did not propagate to bzr yet :( I've checked with rev
109760. For some reason I had problems building git version on Windows a
while ago and I didn't try since then.

-- 
Mikhail

Re: [O] [babel, ess] How can I make S-RET to be multi-session friendly?

[Mikhail Titov]

Bastien b...@gnu.org writes:

 I would say that after applying changes to my-ess-eval and to
 org-babel-edit-prep:R as suggested by Andrew, it looks like everything
 is working right for me.

 I'v been bold and I pushed the change Andrew suggested.

 Thanks for reporting this and for testing around -- and thanks
 to Andrew for the exploration and the fix! 

Though not related to Org, I noticed that ess-make-buffer-current calls
(update-ess-process-name-list) thus making a call for it in my-ess-eval,
probably, somewhat redundant, right?

Another thing that somewhat bugs me is that if R process quits (or
probably dies as well) when editing source code block in a separate
buffer, the subsequent S-RET will silently execute a line in a wrong
buffer/process. If there are no buffers with R process, it will create
the default *R* named buffer. It might be exotic but I think it is an
issue.

Does it mean that there is a bug in ess-make-buffer-current function
somewhere? Something, probably, re-associates a buffer to another
process, does it?

I think it might be relevant that code editing buffer local variable
ess-local-process-name is non-nil when associated process quits. This
results in first ess-make-buffer-current in my-ess-eval silently
launching *R*.

I'm not sure if it is too much to fix. Perhaps hitting C-c ' twice to
re-start editing is a reasonable workaround.

Eric Schulte eric.schu...@gmx.com writes:

 You can find the name of the original org-mode buffer by running the
 following snippet of elisp within the edit buffer.

 ;; -*- emacs-lisp -*-
 (marker-buffer org-edit-src-beg-marker)

 The `org-src-in-org-buffer' macro may be used from an edit buffer to run
 elisp inside the code block, in the org-mode buffer of the edit buffer.
 e.g., the following 

 ;; -*- emacs-lisp -*-
 (org-src-in-org-buffer (message --%S (org-babel-get-src-block-info)))

Where is org-src-in-org-buffer macro defined. Searching all dot el files
in org folder does not show anything neither does C-h f show anything
similar.

-- 
Mikhail

Re: [O] [babel, ess] How can I make S-RET to be multi-session friendly?

[Mikhail Titov]

Eric Schulte eric.schu...@gmx.com writes:

 Thanks for sending this along, unfortunately ob-R.el is currently
 without a core maintainer

Quite a sad situation, many good modules lack maintainers :(

, so I'm not sure who on list would have the expertise to review your
submission.  Although hopefully those experiencing the problem can at
least check if it works for them.

I'm not an expert but I gave it a shot.

 It seems that for me, the inferior ess process is not being properly
 associated with the src edit buffer.  It is being set correctly by
 org-babel-R-associate-session, and then being set a second time
 incorrectly by org-babel-edit-prep:R.  Commenting out line 5 in
 org-babel-edit-prep:R seems to fix this issue, although I'm honestly
 not sure if or what it breaks.  Everything seems ok for me, but ymmv.

 Heres the change:
 #+begin_src emacs-lisp
   (defun org-babel-edit-prep:R (info)
 (let ((session (cdr (assoc :session (nth 2 info)
   (when (and session (string-match ^\\*\\(.+?\\)\\*$ session))
 (save-match-data (org-babel-R-initiate-session session nil))
 ;;(setq ess-local-process-name (match-string 1 session)
 )))
 #+end_src


 Perhaps replacing the commented setq ess-local-process-name line with
 ess-switch-process could solve this problem?  Could the process name be
 found programatically, perhaps using the regexp solution above.


 Is there any one having such issues, or who can weigh in on what
 exactly is happening here?

 Without making the above change, it is possible to manually attach an
 ess process to the current src buffer by using the command:

 C-c C-s (ess-switch-process)

 You'll have to specify the process name, rather than the buffer name,
 and the session must have already been started.

I would say that after applying changes to my-ess-eval and to
org-babel-edit-prep:R as suggested by Andrew, it looks like everything
is working right for me. Once I hit C-c ' I see properly named buffer
appear with new process. Then if I hit S-RET it asks me what session to
use and since I have ido mode, it already highlights proper session
name, so I just hit RET. Perhaps it worth recommending to use ido?

Note that I do not have to enter process name.

If I quite R, while editing code in a separate buffer, and hit S-RET it
is executed in the wrong one without any question being asked :(

I'm running somewhat recent bzr version of Emacs with default Org in it.

-- 
Mikhail

Re: [O] [babel, ess] How can I make S-RET to be multi-session friendly?

[Mikhail Titov]

Eric Schulte eric.schu...@gmx.com writes:

 There is a wonderful post[1] on how to make S-RET to do handy things in
 ESS mode. However I often find myself working on several Org documents
 from different folders.

 It is quite inconvenient to change a directory in =*R*= buffer each
 time I work on different document.

 Is there a neat way to somehow reuse Org mode property =session= that I
 set buffer wide?


 I'm not sure what you mean by reuse.  All of the information for how
 to set header arguments in available at (info (org) Using header
 arguments)

Here is the outline of what I have and what I'm doing.

As I mentioned I set default :session header for R to *R*. In my file I have
something like

#+PROPERTY: session *Rreport*

Whenever I C-c C-c on code block, I can see that *R* buffer
was created instead of *Rreport* !

Now, if I edit my code block with C-c ' and hit S-RET on any line, it
evaluates in *R* whereas I'd prefer it to be *Rreport* somehow. I
understand that I'm trying to somewhat mix ob with plain
ESS. Nevertheless I wonder if it is somehow possible.

 Also for some reason

 #+PROPERTY: session *Rsomename*

 does not override session name set in
 =org-babel-default-header-args:R= even after =C-c C-c= on it when I
 re-evaluate babel code block with =C-c C-c= on code block, while
 explicit block header =:session *Rsomename*= makes difference.


 Yes, the order of precedence is

 system-level  buffer/subtree-level  language-level 
 code-block-level

Then I'd say buffer level does NOT override system-level for some
reason. I just re-built Emacs from bzr to make sure I'm running somewhat
recent Org.

Another weird thing is that when I tried to use Org from git (and not
the stock one), Emacs freezes deadly on
(org-clock-persistence-insinuate) unless I kill ntvdm.exe with Task
Manager (I'm on Windows). But I guess it is a separate story.

 ,[ snippet from dot emacs ]
 | (setq org-babel-default-header-args:R
 |   '((:results . output) (:session . *R*)))
 `


 Given that (:session . *R*) will be used by default you could simply
 remove it from your custom setting for org-babel-default-header-args.

This made a trick. Now indeed I have *Rreport* after C-c C-c on code
block. However after C-c ' whenever I attempt to S-RET, yet another *R*
is launched every time instead of evaluating a line.

So the question perhaps is:

How to alter [1] such that when I edit code block with C-c ' , S-RET
executes lines in a proper session. I believe all information is in
there, I just have no clue how would I extract it, e.g. to which main
buffer that code editing buffer (I don't know the right name for it)
belongs to, and what session header is set to in that buffer.

If there is a way to fetch those, perhaps I'd be able to alter original
set up in [1].

 Footnotes: 
 [1]
 http://www.kieranhealy.org/blog/archives/2009/10/12/make-shift-enter-do-a-lot-in-ess/

-- 
Mikhail

[O] [babel, ess] How can I make S-RET to be multi-session friendly?

[Mikhail Titov]

Hello!

There is a wonderful post[1] on how to make S-RET to do handy things in
ESS mode. However I often find myself working on several Org documents
from different folders.

It is quite inconvenient to change a directory in =*R*= buffer each time
I work on different document.

Is there a neat way to somehow reuse Org mode property =session= that I
set buffer wide?

Also for some reason

#+PROPERTY: session *Rsomename*

does not override session name set in =org-babel-default-header-args:R=
even after =C-c C-c= on it when I re-evaluate babel code block with =C-c
C-c= on code block, while explicit block header =:session *Rsomename*=
makes difference.

,[ snippet from dot emacs ]
| (setq org-babel-default-header-args:R
|   '((:results . output) (:session . *R*)))
`

I'm running Org-mode version 7.8.10 (release_7.8.10-658-g451191.dirty)

Footnotes: 
[1]  
http://www.kieranhealy.org/blog/archives/2009/10/12/make-shift-enter-do-a-lot-in-ess/

-- 
Mikhail

Re: [O] How to integrate org-mode in a MS Windows-/Office-based environment?

[Mikhail Titov]

M elwood...@web.de writes:

 So unfortunately I'll have to find a way to integrate as good as possible.
 (I had tried to use MS Outlook 2007 for managing tasks for some weeks but I
 was missing a lot of features I got used to from org-mode, so I installed
 org-mode.

 One example of helpful integration: if I send or get an e-mail which I want
 to follow-up on later, I want to track that in org-mode and I want to have a
 way to quickly find the original message in Outlook again (to reply or
 forward it or whatever), which can be done with hyperlinks.

You can set up Gnus if Exchange server is available via IMAP otherwise
see Q 3.10 [1]. With Gnus you can easily insert links right to your
e-mail. Indeed the ability to bookmark an e-mail is something I would
miss without Org mode.

[1] http://gnus.org/manual/gnus_397.html#SEC446

 I'm sure there are a lot more useful tricks which can help in daily work, e.
 g. a vba macro which copies the path to the currently open word or excel
 document into the clipboard or even directly opens org-capture to add some
 note or task which is linked to this document...

You can use dired to navigate to your word document in the first place
and make a link using dired.

-- 
Mikhail

Re: [O] Org variables in LaTeX - how?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Rainer M Krug
 Sent: Thursday, June 07, 2012 6:32 AM
 To: emacs-orgmode
 Subject: [O] Org variables in LaTeX - how?
 
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Hi
 
 I must admit, I don't know the inner workings of LaTeX, so this might be
 impossible, but anyway:
 
 I have the following two variables:
 
 
 #+PROPERTY: var VER=89
 #+PROPERTY: var+ STATE=up-to-date
 
 I create a file in one code block via sh, named
 FILE=./../nsa.$VER.$STATE.tar.gz
 
 Now I would likle to attach this file to the pdf:
 
 #+LATEX_HEADER:\\usepackage{attachfile2}
 #+BEGIN_LaTeX
   \textattachfile[print=false,color=0.5 0.5
 0.5]{./../nsa.VER.STATE.tar.gz}{R source files}
 #+END_LaTeX
 
 How can I use the variables in a LaTeX block?
 Using the ove does obviously not work, but
 
 #+BEGIN_LaTeX
   \textattachfile[print=false,color=0.5 0.5 0.5]{./../nsa.98.up-to-
 date.tar.gz}{R source files}
 #+END_LaTeX
 
 does.
 
 So my question: Can I, and if yes how, use org variables in LaTeX code?

You should generate latex code with let's say elisp (or some other language)
fragment that will output :results latex

Mikhail

Re: [O] python/babel inline images

[Mikhail Titov]

 -Original Message-
 From: henry atting [mailto:nsmp...@online.de]
 Sent: Thursday, June 07, 2012 3:43 AM
 To: Mikhail Titov
 Cc: 'henry atting'; emacs-orgmode@gnu.org
 Subject: Re: python/babel inline images
 
  The code itself works flawlessly. So
  the workaround which I already have used is to link to the resulting
  image. The only drawback with this solution is that after every
  evaluation I have to remove the empty `'Results:'
 
  You can use :results silent
 
 This is great! Actually this solves my problem which means: create a link
 to the file and set results to silent.

This has an implication of inability to cache results in case you might want
it. I personally would just leave empty #+RESULTS: block as is and I would
place link manually two lines below it (leave 1 blank line so re-evaluation
won't delete your link).

 
  but the heck with
  it, I can live with it happily till the end of my days.
  However I find that some inconsistency lies therein. Before
  python/matplotlib I used gnuplot with which babel had no problem of
  this type.
 
  Try using
 
  ... :file exp_csv.svg
  ...
  plot.savefig(file=sys.stdout)
 
 This does not compile, the compiler complains about missing arguments.
 I have to write it like this:
 
 plot.savefig(file.svg, format='svg')

I never used that library but it makes sense:-) The only problem with this
solution that you should make sure nothing else goes to stdout. I think it
is a huge shortcoming.

 So, just to mention the current state of affairs (with a simple
 example):
 
 --8---cut here---start-8---
 #+begin_src python   :results output
 from pylab import *
 
 t = arange(0.0, 2.0, 0.01)
 s = sin(2*pi*t)
 plot(t, s)
 show()
 savefig(file.svg, format='svg')
 #+end_src
 --8---cut here---start-8---
 
 The above code works. But if I set `:file' to `file.svg' with every
 evaluation the link to the file is placed after #+RESULTS: but the
 file itself is empty.

As William LECHELLE pointed out that in this case file captures the output
of the savefig() call which does not output anything to stdout. So it is
expected.

 If the code is evaluated without `:file
 file.svg' the evaluation simply works and the file.svg appears in the
 working directory.

I think this is the best way to proceed.

M.

Re: [O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Wednesday, June 06, 2012 6:06 PM
 To: 'Eric Schulte'
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] session initialization (was RE: python/babel
inline
 images)
 
 ...
 
 How would I reliably refer to the org doc buffer from where everything was
 called? The following works just fine in session initialization code for
 Matlab but not for Octave
 
 (file-name-directory (buffer-file-name (other-buffer)))
 
 At this point, (current-buffer) refers to the one with inferior process.

So I ended up using the following in session initialization for inferior
process to get a current folder of a document from where calculations
initiated

(file-name-directory
   (car (delq nil (mapcar #'buffer-file-name (buffer-list)

It works. But I have a feeling that it is not a reliable method. Any
suggestions?

M.

Re: [O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Thursday, June 07, 2012 5:44 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org; 'Eric Schulte'
 Subject: Re: [O] [babel] session initialization (was RE: python/babel
inline
 images)
 
  ...
 
  How would I reliably refer to the org doc buffer from where everything
was
  called? The following works just fine in session initialization code
for
  Matlab but not for Octave
 
 
  (file-name-directory
 (car (delq nil (mapcar #'buffer-file-name (buffer-list)
 
  It works. But I have a feeling that it is not a reliable method. Any
  suggestions?
 
 
 I would recommend using the `default-directory' variable.  That should
 hold the value of the directory of the Org-mode file or the value of the
 :dir header argument if present.

Huh... now it works... I remember I've tried before but for some reason it
was nil.. maybe typo though I have AC.

The only trick [1] is to use (file-truename default-directory) as Matlab
does not like ~.

Thanks!

M. 

[1]
http://stackoverflow.com/questions/291976/relative-path-to-absolute-path-in-
elisp

Re: [O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Thursday, June 07, 2012 6:03 PM
 To: 'Eric Schulte'
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] session initialization (was RE: python/babel
inline
 images)
 
   ...
  
   How would I reliably refer to the org doc buffer from where
everything
 was
   called? The following works just fine in session initialization code
 for
   Matlab but not for Octave
  
  
   (file-name-directory
  (car (delq nil (mapcar #'buffer-file-name (buffer-list)
  
   It works. But I have a feeling that it is not a reliable method. Any
   suggestions?
  
 
  I would recommend using the `default-directory' variable.  That should
  hold the value of the directory of the Org-mode file or the value of the
  :dir header argument if present.
 
 Huh... now it works... I remember I've tried before but for some reason it
 was nil.. maybe typo though I have AC.
 
 The only trick [1] is to use (file-truename default-directory) as Matlab
 does not like ~.

Turns out this does not work for octave for some reason. default-directory
points to my home folder.

Also I'm getting ansi-color-process-output: Marker does not point anywhere
for Octave. So I have to C-c a couple of times on the block for the first
time. First evaluation just launches session but breaks because of that
error. Second time (when session is up) C-c works just fine and dumps
result. Non-session version of Octave works as expected. I wonder if it is
something Windows-specific... I can see test on :session for Octave and
Achim Gratz said it passed tests.

The problem occurs to me with git version of ob-octave.el as well. So I'm
confident it is not me who broke something during experiments :-)

Any idea? Matlab works just fine (session)!

I'm afraid I'll leave all the things as is for now. Maybe someone else can
fix it later.

M.
 

[O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Wednesday, June 06, 2012 12:20 AM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org; 'henry atting'
 Subject: Re: [O] python/babel inline images
 
 Mikhail Titov m...@gmx.us writes:
 
  -Original Message-
  From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
  bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
  Sent: Tuesday, June 05, 2012 9:57 AM
  To: henry atting
  Cc: emacs-orgmode@gnu.org
  Subject: Re: [O] python/babel inline images
 
  I'm not python expert, but the code block should be run in your current
  directory, e.g., the following outputs the current working path
expected
  for me.
 
  #+begin_src sh
pwd
  #+end_src
 
  If you want to explicitly pass the current directory to your code block
  as an argument, you could try something like the following
 
  #+begin_src python :var mydir=(file-name-directory (buffer-file-name))
return mydir
  #+end_src
 
 
  I've noticed some inconsistency between various languages in this
aspect.
  For instance, ob-R starts session in proper working directory, while all
  looks like everything (?) else does not.
 
  Should not it be somewhat standardized? I think it make sense to always
cd
  to org doc folder.
 
 
 Most languages should and (at least those I use regularly) do run in the
 directory of the containing Org-mode file.  Which languages do not?

I'm working on ob-octave.el which does not. So I'll fix it in this case.
Which leads me to another question I was about to ask. How to comint
commands in org-babel-XXX-initiate-session as session is not assigned yet?
Right now I have something like the following in that function

  (comint-send-string
   (get-buffer-process (current-buffer))
   set(0, 'defaultfigurevisible', 'off');\n)

I do it there as it does not make sense to call for each block. I was about
to write that ob-R does show stuff but I believe it was in earlier versions
of ob-R.el or something as I've checked and indeed nothing appears on screen
as code being wrapped in a device output block.

Also IIRC ob-sh does not change directory though I tried it on Windows with
cmd.exe . Worth mentioning that it tangles into dot sh instead of dot bat or
dot cmd on that platform. It misses platform specific

(defvar org-babel-tangle-lang-exts) 
(if (string-equal system-type windows-nt) 
  (add-to-list 'org-babel-tangle-lang-exts '(sh . bat))
)

P.S. I feel like I'm hijacking the thread

M.

Re: [O] python/babel inline images

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of henry atting
 Sent: Wednesday, June 06, 2012 10:19 AM
 To: emacs-orgmode@gnu.org
 Subject: Re: [O] python/babel inline images
 
 I don't think its a path problem.

Indeed

#+begin_src python :results output
import os
print(os.getcwd())
#+end_src

Shows location of my org doc.

 The code itself works flawlessly. So
 the workaround which I already have used is to link to the resulting
 image. The only drawback with this solution is that after every
 evaluation I have to remove the empty `'Results:'

You can use :results silent

 but the heck with
 it, I can live with it happily till the end of my days.
 However I find that some inconsistency lies therein. Before
 python/matplotlib I used gnuplot with which babel had no problem of
 this type.

Try using

... :file exp_csv.svg
...
plot.savefig(file=sys.stdout)


#+begin_src python :results output :file zzz.xxx
import os, sys
print(os.getcwd(), file=sys.stdout)
#+end_src

#+RESULTS:
[[file:zzz.xxx]]


Meanwhile I've noticed that I can't return back from editing python code in
a sub-editing buffer. C-c ' does not work and M-x org-edit-src-exit says
This is not a sub-editing buffer, something is wrong.

Re: [O] python/babel inline images

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Wednesday, June 06, 2012 2:25 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org; 'henry atting'
 Subject: Re: [O] python/babel inline images
 
  Meanwhile I've noticed that I can't return back from editing python code
in
  a sub-editing buffer. C-c ' does not work and M-x org-edit-src-exit says
  This is not a sub-editing buffer, something is wrong.
 
 
 This works on my system, perhaps the problem is due to something in your
 configuration.  Do you still notice this problem when launching emacs
 with the -Q option.

Huh... -Q solves it. I'm loading CEDET early in dot emacs for matlab-emacs
(as per manual) and it does something nasty that ruins normal behavior of
C-c '. Bummer.

Outdated eieio 1.3 shadowed to meet minimum version 1.4
Outdated semantic 2.0 shadowed to meet minimum version 2.1
Outdated srecode 1.0 shadowed to meet minimum version 1.1
Outdated ede 1.0 shadowed to meet minimum version 1.1
Outdated speedbar 1.0 shadowed to meet minimum version 1.0.4
Setting up CEDET packages...done

M.

Re: [O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Wednesday, June 06, 2012 2:02 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org; 'henry atting'; 'Eric Schulte'
 Subject: Re: [O] [babel] session initialization (was RE: python/babel
inline
 images)
 
  Right now I have something like the following in that function
 
(comint-send-string
 (get-buffer-process (current-buffer))
 set(0, 'defaultfigurevisible', 'off');\n)
 
  I do it there as it does not make sense to call for each block. I was
about
  to write that ob-R does show stuff but I believe it was in earlier
versions
  of ob-R.el or something as I've checked and indeed nothing appears on
screen
  as code being wrapped in a device output block.
 
 
 I'm not aware of a way to run code on the start of a session.  I do see
 how this could be a useful addition.

So the fragment above does look legitimate to you? I just add

(format cd('%s');\n (file-name-directory (buffer-file-name)))

and problem solved? Well... for sessions. I don't know if it is common to
use non-session based calculations...

  Also IIRC ob-sh does not change directory though I tried it on Windows
with
  cmd.exe.
 
 Granted I only run on linux, but (on linux) ob-sh *does* run in the
 directory of the containing Org-mode file.
 
  Worth mentioning that it tangles into dot sh instead of dot bat or dot
  cmd on that platform. It misses platform specific
 
  (defvar org-babel-tangle-lang-exts)
  (if (string-equal system-type windows-nt)
(add-to-list 'org-babel-tangle-lang-exts '(sh . bat))
  )
 
 
 OK, could you convert the above into a patch which we could apply to
 ob-sh?

I think there should be more than that. I do sometimes use bash from msys on
Win32 so I'd expect sh as a tangled file name extension in this case. I
believe it can be accomplished as with matlab / octave by adding a new
language cmd that will reuse most of sh. I'll see what I can do.

M.

Re: [O] [babel] session initialization (was RE: python/babel inline images)

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Wednesday, June 06, 2012 2:42 PM
 To: 'Eric Schulte'
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] session initialization (was RE: python/babel
inline
 images)
 
  -Original Message-
  From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
  bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
  Sent: Wednesday, June 06, 2012 2:02 PM
  To: Mikhail Titov
  Cc: emacs-orgmode@gnu.org; 'henry atting'; 'Eric Schulte'
  Subject: Re: [O] [babel] session initialization (was RE: python/babel
 inline
  images)
 
   Right now I have something like the following in that function
  
   (comint-send-string
(get-buffer-process (current-buffer))
set(0, 'defaultfigurevisible', 'off');\n)
  
   I do it there as it does not make sense to call for each block. I was
 about
   to write that ob-R does show stuff but I believe it was in earlier
 versions
   of ob-R.el or something as I've checked and indeed nothing appears on
 screen
   as code being wrapped in a device output block.
  
 
  I'm not aware of a way to run code on the start of a session.  I do see
  how this could be a useful addition.
 
 So the fragment above does look legitimate to you? I just add
 
 (format cd('%s');\n (file-name-directory (buffer-file-name)))
 
 and problem solved? Well... for sessions. I don't know if it is common to
 use non-session based calculations...

How would I reliably refer to the org doc buffer from where everything was
called? The following works just fine in session initialization code for
Matlab but not for Octave

(file-name-directory (buffer-file-name (other-buffer)))

At this point, (current-buffer) refers to the one with inferior process.

M.

[O] [babel] Why #+name: is not a member of params?

[Mikhail Titov]

Hello!

I’d like to insert a comment into tangle output with a block name. I thought I 
could easily access it (like from org-babel-expand-body:XXX function) with

(cdr (assq :name params))

But apparently it does not work. When I do C-c C-v C-v trying to expand body, I 
get nil as it is not there.

Did I miss something?

I want that so each block appears in individual Matlab code cell [1].

[1] http://www.mathworks.com/help/techdoc/matlab_env/brqxeeu-259.html

Mikhail

Re: [O] [babel] Why #+name: is not a member of params?

[Mikhail Titov]

 -Original Message-
 From: Eric Schulte [mailto:eric.schu...@gmx.com]
 Sent: Tuesday, June 05, 2012 7:42 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] Why #+name: is not a member of params?
 
 Mikhail Titov m...@gmx.us writes:
 
  Hello!
 
  I’d like to insert a comment into tangle output with a block name. I thought
 I could easily access it (like from org-babel-expand-body:XXX function) with
 
  (cdr (assq :name params))
 
 ...
 
 The code block name is not a member of params.  Params only holds header
 arguments, not other meta data like the name.  The code block name is
 stored in the `info' list which is active while the code block is being
 processed, so you could access it with something like the following,
 although which is relying on an implementation detail that is not part
 of the formal spec (i.e., cheating) and could change.
 
 #+name: foo
 #+begin_src emacs-lisp
   (nth 4 info)
 #+end_src
 
 #+RESULTS: foo
 : foo

Thank you, Eric!

Marvelous! It does what I want. I see its definition in ob.el .

M. 

Re: [O] python/babel inline images

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Tuesday, June 05, 2012 9:57 AM
 To: henry atting
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] python/babel inline images
 
 I'm not python expert, but the code block should be run in your current
 directory, e.g., the following outputs the current working path expected
 for me.
 
 #+begin_src sh
   pwd
 #+end_src
 
 If you want to explicitly pass the current directory to your code block
 as an argument, you could try something like the following
 
 #+begin_src python :var mydir=(file-name-directory (buffer-file-name))
   return mydir
 #+end_src
 

I've noticed some inconsistency between various languages in this aspect.
For instance, ob-R starts session in proper working directory, while all
looks like everything (?) else does not.

Should not it be somewhat standardized? I think it make sense to always cd
to org doc folder.

M.

Re: [O] [babel, patch] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Achim Gratz
 Sent: Monday, May 28, 2012 1:24 PM
 To: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel, patch] ob-octave does not catch EOE from
matlabShell
 on MS Windows
 
 Eric Schulte writes:
  Thanks for sending along the patch and the variable re-definition.  If I
  understand correctly then the patch should be applied for any system,
  but the variable definition need only be applied on windows systems.  Is
  that correct?
 
 The variable re-definition seems to be be needed for matlab-shell, I
 don't know if that would be restricted to Windows.
 
  Can anyone confirm that matlab/octave code blocks are still functional
  on a GNU/Linux machine after the above patch and redefinition have been
  applied?  I do not use octave/matlab myself and can't verify this.
 
 The octave tests still pass on openSUSE with the patch applied along
 with all the other tests (except R, since I'm missing ESS).

I wonder how it still passes the test...

I think my patch unintentionally breaks octave. It probably should have been
just

 org-babel-octave-eoe-output

instead of

 (if matlabp
 org-babel-octave-eoe-output
   org-babel-octave-eoe-indicator) 

or other way around.

I apologize for bringing it all over to the list as I'm not proficient in
elisp yet.

I feel like ob-octave needs an overhaul in general as it does not respect
many header arguments like :width, :height, and graphics format (always
png). Also it would be nice if it removed extra prompts left in results as
does ob-R.el .

I'll post improved patch once I feel it is ready.

Eric, so for now, just hold on with the application of what I've sent.

Mikhail

Re: [O] [babel, patch] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

 -Original Message-
 From: Eric Schulte [mailto:eric.schu...@gmx.com]
 Sent: Monday, May 28, 2012 10:57 AM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel, patch] ob-octave does not catch EOE from
matlabShell
 on MS Windows
 
 ...
 
  It looks like org-babel-octave-eoe-output and org-babel-octave-eoe-
 indicator
  were swapped around in org-babel-octave-evaluate-session .
 
  I have the following in dot emacs
 
  (setq org-babel-octave-eoe-output 
  ans =
 
  org_babel_eoe
 
  )
 
  For the sake of completeness I'm attaching the patch. Also one should
 override
 
  (setq org-babel-matlab-emacs-link-wrapper-method
 %s
  if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans);
 fclose(fid); else, save -ascii %s ans ; end
  delete('%s')
  )
 
  as matlabShell does not like commands split across multiple lines.
 
 
 Thanks for sending along the patch and the variable re-definition.

I was in the hurry and the second variable should have been 

(setq org-babel-octave-wrapper-method
  %s
if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans);
fclose(fid); else, dlmwrite('%s', ans, '\\t'); end)

and not org-babel-matlab-emacs-link-wrapper-method . The only difference
from what is already in there, is that it should be a single line (with ;
delimiters). It might be a limitation of matlabShell.

From what I understand EmacsLink is something outdated and not supported
anymore as there is matlab-emacs mode.

Also the patch was missing yet another change to use single quotes instead
of double quotes when making default figures invisible. I'm attaching the
patch I ended up using.

  If I
 understand correctly then the patch should be applied for any system,
 but the variable definition need only be applied on windows systems.  Is
 that correct?

Unfortunately I don't have Matlab installed on my home GNU/Linux computer,
I'll see if I'm eligible and can get one.

What bugs me though is that I can't use both octave and matlab as they use
same variable (org-babel-octave-eoe-output) which should be set to different
values. In org-babel-comint-with-output macro (ob-comint.el) it is used to
check if shell/REPL is done with evaluation and ready for input. I wonder if
it is possible to generalize org-babel-octave-eoe-output for both matlab and
octave as the only difference is the bunch of newlines in Matlab output. One
may write a regexp that matches both, however (regexp-quote
,eoe-indicator) in aforementioned macro confuses me. So it got to be a
plain string.

M.

 Can anyone confirm that matlab/octave code blocks are still functional
 on a GNU/Linux machine after the above patch and redefinition have been
 applied?  I do not use octave/matlab myself and can't verify this.
 
 If they don't break anything I'm happy to apply these patches.
 
 Thanks,
 
 --
 Eric Schulte
 http://cs.unm.edu/~eschulte


ob-octave_matlab_updated.patch
Description: Binary data

Re: [O] [babel] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Thursday, May 24, 2012 4:31 PM
 To: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] ob-octave does not catch EOE from matlabShell on MS
 Windows
 
  ...
 
  I have a simple test block like
 
  #+begin_src matlab :session *MATLAB*
  a=2
  #+end_src
 
  When I try to execute it with C-c C-c , emacs never returns unless I hit C-
 g.
  If I do M-x toggle-debug-on-quit RET I see that for some reason it keeps
  waiting for EOE.

It looks like org-babel-octave-eoe-output and org-babel-octave-eoe-indicator 
were swapped around in org-babel-octave-evaluate-session .

I have the following in dot emacs

(setq org-babel-octave-eoe-output 
ans =

org_babel_eoe

)

M.

 
  ...
 
  Here is what I see in *MATLAB* buffer:
 
  8-*MATLAB*--8-
   a=2
  if ischar(ans), fid = fopen('c:/DOCUME~1/user/LOCALS~1/Temp/babel-
  7560HUp/matlab-7560PPd', 'w'); fprintf(fid, '%s\n', ans); fclose(fid); else,
  dlmwrite('c:/DOCUME~1/user/LOCALS~1/Temp/babel-7560HUp/matlab-7560PPd', ans,
  '\t'); end
  'org_babel_eoe'
 
  a =
 
   2
 
   
  ans =
 
  org_babel_eoe
 
  
  8-*MATLAB*--8-
 
 I feel like it is about
 
 (defvar org-babel-octave-eoe-output ans = org_babel_eoe)
 
 as Matlab's return has newlines. I'm not sure so far how to make universal
 regex for re-search-forward in org-babel-comint-with-output .
 
 Mikhail
 
 
 

Re: [O] [babel, patch] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Friday, May 25, 2012 11:31 AM
 To: emacs-orgmode@gnu.org
 Subject: Re: [O] [babel] ob-octave does not catch EOE from matlabShell on MS
 Windows
 
   ...
  
   I have a simple test block like
  
   #+begin_src matlab :session *MATLAB*
   a=2
   #+end_src
  
   When I try to execute it with C-c C-c , emacs never returns unless I hit
 C-
  g.
   If I do M-x toggle-debug-on-quit RET I see that for some reason it keeps
   waiting for EOE.
 
 It looks like org-babel-octave-eoe-output and org-babel-octave-eoe-indicator
 were swapped around in org-babel-octave-evaluate-session .
 
 I have the following in dot emacs
 
 (setq org-babel-octave-eoe-output 
 ans =
 
 org_babel_eoe
 
 )

For the sake of completeness I'm attaching the patch. Also one should override

(setq org-babel-matlab-emacs-link-wrapper-method
   %s
if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); 
fclose(fid); else, save -ascii %s ans ; end
delete('%s')
)

as matlabShell does not like commands split across multiple lines.

M.



ob-octave_matlab.patch
Description: Binary data

[O] [babel] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

Hello!

I was trying hard to set up Matlab R2011a to work with my Emacs 24.1.50.1 (org 
version is release_7.8.09-532-gb797c8.dirty) and finally I was able to use it 
from M-shell but not from orgmode yet. I've edited emacs wiki [1] to reflect 
somewhat working matlab-mode setup on win32. Namely I use [2] as matlab shell.

I have a simple test block like

#+begin_src matlab :session *MATLAB*
a=2
#+end_src

When I try to execute it with C-c C-c , emacs never returns unless I hit C-g. 
If I do M-x toggle-debug-on-quit RET I see that for some reason it keeps 
waiting for EOE.

I'd appreciate any suggestion as what to try (other than Octave which has its 
own tricks on Win32). I'm lost.

[1] http://www.emacswiki.org/emacs/MatlabMode#toc3
[2] http://www.cs.umb.edu/~ram/matlabShell/index.html

--
Mikhail


Here is what I see in *MATLAB* buffer:

8-*MATLAB*--8-
 a=2
if ischar(ans), fid = 
fopen('c:/DOCUME~1/user/LOCALS~1/Temp/babel-7560HUp/matlab-7560PPd', 'w'); 
fprintf(fid, '%s\n', ans); fclose(fid); else, 
dlmwrite('c:/DOCUME~1/user/LOCALS~1/Temp/babel-7560HUp/matlab-7560PPd', ans, 
'\t'); end
'org_babel_eoe'

a =

 2

  
ans =

org_babel_eoe


8-*MATLAB*--8-


8-*Bactrace*--8-
Debugger entered--Lisp error: (quit)
  accept-process-output(#process MATLAB)
  (while (progn (goto-char comint-last-input-end) (not (save-excursion (and 
(re-search-forward (regexp-quote (if matlabp org-babel-octave-eoe-indicator 
org-babel-octave-eoe-output)) nil t) (re-search-forward comint-prompt-regexp 
nil t) (accept-process-output (get-buffer-process (current-buffer
  (progn (goto-char (process-mark (get-buffer-process (current-buffer (let 
((start (point)) (end (point-max))) (setq dangling-text (buffer-substring start 
end)) (delete-region start end)) (insert full-body) (comint-send-input nil t) 
(while (progn (goto-char comint-last-input-end) (not (save-excursion (and 
(re-search-forward (regexp-quote ...) nil t) (re-search-forward 
comint-prompt-regexp nil t) (accept-process-output (get-buffer-process 
(current-buffer (goto-char (process-mark (get-buffer-process 
(current-buffer (insert dangling-text))
  (unwind-protect (progn (goto-char (process-mark (get-buffer-process 
(current-buffer (let ((start (point)) (end (point-max))) (setq 
dangling-text (buffer-substring start end)) (delete-region start end)) (insert 
full-body) (comint-send-input nil t) (while (progn (goto-char 
comint-last-input-end) (not (save-excursion (and (re-search-forward ... nil t) 
(re-search-forward comint-prompt-regexp nil t) (accept-process-output 
(get-buffer-process (current-buffer (goto-char (process-mark 
(get-buffer-process (current-buffer (insert dangling-text)) (remove-hook 
(quote comint-output-filter-functions) (quote my-filt)))
  (progn (fset (quote my-filt) (function* (lambda (text) (block my-filt (setq 
string-buffer (concat string-buffer text)) (add-hook (quote 
comint-output-filter-functions) (quote my-filt)) (unwind-protect (progn 
(goto-char (process-mark (get-buffer-process (current-buffer (let ((start 
(point)) (end (point-max))) (setq dangling-text (buffer-substring start end)) 
(delete-region start end)) (insert full-body) (comint-send-input nil t) (while 
(progn (goto-char comint-last-input-end) (not (save-excursion (and ... ... 
(accept-process-output (get-buffer-process (current-buffer (goto-char 
(process-mark (get-buffer-process (current-buffer (insert dangling-text)) 
(remove-hook (quote comint-output-filter-functions) (quote my-filt
  (unwind-protect (progn (fset (quote my-filt) (function* (lambda (text) (block 
my-filt (setq string-buffer (concat string-buffer text)) (add-hook (quote 
comint-output-filter-functions) (quote my-filt)) (unwind-protect (progn 
(goto-char (process-mark (get-buffer-process (current-buffer (let ((start 
(point)) (end (point-max))) (setq dangling-text (buffer-substring start end)) 
(delete-region start end)) (insert full-body) (comint-send-input nil t) (while 
(progn (goto-char comint-last-input-end) (not (save-excursion ...))) 
(accept-process-output (get-buffer-process (current-buffer (goto-char 
(process-mark (get-buffer-process (current-buffer (insert dangling-text)) 
(remove-hook (quote comint-output-filter-functions) (quote my-filt (if 
--cl-letf-bound-- (fset (quote my-filt) --cl-letf-save--) (fmakunbound (quote 
my-filt
  (let* ((--cl-letf-bound-- (fboundp (quote my-filt))) (--cl-letf-save-- (and 
--cl-letf-bound-- (symbol-function (quote my-filt) (unwind-protect (progn 
(fset (quote my-filt) (function* (lambda (text) (block my-filt (setq 
string-buffer ...) (add-hook (quote comint-output-filter-functions) (quote 
my-filt)) (unwind-protect (progn (goto-char (process-mark (get-buffer-process 
...))) (let ((start ...) (end ...)) (setq dangling-text (buffer-substring start 

Re: [O] [babel] ob-octave does not catch EOE from matlabShell on MS Windows

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Thursday, May 24, 2012 4:02 PM
 To: emacs-orgmode@gnu.org
 Subject: [O] [babel] ob-octave does not catch EOE from matlabShell on MS
 Windows
 
 ...

 I have a simple test block like
 
 #+begin_src matlab :session *MATLAB*
 a=2
 #+end_src
 
 When I try to execute it with C-c C-c , emacs never returns unless I hit C-g.
 If I do M-x toggle-debug-on-quit RET I see that for some reason it keeps
 waiting for EOE.

 ...
 
 Here is what I see in *MATLAB* buffer:
 
 8-*MATLAB*--8-
  a=2
 if ischar(ans), fid = fopen('c:/DOCUME~1/user/LOCALS~1/Temp/babel-
 7560HUp/matlab-7560PPd', 'w'); fprintf(fid, '%s\n', ans); fclose(fid); else,
 dlmwrite('c:/DOCUME~1/user/LOCALS~1/Temp/babel-7560HUp/matlab-7560PPd', ans,
 '\t'); end
 'org_babel_eoe'
 
 a =
 
  2
 
  
 ans =
 
 org_babel_eoe
 
 
 8-*MATLAB*--8-

I feel like it is about

(defvar org-babel-octave-eoe-output ans = org_babel_eoe)

as Matlab's return has newlines. I'm not sure so far how to make universal 
regex for re-search-forward in org-babel-comint-with-output .

Mikhail
 

Re: [O] Unable to Style RESULTS Blocks

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Thomas S. Dye
 Sent: Monday, May 21, 2012 12:58 PM
 To: Jeff Rush
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] Unable to Style RESULTS Blocks
 
  Using org-babel, I cannot figure out how to make the export of the
  results of execution appear in LaTeX as a shaded box, like I see on so
  many of the org-mode websites.
 
  #+name: example
  #+BEGIN_SRC python -n :results output :exports both
print Hello World
  #+END_SRC
 
  #+results: example
  : Hello World
 
  The results are exported as:
 
  \begin{verbatim}
   Hello World
  \end{verbatim}
 
  which lacks any shading/borders.  The org-mode documentation at:
 
http://orgmode.org/worg/org-tutorials/org-latex-export.html
 
  shows this example but the example expects the results to be wrapped in
  a 'results' environment instead of the 'verbatim' environment I'm
seeing.
 
  #+LaTeX_HEADER: \usepackage{framed}
  #+LaTeX_HEADER: \usepackage{xcolor}
  #+LaTeX_HEADER: \definecolor{shadecolor}{gray}{.95}
  #+LaTeX_HEADER: \newenvironment{results}{\begin{shaded}}{\end{shaded}}
 
  I'm running org-mode 7.8.03 under Linux, and I've defined my own LaTeX
  document class to format the other parts of my document.  I am new to
  LaTeX though.  I just expected the formatting of source and results to
  be a well-solved problem w/good looking defaults in org-mode.
 
  -Jeff
 
 You can wrap a results block any way you like with the :wrap header
 argument, e.g.,
 
 #+name: example
 #+BEGIN_SRC python -n :results output :exports both :wrap results
   print Hello World
 #+END_SRC
 
 #+RESULTS: example
 #+BEGIN_results
 Hello World
 #+END_results
 
 Or,
 
 #+name: example
 #+BEGIN_SRC python -n :results output :exports both :wrap foo
   print Hello World
 #+END_SRC
 
 #+RESULTS: example
 #+BEGIN_foo
 Hello World
 #+END_foo
 
 If you have loaded org-special-blocks, then
 
 #+LaTeX_HEADER: \usepackage{framed}
 #+LaTeX_HEADER: \usepackage{xcolor}
 #+LaTeX_HEADER: \definecolor{shadecolor}{gray}{.95}
 #+LaTeX_HEADER: \newenvironment{results}{\begin{shaded}}{\end{shaded}}
 #+LaTeX_HEADER: \newenvironment{foo}{\begin{framed}}{\end{framed}}

Or even better, use LaTeX package minted [1]. Install all the stuff
including pigments and add to you dot emacs the following

(setq org-export-latex-listings 'minted)

[1] http://code.google.com/p/minted/

Re: [O] How to get to work non-interactive publishing?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Eric Schulte
 Sent: Saturday, May 19, 2012 5:39 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] How to get to work non-interactive publishing?
 
  I can publish project if I don’t use –-batch . So the following works
  just fine: emacs -nw --eval '(org-publish-project myproj)'
 
  However nothing happens if I try emacs --batch --eval '(org-publish-
 project myproj)'
 ...
  Using batch mode shouldn't be causing any problems with the export
  process, is it possible that something in your personal config is not
  compatible with batch-mode
 ...
  I really did not want to create a separate init file as I was quite
  happy with existing dot emacs. You are right. Something was in the way.
  After I created a separate file that loads only necessary stuff, it
  published fine.
 
 
 Happy it works, if you find the offending element of your persona
 configuration you could remove it and continue to use your personal
 config for batch publishing.
 
  So weird emacs did not give any error before that something is not
  quite right. Is there an option for emacs so that some module can say
  it can't work in a batch mode?
 
 
 I don't believe that there is an automated way to raise such warnings.
 You could do a binary search through your init.

Part of my question was if there is an easy way to find it other than by 
dichotomy? I guess not :-)

  I mean what is the point to make a separate init file other than
  speed?
 
 
 Your main init file is used to customize Emacs for interactive editing,
 many (if not most) of these settings won't apply to batch evaluation.
 
 By separating your personal customization from the project init file
 used for publishing it becomes possible to distribute your project with
 the publication init file without sharing your personal configuration.

That makes it clear.

Another weird issue I experience when batch-publishing is that even with a 
separate init file, I get different htmlization of babel blocks. I mean if I 
load

emacs -nw -Q -l myinit.el project_part.org

and publish that with C-c C-e P , then I get nicely colored babel block in HTML 
starting like

pre class=src src-R  span style=color: #cd00cd;library/span(RODBC)

However, if I do

emacs -Q --batch -l myinit.el -f 'org-publish-all'

then I get something like

pre class=src src-Rspan style=font-weight: bold; text-decoration: 
underline;library/span(RODBC)

It seems odd to me that same config results in different outputs when 
publishing interactively and in a batch mode. I would prefer colored output.

What should I pay attention to? I have a feeling that something is not loaded 
which does in interactive mode, or vice versa.

Mikhail

Re: [O] How to get to work non-interactive publishing?

[Mikhail Titov]

 -Original Message-
 From: Eric Schulte [mailto:eric.schu...@gmx.com]
 Sent: Monday, May 21, 2012 1:11 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] How to get to work non-interactive publishing?
 
 ...

  Another weird issue I experience when batch-publishing is that even
  with a separate init file, I get different htmlization of babel
  blocks. I mean if I load
 
  emacs -nw -Q -l myinit.el project_part.org
 
  and publish that with C-c C-e P , then I get nicely colored babel block in
 HTML starting like
 
  pre class=src src-R  span style=color: #cd00cd;library/span(RODBC)
 
  However, if I do
 
  emacs -Q --batch -l myinit.el -f 'org-publish-all'
 
  then I get something like
 
  pre class=src src-Rspan style=font-weight: bold; text-decoration:
 underline;library/span(RODBC)
 
  It seems odd to me that same config results in different outputs when
  publishing interactively and in a batch mode. I would prefer colored
  output.
 
  What should I pay attention to? I have a feeling that something is not
 loaded which does in interactive mode, or vice versa.
 
 
 The library used to colorize source code relies on the actual Emacs
 colorization mechanisms, which aren't available in batch mode.  The best
 solution in this case is to save your colorized CSS information into a
 .css file with `org-export-htmlize-generate-css', and then use that file
 in all of your exports by setting `org-export-htmlize-output-type' to
 'css.  This way your fontification will be consistent across batch or
 regular export.

Thank you for the explanation!

Also I just noticed [1]. For now, I can just use -nw and (kill-emacs) after 
publishing is done and deal with CSS fine tuning later.

[1] http://stackoverflow.com/questions/3591337/emacs-htmlize-in-batch-mode

M.

Re: [O] How to get to work non-interactive publishing?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Monday, May 21, 2012 4:06 PM
 To: 'Eric Schulte'
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] How to get to work non-interactive publishing?
 
 ...

  The library used to colorize source code relies on the actual Emacs
  colorization mechanisms, which aren't available in batch mode.  The best
  solution in this case is to save your colorized CSS information into a
  .css file with `org-export-htmlize-generate-css', and then use that file
  in all of your exports by setting `org-export-htmlize-output-type' to
  'css.  This way your fontification will be consistent across batch or
  regular export.
 
 Thank you for the explanation!
 
 Also I just noticed [1]. For now, I can just use -nw and (kill-emacs) after
 publishing is done and deal with CSS fine tuning later.

Did not read careful enough about crontab. I'll go CSS way.

 
 [1] http://stackoverflow.com/questions/3591337/emacs-htmlize-in-batch-mode
 
 M.
 

Re: [O] Unable to Style RESULTS Blocks

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Thomas S. Dye
 Sent: Monday, May 21, 2012 4:40 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org; 'Jeff Rush'
 Subject: Re: [O] Unable to Style RESULTS Blocks
 
 
  Or even better, use LaTeX package minted [1]. Install all the stuff
  including pigments and add to you dot emacs the following
 
  (setq org-export-latex-listings 'minted)
 
  [1] http://code.google.com/p/minted/
 
 In my experience, minted marks up exported source code blocks.  I
 haven't seen it do the same for results blocks, but would be interested
 to learn if this is possible and how to make it work.

My apologies. After reading your reply, I've realized that I misread the
question. I thought it was about the background in block source export
result.

M.

Re: [O] How to get to work non-interactive publishing?

[Mikhail Titov]

On 05/18/2012 07:19 AM, Eric Schulte wrote:
 I can publish project if I don’t use –-batch . So the following works
 just fine: emacs -nw --eval '(org-publish-project myproj)'

 However nothing happens if I try emacs --batch --eval '(org-publish-project 
 myproj)'

 Does anybody have an idea how to pin point the problem? It just
 returns almost instantaneously with no output to stderr.

 I do use ESS, and I have lots of R code some of which is intentionally
 non-cached. I’m running GNU Emacs 24.1.50.2 (revno: 108254) with
 default orgmode if it makes any difference.
 Using batch mode shouldn't be causing any problems with the export
 process, is it possible that something in your personal config is not
 compatible with batch-mode?  I have a number of projects in which I
 export using a batch Emacs process (generally from a make file).  My
 Makefile rules tend to look like the following.

 EMACS=emacs
 BATCH_EMACS=$(EMACS) --batch -Q -l init.el document.org

 ...

 document.tex: document.org init.el
 $(BATCH_EMACS) -f org-export-as-latex

 where init.el contains all of the init necessary for the particular
 project.  For a complete working example see the replication materials
 at http://www.jstatsoft.org/v46/i03.
I really did not want to create a separate init file as I was quite
happy with existing dot emacs. You are right. Something was in the way.
After I created a separate file that loads only necessary stuff, it
published fine.

So weird emacs did not give any error before that something is not quite
right. Is there an option for emacs so that some module can say it can't
work in a batch mode?

I mean what is the point to make a separate init file other than speed?

M.

Re: [O] [babel] java headless support is missing for most graphing languages

[Mikhail Titov]

On 05/19/2012 02:51 AM, Bastien wrote:
 I’ve noticed that at least ditaa and plantuml fail to evaluate with
 babel.
 What version of Org are you using?
Hello, Bastien!

It is 7.8.09 from default emacs 24.1.50.2 (revno: 108254). I have no X11
server running.

M.

Re: [O] [babel] java headless support is missing for most graphing languages

[Mikhail Titov]

On 05/19/2012 05:41 PM, Eric Schulte wrote:
 I’ve noticed that at least ditaa and plantuml fail to evaluate with
 babel.
 What version of Org are you using?
 Hello, Bastien!

 It is 7.8.09 from default emacs 24.1.50.2 (revno: 108254). I have no X11
 server running.

 If I understand correctly you were able to execute successfully after
 adjusting your ditaa header arguments.  Is that correct?
Hi Eric!

Yes, it works for ditaa. However I was unable to do that for plantuml as
it does not respect :java alist (?) element in a similar fashion. I had
to edit ob-plantuml.el for that as it has hardcoded java -jar so no
way to insert anything in-between.
 If so then I believe ob-ditaa should be left as is, given that it works
 for most cases out of the box, and that you were able to easily adjust
 it to work without an X server.
I am confident that for all folks working with orgmode remotely using,
let's say, SSH connection without X11 tunneling, blocks calling such
java tools will fail. So I'd call it a bug. Either there should be a way
to supply :java to other similar languages, or headless option should
be set by default.

M.

Re: [O] [babel] java headless support is missing for most graphing languages

[Mikhail Titov]

On 05/19/2012 07:39 PM, Eric Schulte wrote:
 I am confident that for all folks working with orgmode remotely using,
 let's say, SSH connection without X11 tunneling, blocks calling such
 java tools will fail. So I'd call it a bug. Either there should be a way
 to supply :java to other similar languages, or headless option should
 be set by default.

 I just added a :java option to plantuml which may be used in the same
 manner as the :java option for ditaa.  I'm not sure which other
 languages would benefit from such an option, but I agree that each java
 language should provide a way to pass command line options to the java
 executable.
Thank you! I quickly checked, indeed it is only ob-java, ob-ditaa, and
ob-plantuml  that use java. plantuml was the only one that missed java
command line options.

Nevertheless I'd say it won't hurt to have headless option set by
default. I don't insist :-)

M.

[O] [babel] java headless support is missing for most graphing languages

[Mikhail Titov]

Hello!

I’ve noticed that at least ditaa and plantuml fail to evaluate with babel.

While for ditaa I can override :java list item with something like

(setq org-babel-default-header-args:ditaa
  '((:results . file)
(:exports . results)
(:java . -Dfile.encoding=UTF-8 -Djava.awt.headless=true)))

However plantuml is handling differently. Curiously enough it runs just fine 
without stdin/stdout redirection from the command line. However if I tried to 
use input/output redirection like in ob-plantuml.el , it complains like the 
following:  Exception in thread main java.lang.InternalError: Can't connect 
to window server - not enough permissions.

I propose to add by default “-Djava.awt.headless=true” to all “language” 
handlers supported by org-babel. I think it won’t hurt and will make working 
from CLI more enjoyable out of box.

Mikhail

[O] How to get to work non-interactive publishing?

[Mikhail Titov]

Hello!

I can publish project if I don’t use –-batch . So the following works just 
fine:emacs -nw --eval '(org-publish-project myproj)'

However nothing happens if I try emacs --batch --eval '(org-publish-project 
myproj)'

Does anybody have an idea how to pin point the problem? It just returns almost 
instantaneously with no output to stderr.

I do use ESS, and I have lots of R code some of which is intentionally 
non-cached. I’m running GNU Emacs 24.1.50.2 (revno: 108254) with default 
orgmode if it makes any difference.

Thank you,
Mikhail

Re: [O] [beamer] What is the easiest way to inject latex code between block environments?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Tuesday, April 17, 2012 11:46 PM
 To: John Hendy
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] [beamer] What is the easiest way to inject latex code
between
 block environments?
 
  I would like to explicitly define heights for columns that contain
blocks
 to be able to use \vfill [1] in-between blocks. And here comes the
problem. I
 kind of need to inject

Here is the dirty hack if someone else is also making posters with orgmode 
beamerposter.
Unfortunately I know AWK better than elisp so don't condemn me :-) It does a
perfect job for me. I don't know if can be hooked to pipe through before
writing TeX output.

8--
---8-
#!/usr/bin/awk -f
# Post-process orgmode output before final call to pdflatex while using
beamerposter

BEGIN {
end_block = 0   # 1 if previous line was \end{block}
columns = 0 # 1 if probably \vbox will be needed, 2 if
it is needed
RS = \r\n # I'm on Windows
height = .98\\textheight   # FIXME
}

/^\\frametitle{.+}$/ { next}# frametitle removal from the only frame

/^\\begin{columns}/ { columns = 1 }
/^\\begin{column}/  columns { columns = 2 }

/^%% .+/  columns == 2 { print \\vbox to  height  {%; columns = 0 } #
we rely on orgmode comments :(

/^\\end{block}$/ { end_block = 1 }

/^\\begin{block}/  end_block { print \\vfill; end_block = 0 }

/^\\end{column}$/  end_block { print }%; columns = 1; end_block = 0 }

{ print }
8--
---8-

Mikhail

[O] [beamer] What is the easiest way to inject latex code between block environments?

[Mikhail Titov]

Hello!

I would like to explicitly define heights for columns that contain blocks to be 
able to use \vfill [1] in-between blocks. And here comes the problem. I kind of 
need to inject

#+latex: \vfill

before new block

** block2

but after \end{block} was emitted, not before. Is there an easy way to approach 
that?

[1] 
http://tex.stackexchange.com/questions/15244/why-does-vfill-not-work-inside-a-beamer-column

Mikhail

Re: [O] [beamer] What is the easiest way to inject latex code between block environments?

[Mikhail Titov]

On Apr 17, 2012, at 8:23 PM, John Hendy jw.he...@gmail.com wrote:

 On Tue, Apr 17, 2012 at 8:19 PM, John Hendy jw.he...@gmail.com wrote:
 On Tue, Apr 17, 2012 at 8:08 PM, Mikhail Titov m...@gmx.us wrote:
 Hello!
 
 I would like to explicitly define heights for columns that contain blocks 
 to be able to use \vfill [1] in-between blocks. And here comes the problem. 
 I kind of need to inject
 
 #+latex: \vfill
 
 before new block
 
 ** block2
 
 but after \end{block} was emitted, not before. Is there an easy way to 
 approach that?
 
 Everything in org-mode gets treated as belonging to the parent
 headline. I don't think there's an easy way to do this except by
 tweaking the .tex file after export and re-compiling via LaTeX
 directly.

That is how I'm proceeding now as I don't have time to hack now:(

 I could be wrong, but I believe it's the same principle as why the
 answer to these questions is No:
 -- http://orgmode.org/worg/org-faq.html#closing-outline-sections

I wonder if a special case can be made via some extra property and some changes 
to orgmode code (or with hooks?). It should be possible as I need just quite 
specific command and not arbitrary text embedded. 

 In other words... everything is always in some headline and what
 you're trying to do is escape a headline to enter text in kind of a
 no man's land. Sorry to say, I don't think it's possible.
 
 
 Actually, I was picturing doing this in between /frames/, not blocks.

That is how beamerposter is organized. 

 Since you're in a frame, you can just write the LaTeX syntax directly
 inside of your frame headline?

I was trying to escape to orgmode from plain latex not to return that far back 
;)

M

[O] [latex, beamerposter] Muticolumn poster with multicolumn blocks or BMCOL and B_columns coexistance, is it possible?

[Mikhail Titov]

All:

I realized I have a need for 2 columns in a block. However when I tried to use 
B_columns and B_column besides BMCOL that were alreasy in there, it failed to 
generate proper LaTeX source. Below is the trimmed down example that fails to 
work properly on 7.8.09 . Do I miss something?

#-*- buffer-file-coding-system: utf-8; TeX-master: t -*-
#+Title: Test for multicolumn blocks in multicolumn poster
#+LaTeX_CLASS: beamer
#LaTeX_CLASS_OPTIONS: [presentation]
#+BEAMER_FRAME_LEVEL: 1
#+STARTUP: beamer

#BEAMER_HEADER_EXTRA: \usetheme{I6dv} %mlt}
#\usecolortheme{default}
#+COLUMNS: %45ITEM %10BEAMER_env(Env) %10BEAMER_envargs(Env Args) 
%4BEAMER_col(Col) %8BEAMER_extra(Extra)
#+PROPERTY: BEAMER_col_ALL 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 :ETC
#+OPTIONS: toc:nil

#+latex_header: 
\usepackage[orientation=landscape,size=custom,width=182.88,height=101.6,scale=1.5]{beamerposter}

#+LATEX_HEADER: \renewcommand\maketitle{}
# http://blog.zindel.org/?p=99
#+latex_header: \def\newblock{\hskip .11em plus .33em minus .07em}


# C-c C-x C-c for column view
* Poster

** Left   :BMCOL:B_ignoreheading:
   :PROPERTIES:
   :BEAMER_col: 0.32
   :BEAMER_env: ignoreheading
   :END:

*** 1 Left  :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:

 Columns  :B_columns:
 :PROPERTIES:
 :BEAMER_env: columns
 :END:
* .5   :B_column:
  :PROPERTIES:
  :BEAMER_env: column
  :END:
- intro left. Comment stuff above till including Columns to make it compilable
* .4   :B_column:
  :PROPERTIES:
  :BEAMER_env: column
  :END:
- intro right. Comment stuff above.

** Center :BMCOL:B_ignoreheading:
   :PROPERTIES:
   :BEAMER_col: 0.32
   :BEAMER_env: ignoreheading
   :END:

*** 2 Center:B_block:
:PROPERTIES:
:BEAMER_env: block
:END:

- Central block

** Right  :BMCOL:B_ignoreheading:
   :PROPERTIES:
   :BEAMER_col: 0.32
   :BEAMER_env: ignoreheading
   :END:

*** 3 right block   :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:

- hello

Mikhail

Re: [O] [beamerposter] How do I suppress frame title?

[Mikhail Titov]

On 04/13/2012 12:04 AM, Bastien wrote:
 I’m trying to use orgmode with beamerposter LaTeX package [1] to make a
 poster. I’ve managed to remove toc and override \maketitle . However I
 can’t seem to find a way to suppress a title from the only high level
 section * Poster. I've tried to add :B_ignoreheading: via C-c C-b i
 with no success :(
 Unless I missed something, there is no option to suppress this frame
 title, sorry.

I just found a quick workaround - to use *  that is asterisk followed
by a space. It still generates frame but does not insert any title. I
feel like it might be even a bug. But it works since it is the only
frame I have.

I was trying to wrap frametitle ( subtitle) generation in org-beamer.el
into conditional like below but I failed miserably at it.

  (if (not (equal (cdr (assoc BEAMER_env props))
ignoreheading))
  (progn
  (cons T (if (string-match \\S- text)
\n\\frametitle{%s} ))
  (cons S (if (string-match  text)
\n\\framesubtitle{%s} ))
))

M.

Re: [O] [beamerposter] How do I suppress frame title?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of suvayu ali
 Sent: Friday, April 13, 2012 3:52 AM
 To: Mikhail Titov
 Cc: Bastien; emacs-orgmode@gnu.org
 Subject: Re: [O] [beamerposter] How do I suppress frame title?
 
  I just found a quick workaround - to use *  that is asterisk followed
  by a space. It still generates frame but does not insert any title. I
  feel like it might be even a bug. But it works since it is the only
  frame I have.
 
  I was trying to wrap frametitle ( subtitle) generation in org-beamer.el
  into conditional like below but I failed miserably at it.
 
   (if (not (equal (cdr (assoc BEAMER_env props))
  ignoreheading))
   (progn
   (cons T (if (string-match \\S- text)
 \n\\frametitle{%s} ))
   (cons S (if (string-match  text)
 \n\\framesubtitle{%s} ))
 ))
 
 Your solution works, and I have used it before to get a backup slide
 marker saying just bakup slides in the centre before.

Do you mean former or latter one? When I try to change org-beamer.el as 
described above, I get Invalid format operation %a since I do something badly 
wrong. I was trying to mess with this [1] code. I don't know elisp well enough. 
I guess I can't do it that way.

[1] 
http://orgmode.org/w/?p=org-mode.git;a=blob;f=lisp/org-beamer.el;h=966db82debdf21bad0777372c06bc7cb84735cfb;hb=HEAD#l274

 But I think
 there can be a cleaner solution with pre/post-process hooks. For an
 example of such a hook with LaTeX export, see:
 
 https://github.com/suvayu/.emacs.d/blob/master/org-mode-config.el#L234
 
 Here I ignore headings for bibiliographies and appendices.

I am afraid I don't quite follow your code. I think you deal with plain latex 
export while mine question deals with some beamer details.

M.

[O] [beamerposter] How do I suppress frame title?

[Mikhail Titov]

Hello!

I’m trying to use orgmode with beamerposter LaTeX package [1] to make a poster. 
I’ve managed to remove toc and override \maketitle . However I can’t seem to 
find a way to suppress a title from the only high level section * Poster. 
I've tried to add :B_ignoreheading: via C-c C-b i with no success :(

Is it possible? It is not a big deal just to remove frametitle from the final 
version but nevertheless.

[1] http://www-i6.informatik.rwth-aachen.de/~dreuw/latexbeamerposter.php

Mikhail

Re: [O] Links to Gnus articles don't export correctly

[Mikhail Titov]

Jason:

I just noticed that behavior. Take a look at
[[http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17-2-2][latex
export tutorial]]. Just override defaults from org-gnus.el

#+begin_src lisp
(org-add-link-type gnus 'org-gnus-open)
#+end_src

-- 
Mikhail

Re: [O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

 -Original Message-
 From: Bernt Hansen [mailto:be...@norang.ca]
 Sent: Thursday, December 15, 2011 5:00 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] Export all clocks or find last clock out. Is it possible?
 
  I'm not sure what happened, but now I see only Log mode is on  Log
  mode is off when I press `v c` in agenda :( Any ideas what is messed
  up?
 
 Is your agenda limited by tags or a restriction that has no log data?

Just to let you know. Somehow I got wrong org-agenda-files (Saving emacs
config does that?). Everything is working as expected after I removed
corresponding line from dot emacs as I have proper one included from my
customizations in myorg.el loaded earlier.

Thanks again!
M.

Re: [O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

 -Original Message-
 From: emacs-orgmode-bounces+mlt=gmx...@gnu.org [mailto:emacs-orgmode-
 bounces+mlt=gmx...@gnu.org] On Behalf Of Mikhail Titov
 Sent: Sunday, December 11, 2011 5:20 PM
 To: Bernt Hansen
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] Export all clocks or find last clock out. Is it possible?
 
  You can view your clocked items in the agenda
 
 agenda view
/ show week view
   / / validate clocks
  / / /
 / / /\
  C-c a a w v c
 Thanks a lot! I was able to rebuild agenda for the year and check
 clocks! Perhaps I missed details on agenda commands while I was reading
 manual. Just `v c` is what I was missing.

I'm not sure what happened, but now I see only Log mode is on  Log mode is 
off when I press `v c` in agenda :( Any ideas what is messed up?

M.

Re: [O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

On 12/11/2011 07:05 AM, Olaf Dietsche wrote:
 As already suggested by Puneeth `org-clock-goto' (with prefix: C-u C-c
 C-x C-j) lists the most recently used clocks and C-u C-c C-x C-j 1 jumps
 to the last clocked task.
For some reason it also shows empty Recent Tasks list :(
 `org-clock-history-length' sets the number of tasks shown.

 (custom-set-variables
  '(org-clock-history-length 28))
I evaluated this expression. But it does not make any difference.
 Besides the org manual, Bernt Hansen has an excellent website
 http://doc.norang.ca/org-mode.html covering his workflow with orgmode.
 Look out for `org-clock-goto' in 1.5 Key Bindings and 15.19 Speed
 commands.
I do have some of Bernt's commands in my dot emacs. As I said, while I'm
working on a file, everything is nice: I can jump to most recent task
with F11 even when it is clocked out. But not when I open an old file.

Also I do have the following in dot emacs

(setq org-clock-persist 'history)
 (org-clock-persistence-insinuate)


But I feel like it is only for most recent file that has no clock out yet.

I'm not consistent with org-mode and I use it for only one project for
timing so far :( Most of the time I spend outside of emacs and I simply
forget to clock a task or even start emacs sometimes. I feel like I'm on
my own if I don't follow org-mode rules all the time and I want to back
fill things I've done in the past.

Mikhail

Re: [O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

On 12/11/2011 04:25 PM, Bernt Hansen wrote:
 Mikhail Titov m...@gmx.us writes:

 Also how can I navigate to the last clock out?

 I know I can do some exercise with awk or perl, but perhaps there should
 be a better solution. I tried to google but I can't find anything :(
 I know I can do some exercise with awk or perl, but perhaps there should
 be a better solution. I tried to google but I can't find anything :(
 You can view your clocked items in the agenda

agenda view
   / show week view
  / / validate clocks
 / / /
/ / /\
 C-c a a w v c
Thanks a lot! I was able to rebuild agenda for the year and check
clocks! Perhaps I missed details on agenda commands while I was reading
manual. Just `v c` is what I was missing.

Can I see somehow see an agenda for previous month after I pressed `v
m`? I had to switch to year view in my case.

Mikhail

[O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

Hello!

I wonder if I can see all clocks in a table or export them somehow as
csv or alike?

Also how can I navigate to the last clock out?

I know I can do some exercise with awk or perl, but perhaps there should
be a better solution. I tried to google but I can't find anything :(

--
Mikhail

Re: [O] Export all clocks or find last clock out. Is it possible?

[Mikhail Titov]

On 12/11/2011 01:10 AM, Puneeth Chaganti wrote:
 On 12/11/11, Mikhail Titov m...@gmx.us wrote:
 Hello!

 I wonder if I can see all clocks in a table or export them somehow as
 csv or alike?
 Look at `org-clock-report' function [
 http://orgmode.org/manual/The-clock-table.html ]
This does not show all clocks. I've tried clock table with :timestamp.
It shows task time and deadlines and alike but not all clock-in 
clock-out for a task.
 Also how can I navigate to the last clock out?
 `org-clock-goto' function can do this for you.

 Use `M-x org-clock-goto' (By default, it is bound to C-c C-x C-j)
This results in No active or recent clock task. Generally it works
find while I'm working on document. But if I open old document, it does
not work for some reason :(

I've tried both your suggestions before and that is why I'm asking here
in the list.

M.

Re: [O] Regression: Empty TODO lines

[Mikhail Titov]

On 11/13/2011 05:30 AM, Carsten Dominik wrote:
 Hi Nicolas,

 commit dfcb6faef11a2439b56b18a6289803361d402130 (Provide more consistent 
 regexps for headlines)
 makes the global TODO list fail on headlines with a TODO keyword but no text 
 following:

 * TODO This one works
 * TODO
   This one fails (note, there is not even a space after TODO.

 While I agree that a TODO line with not text is not good, I think
 it should not break the TODO list view.  I am attaching the backtrace.

I have a related question. How do I escape TODO? I mean if I want to
have a beamer frame named this way, how can I do that? Last time I ended
up writing

** ToDo

Mikhail

Re: [O] How to reuse page keywords for LaTeX with pdfkeywords and hyperref package?

[Mikhail Titov]

Bastien bzg at altern.org writes:
 Hi Mikhail,
 
 Mikhail Titov mlt at gmx.us writes:
 
  In case someone else also wants page keywords to appear in latex export.
  Here is the link to original thread
  http://lists.gnu.org/archive/html/emacs-orgmode/2011-03/msg01429.html .
  There is a patch at the bottom that does that. It assumes that hyperred
  package is used and doesn't check that!
 
 Yes, hyperref is in ̀org-export-latex-default-packages-alist' and is
 available.
 
  I'm not sure if I'm doing it right as I don't know lisp and emacs
  much.
 
 I pushed a commit with a slightly adapted version of your patch.
 
 Please check it does the right thing for you.

Yes! It does exactly what I've wanted and even adds application name to PDF.
Sweet!

 Further improvements in this area: have a defcustom allowing the user 
 to select what hyperref options he wants in the .tex output.  Maybe you
 can improve your ELisp trying to provide a patch for this?   

I'm afraid I don't get it.
I can see org-export-latex-hyperref-format in org-latex.el .
Isn't it already in there?

Mikhail

Re: [O] babel, beamer: Prevent apostrophe/single quote mangling, so examples can be reused from PDF

[Mikhail Titov]

 -Original Message-
 From: Eric Schulte [mailto:schulte.e...@gmail.com]
 Sent: Friday, November 11, 2011 8:21 PM
 To: Mikhail Titov
 Cc: emacs-orgmode@gnu.org
 Subject: Re: [O] babel, beamer: Prevent apostrophe/single quote mangling,
 so examples can be reused from PDF
 
 I have seen a similar issue in which code *executed* by R returns weird
 nasty quotes.  The following works for me to remove these quotes before
 the confuse TeX.
 
 ;; Replace nasty single-quotes returned by R.
 (add-hook 'org-export-latex-final-hook
   (lambda () (replace-regexp ’ ')))
 
 Hope this helps -- Eric

Probably it was another issue. I've double checked in another text editor that 
I'm getting correct apostrophes in tex output. I tried with or without your 
code in dot emacs (I restarted emacs). It is something in LaTeX or some package 
that triggers it:(

I've came across this 
http://www.cs.sfu.ca/~ggbaker/reference/characters/#single . It says that for 
typewriter font LaTeX won't substitute apostrophe with closing single quote. 
However I thought that verbatim as produced by babel implies typewriter font.

Mikhail

[O] Is LaTeX pdf export that uses pgfSweave possible?

[Mikhail Titov]

Hello!

First of all I’m not good at lisp as of now. I’d like to have an extra export 
option when I press C-c C-e that would create dotRnw file instead of 
dottex, pass it through pgfSweave in running R session.

I have the following to use pgfSweave in R session:

---8---8---
 
(defun ess-swv-pgfweave ()
   Run pgfSweave on the current .Rnw file.
   (interactive)
   (ess-execute library(pgfSweave))
   (ess-swv-run-in-R pgfSweave))

(define-key noweb-minor-mode-map \M-ns 'ess-swv-pgfweave)

(easy-menu-add-item noweb-minor-mode-menu '(Sweaving, Tangling, ...) 
[pgfSweave ess-swv-pgfweave t])
---8---8---

So I thought I'd somehow hook up altogether as I like an idea of folding things 
while make Beamer slides, but same time I like neatness of pgfSweave...

I don't know if there might be problems passing through constructs like

stuff=
stuff
@

untouched into dotRnw file.

I'm aware of babel for R but I can't use LaTeX in plots with it :(

Mikhail

Re: [O] Table alignment

[Mikhail Titov]

   1. Rename .emacs to renamed.el
   2. Start vanilla emacs
   3. Open your renamed.el file
   4. Select region of intereset
   5. Evaluate region with M-x eval-region
   6. See if it is still working
   7. Go to 4


On 08/31/2011 12:46 AM, Vikas Rawal wrote:
 There is something in my .emacs that messes up table alignment in
 org. Have been struggling to find it. If I remove my .emacs, table
 alignment is fine. I have tried commenting parts of .emacs to identify
 the offending lines. But somehow I am missing it.

 A copy of my .emacs is at: http://dl.dropbox.com/u/10112644/dotemacs

 Will be grateful if somebody could help? Is there a way I can load my
 .emacs segment by segment and see when the problem appears?

 Vikas

Re: [O] How to reuse page keywords for LaTeX with pdfkeywords and hyperref package?

[Mikhail Titov]

In case someone else also wants page keywords to appear in latex export.
Here is the link to original thread
http://lists.gnu.org/archive/html/emacs-orgmode/2011-03/msg01429.html .
There is a patch at the bottom that does that. It assumes that hyperred
package is used and doesn't check that!
I'm not sure if I'm doing it right as I don't know lisp and emacs much.

Mikhail

From ee027f75db3df6b16ccb2e8f96916fe7274655f3 Mon Sep 17 00:00:00 2001
From: Mikhail Titov m...@gmx.us
Date: Sat, 27 Aug 2011 11:59:06 -0500
Subject: [PATCH] Set keywords and subject fields in pdf

---
 lisp/org-latex.el |   13 +
 1 files changed, 13 insertions(+), 0 deletions(-)

diff --git a/lisp/org-latex.el b/lisp/org-latex.el
index 17626b5..4c35528 100644
--- a/lisp/org-latex.el
+++ b/lisp/org-latex.el
@@ -1391,6 +1391,10 @@ OPT-PLIST is the options plist for current buffer.
   (let ((toc (plist-get opt-plist :table-of-contents))
 (author (org-export-apply-macros-in-string
  (plist-get opt-plist :author)))
+(description (org-export-apply-macros-in-string
+ (plist-get opt-plist :description)))
+(keywords (org-export-apply-macros-in-string
+ (plist-get opt-plist :keywords)))
 (email (replace-regexp-in-string
 _ _
 (org-export-apply-macros-in-string
@@ -1428,6 +1432,15 @@ OPT-PLIST is the options plist for current buffer.
  (format-time-string
   (or (plist-get opt-plist :date)
   org-export-latex-date-format)))
+ ;; add pdf things
+ \\hypersetup{\n
+ ;;  pdfinfo={\n   
+ (format   pdfkeywords={%s},\n
+ (org-export-latex-fontify-headline keywords))
+ (format   pdfsubject={%s}\n
+ (org-export-latex-fontify-headline description))
+ ;; }\n
+ }\n
  ;; beginning of the document
  \n\\begin{document}\n\n
  ;; insert the title command
-- 
1.7.4.1

RE: [O] How to reuse page keywords for LaTeX with pdfkeywords and hyperref package?

[Mikhail Titov]

Bastien:

Thank you! I understand that it is not possible right now through simple 
settings. However hyperref is getting added to packages alist at some point. Is 
there a way to dereference org-export-page-keywords let's say in my custom 
LaTeX class definition in my dot emacs file or even in source code. Or is the 
problem in that that variable is not defined that time?

Mikhail

-Original Message-
From: Bastien Guerry [mailto:bastiengue...@googlemail.com] On Behalf Of Bastien
Sent: Tuesday, March 22, 2011 4:54 AM
To: Mikhail Titov
Cc: 'Org mailing list'
Subject: Re: [O] How to reuse page keywords for LaTeX with pdfkeywords and 
hyperref package?

Hi Mikhail,

Mikhail Titov m...@gmx.us writes:

 I would like to be able to have same keywords for both HTML and PDF 
 output. I was a bit surprised that it is not there yet. I’m not a lisp 
 user:( Could someone suggest what needs to be done to use 
 org-export-page-keywords to set the value of pdfkeywords option of 
 hyperref LaTeX package?

This is not possible right now.  You can do it manually by removing hyperref 
from the `org-export-latex-default-packages-alist' variable, and by adding such 
a header in your org file:

#+LATEX_HEADER: \usepackage[dvips, bookmarks, colorlinks=false,
   pdftitle={An example PDF file from LaTeX}, pdfauthor={Diego Santa
   Cruz}, pdfsubject={From LaTeX to PDF}, pdfkeywords={PDF, LaTeX,
hyperlinks, hyperref}]{hyperref} 

But your request makes sense, I might implement it someday.

Best,

--
 Bastien

[O] How to reuse page keywords for LaTeX with pdfkeywords and hyperref package?

[Mikhail Titov]

Hello all!

I would like to be able to have same keywords for both HTML and PDF output. I 
was a bit surprised that it is not there yet. I’m not a lisp user:( Could 
someone suggest what needs to be done to use org-export-page-keywords to set 
the value of pdfkeywords option of hyperref LaTeX package?

Mikhail

RE: [O] broken latex export of footnote from a table cell?

[Mikhail Titov]

Thank you, Nicholas!

That explains everything. I wonder how I didn't come across the link you 
mentioned before. I should have tried that simply in LaTeX.

Mikhail

-Original Message-
From: emacs-orgmode-bounces+mlt=gmx...@gnu.org 
[mailto:emacs-orgmode-bounces+mlt=gmx...@gnu.org] On Behalf Of Nick Dokos
Sent: Saturday, March 12, 2011 1:32 AM
To: Mikhail Titov
Cc: nicholas.do...@hp.com; emacs-orgmode@gnu.org
Subject: Re: [O] broken latex export of footnote from a table cell?

Mikhail Titov m...@gmx.us wrote:

 Hello!
 
 This is my first message. I'm excited about org-mode! Thank you for = 
 developing such a great tool!
 
 However, I found out that I can't have a footnote in a table cell. If 
 I = export such document to LaTeX, I get misplaced footnote:( I'm 
 running MS = Windows XP SP3 32 bit.
 
 -cut-
 #+Title: orgmode to latex epic fail, footnote in a table cell
 
 Works here [fn:: This is a good footnote]. Does it?
 
 #+LATEX: \begin{table}[h]
 | /org-version/ | /emacs-version/ | /Why can't I use bold here with */ 
 | |
 |---+-+|
 |   7.5 |  23.2.1 | some text[fn:: Why am I here?] |
 #+TBLFM: $1=3D'(message org-version)::$2=3D'(message emacs-version)
 #+LATEX: \end{table}
 
 Some text here.
 -cut-
 

Footnotes in tables are difficult. Even if you leave out org completely and 
just look at latex, things are far from simple. There is a FAQ and an answer on 
this topic here:

   http://www.tex.ac.uk/cgi-bin/texfaq2html?label=footintab

As you can see, things are not simple even if you write in latex. None of this 
is implemented in org.

Best advice: don't use footnotes in tables. If you have to use them, add them 
in a post-export pass, possibly by formatting the table outside of org and 
including it from a separate file.

HTH,
Nick

[O] broken latex export of footnote from a table cell?

[Mikhail Titov]

Hello!

This is my first message. I'm excited about org-mode! Thank you for developing 
such a great tool!

However, I found out that I can't have a footnote in a table cell. If I export 
such document to LaTeX, I get misplaced footnote:( I'm running MS Windows XP 
SP3 32 bit.

-cut-
#+Title: orgmode to latex epic fail, footnote in a table cell

Works here [fn:: This is a good footnote]. Does it?

#+LATEX: \begin{table}[h]
| /org-version/ | /emacs-version/ | /Why can't I use bold here with */ |
|---+-+|
|   7.5 |  23.2.1 | some text[fn:: Why am I here?] |
#+TBLFM: $1='(message org-version)::$2='(message emacs-version)
#+LATEX: \end{table}

Some text here.
-cut-

Mikhail