Re: [O] problems with LaTex/BibTex

2012-03-30 Thread suvayu ali
Hey Julian,

On Fri, Mar 30, 2012 at 03:41, Julian Burgos  wrote:
> The "References.bib" is a BibTex file in the same folder as the test file.
>  The citations were entered using RefTex with no problem.  But when
> exporting to pdf, I get the following message in the minibuffer:
> "Exporting to PDF...done, with some errors: [undefined citations]".  The
> pdf produced had, of course, question marks where the citations should be.

Did you customise your org-latex-to-pdf-process to include bibtex? I use
something like this:

(setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode %b"
 "/usr/bin/bibtex %b"
 "pdflatex -interaction nonstopmode %b"
 "pdflatex -interaction nonstopmode %b"))

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] Org Babel C/C++

2012-03-30 Thread Daimrod
Michael Hannon  writes:

> On Wednesday, March 28, 2012 at 4:01 PM Daimrod wrote:
>
>> Eric Schulte  writes:
>>
>>> Applied, Thanks!
>>>
>>> Daimrod  writes:
>>>
 Hi,

 I've made a small patch to ob-C.el so it now includes the current
 directory to the list of directories to be searched for header files.
 Without this, I cannot include a local header file because the
 compilation happens in /tmp and thus gcc or g++ doesn't search for
 header files in the directory I currently work.

 diff --git a/lisp/ob-C.el b/lisp/ob-C.el
 index f1525aa..4f33fc4 100644
 --- a/lisp/ob-C.el
 +++ b/lisp/ob-C.el
 @@ -96,15 +96,14 @@ or `org-babel-execute:C++'."
 (progn
   (with-temp-file tmp-src-file (insert full-body))
   (org-babel-eval
 -    (format "%s -o %s %s %s -I
>> \"%s\""
 +    (format "%s -o %s %s %s"
   (cond
 ((equal org-babel-c-variant 'c)
>> org-babel-C-compiler)
 ((equal org-babel-c-variant 'cpp)
>> org-babel-C++-compiler))
   (org-babel-process-file-name tmp-bin-file)
   (mapconcat 'identity
   (if (listp flags) flags (list flags)) " ")
 -    (org-babel-process-file-name tmp-src-file)
 -    (file-name-directory (expand-file-name
>> (buffer-file-name ""
 +    (org-babel-process-file-name tmp-src-file))
>> ""
   ((lambda (results)
 (org-babel-reassemble-table
   (if (member "vector" (cdr (assoc :result-params
>> params)))
>>
>> Hum, I'm quite embarrassed, this doesn't work when the block is executed
>> during an export. I didn't track it down yet, but (buffer-file-name)
>> returns nil during the export probably because the buffer changes.
>>
>> A workaround would be to use the :flags header argument though it's a
>> bit tedious because it doesn't seem possible to eval elisp during the
>> export.
>>
>> i.e.
>>
>> #+BEGIN_SRC cpp :flags -I (file-name-directory (buffer-file-name))
>> ...
>> #+END_SRC
>>
>
> I ran into this problem a few months ago.  I don't have the elisp skills to
> patch Org mode, but I found something that worked for me:
>
>     http://article.gmane.org/gmane.emacs.orgmode/49356/
>
> -- Mike

This won't work if you use different directories, you'll have to set the
variable org-babel-C++-compiler every time.

IMHO a good solution would be to be able to specify the directory used
to compile, or maybe I should just use a Makefile.




Re: [O] problems with LaTex/BibTex

2012-03-30 Thread Julian Burgos

Yes! That was it.  Thanks!!

On fös 30.mar 2012 08:05, suvayu ali wrote:

Hey Julian,

On Fri, Mar 30, 2012 at 03:41, Julian Burgos  wrote:

The "References.bib" is a BibTex file in the same folder as the test file.
  The citations were entered using RefTex with no problem.  But when
exporting to pdf, I get the following message in the minibuffer:
"Exporting to PDF...done, with some errors: [undefined citations]".  The
pdf produced had, of course, question marks where the citations should be.

Did you customise your org-latex-to-pdf-process to include bibtex? I use
something like this:

(setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode %b"
 "/usr/bin/bibtex %b"
 "pdflatex -interaction nonstopmode %b"
 "pdflatex -interaction nonstopmode %b"))




--
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is




Re: [O] odt-Export and #+CAPTION: [reference text]{caption text}

2012-03-30 Thread Jambunathan K

> It does what I want. 
I have applied my patch to the hotfix branch.

> Unless there is some formatting in the caption.

This is a limitation that we need to live with.  

That said, if you want the short captions in bold, then the right thing
to do would be to apply the style to the index entry and not to
individual captions.  Have you experimented with the styles tab in the
Index creator...I haven't checked it myself though.

> Then you get an invalid content.xml, even if you don't use the new
> feature (ie with a simple '#+CAPTION: a_i').

> minimal example:
>
> #+CAPTION: [*a_i*]{a_i is named =A\_i=}
> #+LABEL: tab:referenced table
> | a | b | c |
> |---+---+---|
> | 1 | 2 | 3 |

If you unzip the file you will see that the short caption goes as an
attribute while long caption goes as body text.

LibreOffice doesn't even allow entering space in the object names.  If
you know of any workarounds that will help "mimic" short captions, I can
add it.



[O] [PATCH] Separate file time from its tasks times

2012-03-30 Thread Sebastien Vauban
2012-03-30  Sebastien Vauban  

* org-clock.el (org-clocktable-write-default): Make the sum
appear visually correct by not mixing the total time per file
and sub-totals.

>From 148cdf141add43798e21925ca852587017f6312a Mon Sep 17 00:00:00 2001
From: Sebastien Vauban 
Date: Fri, 30 Mar 2012 15:07:01 +0200
Subject: [PATCH] Separate file time from its tasks times

---
 lisp/org-clock.el |2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/lisp/org-clock.el b/lisp/org-clock.el
index 7c2c2ab..b7351a7 100644
--- a/lisp/org-clock.el
+++ b/lisp/org-clock.el
@@ -2293,7 +2293,7 @@ from the dynamic block definition."
 properties "|") "|") "")  ;properties columns, maybe
   (if indent (org-clocktable-indent-string level) "") ; indentation
   hlc headline hlc "|"; headline
-  (make-string (min (1- ntcol) (or (- level 1))) ?|)
+  (make-string (min (1- ntcol) (or level)) ?|)
; empty fields for higher levels
   hlc (org-minutes-to-hh:mm-string (nth 3 entry)) hlc ; time
   "|\n"   ; close line
-- 
1.7.9

Best regards,
  Seb

-- 
Sebastien Vauban




[O] [bug] (org-todo-list ) causes exception with sticky agenda buffers.

2012-03-30 Thread Martyn Jago
Hi

I've noticed that if (org-todo-list ) is called programatically where
`org-agenda-sticky' is set to t, an exception is caused:

The exception happens in (org-prepare-agenda ):

--8<---cut here---start->8---
(defun org-prepare-agenda (&optional name)
  (if (org-agenda-use-sticky-p)
  (progn
;; Popup existing buffer
(org-prepare-agenda-window (get-buffer org-agenda-buffer-name))
(message "Sticky Agenda buffer, use `r' to refresh")
(throw 'exit nil))

--8<---cut here---end--->8---

This looks somewhat intentional.
Unfortunately this kills further execution of the calling script.

NOTE: This only appears to happen once the agenda buffer exists (and is buried).

The debug trace follows:

--8<---cut here---start->8---
Debugger entered--Lisp error: (no-catch exit nil)
  throw(exit nil)
  (progn (org-prepare-agenda-window (get-buffer org-agenda-buffer-name)) 
(message "Sticky Agenda buffer, use `r' to refresh") (throw (quote exit) nil))
  (if (org-agenda-use-sticky-p) (progn (org-prepare-agenda-window
  (get-buffer org-agenda-buffer-name)) (message "Sticky Agenda buffer,
  use `r' to refresh") (throw (quote exit) nil)) (setq
  org-todo-keywords-for-agenda nil) ...

--8<---cut here---end--->8---

Calling (org-todo-list ) interactively appears to exhibit the same behavior.

Best, Martyn

---
Org-mode version 7.8.06 (release_7.8.03.594.g013d)
GNU Emacs 24.0.94.1 (x86_64-apple-darwin, NS apple-appkit-1038.36)
 of 2012-02-28 on bob.porkrind.org




Re: [O] [PATCH] Separate file time from its tasks times

2012-03-30 Thread Sebastien Vauban
Hello,

"Sebastien Vauban" wrote:
> 2012-03-30  Sebastien Vauban  
>
>   * org-clock.el (org-clocktable-write-default): Make the sum
>   appear visually correct by not mixing the total time per file
>   and sub-totals.

This can be best understood with an example...

Before:

#+BEGIN: clocktable :maxlevel 4 :scope ("file-abc-tom.org" 
"file-abc-ann.org") :block 2012-02
Clock summary at [2012-03-30 Fri 15:12], for February 2012.

| File | Headline | Time  |   |
|--+--+---+---|
|  | ALL Total time   | 19:15 |   |
|--+--+---+---|
| file-abc-tom.org | File time| 17:15 |   |
|  | Task A   | 17:15 |   |
|  | TODO Subtask A1  |   | 17:15 |
|--+--+---+---|
| file-abc-ann.org | File time| 2:00  |   |
|  | Task B   | 2:00  |   |
|  | TODO Subtask B2  |   |  2:00 |
 #+END:

Now:

#+BEGIN: clocktable :maxlevel 4 :scope ("file-abc-tom.org" 
"file-abc-ann.org") :block 2012-02
Clock summary at [2012-03-30 Fri 15:13], for February 2012.

| File | Headline | Time  |   |   |
|--+--+---+---+---|
|  | ALL Total time   | 19:15 |   |   |
|--+--+---+---+---|
| file-abc-tom.org | File time| 17:15 |   |   |
|  | Task A   |   | 17:15 |   |
|  | TODO Subtask A1  |   |   | 17:15 |
|--+--+---+---+---|
| file-abc-ann.org | File time| 2:00  |   |   |
|  | Task B   |   |  2:00 |   |
|  | TODO Subtask B2  |   |   |  2:00 |
 #+END:

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] odt-Export and #+CAPTION: [reference text]{caption text}

2012-03-30 Thread Martin Gürtler
Hi Jambunathan,

Am Freitag, den 30.03.2012, 18:38 +0530 schrieb Jambunathan K:
> > It does what I want. 
> I have applied my patch to the hotfix branch.
> 
> > Unless there is some formatting in the caption.
> 
> This is a limitation that we need to live with.  

(Unfortunately, this seems to be so for super/subscripts as well.)

I just found out that now the exporter depends on supplying a short
caption, if the caption contains formatting (which also means
subscripts). If you just give it one version (ala #+CAPTION: a_i), and
the caption contains ,say, a subscript, content.xml becomes invalid. It
works only, if you supply it in the form #+CAPTION: []{a_i}. (Probably,
you take the long versionalso for the short one, if only one is
supplied.) I think this should be fixed as it could break existing
documents.

Regards,

Martin




Re: [O] odt-Export and #+CAPTION: [reference text]{caption text}

2012-03-30 Thread Jambunathan K

> I have applied my patch to the hotfix branch.

I am having second thoughts.  I will slightly re-work the patch so it
doesn't bomb the ODT file in unexpected ways.  I will drop a note once I
am done with it.



Re: [O] odt-Export and #+CAPTION: [reference text]{caption text}

2012-03-30 Thread Jambunathan K
Martin Gürtler  writes:

> (Probably,
> you take the long versionalso for the short one, if only one is
> supplied.) I think this should be fixed as it could break existing
> documents.

Our mails crossed and we have arrived at the same conclusion.  Give me
few hours to fix it.



Re: [O] Feature request for noweb mode that strips references on export

2012-03-30 Thread Sean O'Halpin
Hi,

I've tried to use the new :noweb strip-export feature but I can't work
out the magic combination of headers (working with git head, i.e.
commit 67694297fa0f9b32cf4bfe812ba8a5c5cf4a0859).

Here is a stripped down example:

START OF EXAMPLE

* Example

Define method

#+name: boilerplate
#+begin_src ruby
def hello
  "Hello World"
end
#+end_src

Use it

#+name: example
#+begin_src ruby :exports both :noweb strip-export
«boilerplate»

hello
#+end_src

And here is the result:

#+RESULTS: example
: Hello World

END OF EXAMPLE

On export, I expect this to display the result string "Hello World"
after the code "hello" but get nothing. If I change the :noweb
strip-export to :noweb yes, I do get the output (but also the
boilerplate of course).

Is strip-export meant to work like this? If so, could someone please
post a working example?

Thanks,
Sean



Re: [O] Feature request for noweb mode that strips references on export

2012-03-30 Thread Nick Dokos
Sean O'Halpin  wrote:

> 
> #+name: example
> #+begin_src ruby :exports both :noweb strip-export
> =ABboilerplate=BB
> 
> hello
> #+end_src
> 

This may have nothing to do with anything (it may even be an artifact of
mailer misbehavior) but is this supposed to be <>? These
are supposed to be ASCII chars, so if you are using some sort of extended
charset, try changing them and see if that works.

Nick




Re: [O] Feature request for noweb mode that strips references on export

2012-03-30 Thread Daimrod
"Sean O'Halpin"  writes:

> Hi,
>
> I've tried to use the new :noweb strip-export feature but I can't work
> out the magic combination of headers (working with git head, i.e.
> commit 67694297fa0f9b32cf4bfe812ba8a5c5cf4a0859).
>
> Here is a stripped down example:
>
> START OF EXAMPLE
>
> * Example
>
> Define method
>
> #+name: boilerplate
> #+begin_src ruby
> def hello
>   "Hello World"
> end
> #+end_src
>
> Use it
>
> #+name: example
> #+begin_src ruby :exports both :noweb strip-export
> «boilerplate»
>
> hello
> #+end_src
>
> And here is the result:
>
> #+RESULTS: example
> : Hello World
>
> END OF EXAMPLE
>
> On export, I expect this to display the result string "Hello World"
> after the code "hello" but get nothing. If I change the :noweb
> strip-export to :noweb yes, I do get the output (but also the
> boilerplate of course).
>
> Is strip-export meant to work like this? If so, could someone please
> post a working example?
>
> Thanks,
> Sean

If you don't want to export boilerplate you've to use :exports none in
it.

#+name: boilerplate
#+begin_src ruby :exports none
def hello
  "Hello World"
end
#+end_src

Use it

#+name: example
#+begin_src ruby :exports both :noweb strip-export
<>

hello
#+end_src




Re: [O] [babwel] Simplify graph generation and copying?

2012-03-30 Thread Andreas Leha
Rainer M Krug  writes:

> Hi
>
> I do the following to create a graph in R and then convert / copy / do other 
> stuff with it in the
> bash shell:
>
> #+header: :results graphics
> #+header: :file Test.pdf
> #+header: :width 4
> #+header: :height 8
> #+header: :pointsize 8
> #+begin_src R
>   plot(runif(100))
> #+end_src
>
> #+BEGIN_SRC sh :session shell
>   cp Test.pdf Test2.pdf
> #+END_SRC
>
>
> Is there a way of automatically giving the ffile name from the :file 
> parameter tio the second code
> block, so that I just have to change the :file argument when I want a 
> different name for the graph?
>
> Thanks,
>
> Rainer


Hi Rainer,

I am not aware of any possibility to pass the :file parameter from one
code block to another.  But for your use case, the file name is also
the return value of the R code block.  So, you can do:

#+name: mypdfplot
#+header: :results graphics
#+header: :file Test.pdf
#+header: :width 4
#+header: :height 8
#+header: :pointsize 8
#+begin_src R
  plot(runif(100))
#+end_src


#+BEGIN_SRC sh :session shell :var mypdf=mypdfplot()
  cp "$mypdf" Test2.pdf
#+END_SRC

Best,
Andreas




Re: [O] [babel] file header argument includes other variable

2012-03-30 Thread Andreas Leha
Rainer M Krug  writes:

> Hi
>
> I would like to do make the file header argument to be concatenated of a 
> constant string and
> another variable, so effectively:
>
> #+header: :var+ ConNum="10"
> #+header: :results graphics
> #+header: :file SA_VALUEOFConNum.pdf
> #+header: :width 8
> #+header: :height 8
> #+header: :pointsize 8
> #+begin_src R
>   plot(runif(100))
> #+end_src
>
> #+RESULTS:
> [[file:SA_10.pdf]]
>
> Is this possible?
>
> Thanks,
>
> Rainer


Hi Rainer,

I am not aware of any method that directly does what you want.  But depending on
where the value of your variable ConNum is coming from, the
following might be a start for you.  It is based on the possibility to
insert elisp in the header arguments:

#+name: myconnum
- 19

#+header: :var ConNum=myconnum
#+header: :results graphics
#+header: :file (concat "SA_" (sbe myconnum) ".pdf")
#+header: :width 8
#+header: :height 8
#+header: :pointsize 8
#+begin_src R
  plot(runif(100), main=ConNum)
#+end_src

#+RESULTS:
[[file:SA_(19).pdf]]

Best,
Andreas




[O] [PATCH] Allow org-collector to display heading indentation

2012-03-30 Thread Nicolas Girard
Hi all,
attached is a patch which adds a new parameter "indent" to the
propview dynamic bloc, with the following behaviour:

#+BEGIN_SRC org
  ,* Tree
  ,:PROPERTIES:
  ,:COLUMNS: %8ITEM %4prop1 %5prop2
  ,:ID: tree
  ,:END:
  ,** A
  ,:PROPERTIES:
  ,:prop1: 10
  ,:prop2: 20
  ,:END:
  ,*** A1
  ,:PROPERTIES:
  ,:prop1: 15
  ,:prop2: 19
  ,:END:
  ,*** A2
  ,:PROPERTIES:
  ,:prop1: 20
  ,:prop2: 18
  ,:END:
  ,** B
  ,:PROPERTIES:
  ,:prop1: 25
  ,:prop2: 10
  ,:END:
  ,*** B1
  ,:PROPERTIES:
  ,:prop1: 2
  ,:prop2: 4
  ,:END:
  ,*** B2
  ,:PROPERTIES:
  ,:prop1: 3
  ,:prop2: 5
  ,:END:

#+END_SRC

#+BEGIN: propview :id tree :cols (ITEM prop1) :noquote t :indent t
| ITEM   | prop1 |
|+---|
| Tree   | 0 |
| \- A   |10 |
| \-- A1 |15 |
| \-- A2 |20 |
| \- B   |25 |
| \-- B1 | 2 |
| \-- B2 | 3 |
|+---|
||   |
#+END

I wish the indentation to be displayed with nothing but spaces, but
they would be trimmed by org-table guts ; so that's middly satisfying,
but better than nothing :-)

Cheers,

Nicolas


org-collector.el.diff
Description: Binary data


Re: [O] [PATCH] Allow org-collector to display heading indentation

2012-03-30 Thread Achim Gratz
Nicolas Girard writes:
> I wish the indentation to be displayed with nothing but spaces, but
> they would be trimmed by org-table guts ; so that's middly satisfying,
> but better than nothing :-)

Then use a non-breaking space and be fully satisfied.


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

Waldorf MIDI Implementation & additional documentation:
http://Synth.Stromeko.net/Downloads.html#WaldorfDocs




Re: [O] [PATCH] Allow org-collector to display heading indentation

2012-03-30 Thread Nick Dokos
Nicolas Girard  wrote:

> Hi all,
> attached is a patch ...

Attachments with mime type "application/octet-stream" are *not* caught
by patchwork. Please resubmit the patch in a proper attachment: see
http://orgmode.org/worg/org-contribute.html#sec-4-3 for details.

Nick



Re: [O] odt-Export and #+CAPTION: [reference text]{caption text}

2012-03-30 Thread Jambunathan K
Jambunathan K  writes:

>> I have applied my patch to the hotfix branch.
>
> I am having second thoughts.  I will slightly re-work the patch so it
> doesn't bomb the ODT file in unexpected ways.  I will drop a note once I
> am done with it.

Short captions if not provided will take their values from long caption.
See the commit message for more information.

I am not checking in this change to hotfix-7.8.06 branch.  If it bombs
again and someone else complains, I will revoke the fix.

If you need index entries to be in bold, fix the paragraph style.

Btw, I wonder why LibreOffice UI doesn't allow space (apart from other
characters) in the object names. The OpenDocument v1.1 explicitly has
the following example and as you can see the table name has spaces.
Anyways, looks like LibreOffice behaviour is buggy.

,
| 
| ...
| 
`

,
| commit 8a02f48547df4f11b0402aa0a4fe339e3b85c608
| Author: Jambunathan K 
| Date:   Sat Mar 31 02:03:10 2012 +0530
| 
| org-odt.el: Consider short captions not as org text but as plain text
| 
| * lisp/org-lparse.el (org-lparse-insert-org-table): Consider
| short caption as plain text and not as org text.
| * lisp/org-odt.el (org-export-odt-format-formula)
| (org-export-odt-format-image): ditto.
| 
| Fixes earlier checkin.  See
| http://lists.gnu.org/archive/html/emacs-orgmode/2012-03/msg01212.html
| 
| Handling of short captions is only a convenience feature.
| 
| From within LibreOffice one can always create an "unprotected"
| editable index and later manually delete unwanted index entries (for
| example, delete uncaptioned entries which are given automatic names)
| or modify existing entries (for example, fix long captions to their
| short versions).
`




Re: [O] [PATCH] Allow org-collector to display heading indentation

2012-03-30 Thread Nicolas Girard
>From eaf9e5f06279069ed1072425fd020d8f0442d04f Mon Sep 17 00:00:00 2001
From: Nicolas Girard 
Date: Fri, 30 Mar 2012 22:53:13 +0200
Subject: [PATCH] Allow org-collector to display heading indentation

---
 contrib/lisp/org-collector.el |   12 +---
 1 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/contrib/lisp/org-collector.el b/contrib/lisp/org-collector.el
index da612e9..2476d62 100644
--- a/contrib/lisp/org-collector.el
+++ b/contrib/lisp/org-collector.el
@@ -121,6 +121,7 @@ preceeding the dblock, then update the contents of
the dblock."
(scope (plist-get params :scope))
(noquote (plist-get params :noquote))
(colnames (plist-get params :colnames))
+   (indent (plist-get params :indent))
(content-lines (org-split-string (plist-get params :content) "\n"))
id table line pos)
(save-excursion
@@ -135,7 +136,7 @@ preceeding the dblock, then update the contents of
the dblock."
  (setq stringformat (if noquote "%s" "%S"))
  (setq table (org-propview-to-table
   (org-propview-collect cols stringformat conds match 
scope inherit
-(if colnames colnames cols)) 
stringformat))
+(if colnames colnames cols) 
indent) stringformat))
  (widen))
(setq pos (point))
(when content-lines
@@ -171,13 +172,18 @@ variables and values specified in props"
 (when p (cons n p
 inherit

-(defun org-propview-collect (cols stringformat &optional conds match
scope inherit colnames)
+(defun org-propview-collect (cols stringformat &optional conds match
scope inherit colnames indent)
   (interactive)
   ;; collect the properties from every header
   (let* ((header-props
  (let ((org-trust-scanner-tags t) alst)
(org-map-entries
-(quote (cons (cons "ITEM" (org-get-heading t))
+(quote (cons (cons "ITEM"
+   (let ((item (org-get-heading t))
+ (level (- (org-current-level) 1)))
+ (if (and indent (> level 0))
+ (format "\\%s %s"
+ (make-string level ?- ) item) 
item)))
  (org-propview-get-with-inherited inherit)))
 match scope)))
 ;; read property values
-- 
1.7.8.rc1



Re: [O] [PATCH] Separate file time from its tasks times

2012-03-30 Thread Bernt Hansen


Hi Seb,

I think this detail should be part of the commit message text.

Regards,
Bernt

"Sebastien Vauban"
 writes:

> Hello,
>
> "Sebastien Vauban" wrote:
>> 2012-03-30  Sebastien Vauban  
>> 
>>
>>  * org-clock.el (org-clocktable-write-default): Make the sum
>>  appear visually correct by not mixing the total time per file
>>  and sub-totals.
>
> This can be best understood with an example...
>
> Before:
>
> #+BEGIN: clocktable :maxlevel 4 :scope ("file-abc-tom.org" 
> "file-abc-ann.org") :block 2012-02
> Clock summary at [2012-03-30 Fri 15:12], for February 2012.
>
> | File | Headline | Time  |   |
> |--+--+---+---|
> |  | ALL Total time   | 19:15 |   |
> |--+--+---+---|
> | file-abc-tom.org | File time| 17:15 |   |
> |  | Task A   | 17:15 |   |
> |  | TODO Subtask A1  |   | 17:15 |
> |--+--+---+---|
> | file-abc-ann.org | File time| 2:00  |   |
> |  | Task B   | 2:00  |   |
> |  | TODO Subtask B2  |   |  2:00 |
>  #+END:
>
> Now:
>
> #+BEGIN: clocktable :maxlevel 4 :scope ("file-abc-tom.org" 
> "file-abc-ann.org") :block 2012-02
> Clock summary at [2012-03-30 Fri 15:13], for February 2012.
>
> | File | Headline | Time  |   |   |
> |--+--+---+---+---|
> |  | ALL Total time   | 19:15 |   |   |
> |--+--+---+---+---|
> | file-abc-tom.org | File time| 17:15 |   |   |
> |  | Task A   |   | 17:15 |   |
> |  | TODO Subtask A1  |   |   | 17:15 |
> |--+--+---+---+---|
> | file-abc-ann.org | File time| 2:00  |   |   |
> |  | Task B   |   |  2:00 |   |
> |  | TODO Subtask B2  |   |   |  2:00 |
>  #+END:
>
> Best regards,
>   Seb




[O] Please test: Fix global variables names

2012-03-30 Thread Bastien
Here is a patch against hotfix to fix warnings about wrong
variables names (with Emacs 24).

Please test it heavily.

Thanks a lot to Martyn Jago for a preliminary set of patches
for this!

diff --git a/lisp/ob-maxima.el b/lisp/ob-maxima.el
index 63f1e32..8da20af 100644
--- a/lisp/ob-maxima.el
+++ b/lisp/ob-maxima.el
@@ -42,7 +42,8 @@
 
 (defcustom org-babel-maxima-command
   (if (boundp 'maxima-command) maxima-command "maxima")
-  "Command used to call maxima on the shell.")
+  "Command used to call maxima on the shell."
+  :group 'org-babel)
 
 (defun org-babel-maxima-expand (body params)
   "Expand a block of Maxima code according to its header arguments."
diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index 81377ca..f706050 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -91,7 +91,7 @@
 (defvar org-agenda-buffer-name)
 (defvar org-agenda-overriding-header)
 (defvar org-agenda-title-append nil)
-(defvar entry)
+(defvar org-entry)
 (defvar date)
 (defvar org-agenda-undo-list)
 (defvar org-agenda-pending-undo-list)
@@ -4530,8 +4530,8 @@ function from a program - use `org-agenda-get-day-entries' instead."
   (org-compile-prefix-format 'agenda)
   (org-set-sorting-strategy 'agenda)
   (setq args (or args '(:deadline :scheduled :timestamp :sexp)))
-  (let* ((files (if (and entry (stringp entry) (string-match "\\S-" entry))
-		(list entry)
+  (let* ((files (if (and org-entry (stringp org-entry) (string-match "\\S-" org-entry))
+		(list org-entry)
 		  (org-agenda-files t)))
 	 (time (org-float-time))
 	 file rtn results)
@@ -4936,7 +4936,7 @@ holiday will also be skipped."
 	   (not (member (car (calendar-iso-from-absolute d)) skip-weeks
  (not (and (memq 'holidays skip-weeks)
 	   (calendar-check-holidays date)))
- entry)))
+ org-entry)))
 
 (defun org-diary-class (m1 d1 y1 m2 d2 y2 dayname &rest skip-weeks)
   "Like `org-class', but honor `calendar-date-style'.
diff --git a/lisp/org-beamer.el b/lisp/org-beamer.el
index e6084d2..7882b27 100644
--- a/lisp/org-beamer.el
+++ b/lisp/org-beamer.el
@@ -235,7 +235,7 @@ in org-export-latex-classes."
 	 (envs (append org-beamer-environments-extra
 		   org-beamer-environments-default))
 	 (props (org-get-text-property-any 0 'org-props text))
-	 (in "") (out "") option action defaction environment extra
+	 (in "") (out "") org-beamer-option org-beamer-action org-beamer-defaction org-beamer-environment org-beamer-extra
 	 columns-option column-option
 	 env have-text ass tmp)
 (if (= frame-level 0) (setq frame-level nil))
@@ -266,10 +266,10 @@ in org-export-latex-classes."
 
   (setq in (org-fill-template
 		"\\begin{frame}%a%A%o%T%S%x"
-		(list (cons "a" (or action ""))
-		  (cons "A" (or defaction ""))
-		  (cons "o" (or option org-beamer-frame-default-options ""))
-		  (cons "x" (if extra (concat "\n" extra) ""))
+		(list (cons "a" (or org-beamer-action ""))
+		  (cons "A" (or org-beamer-defaction ""))
+		  (cons "o" (or org-beamer-option org-beamer-frame-default-options ""))
+		  (cons "x" (if org-beamer-extra (concat "\n" org-beamer-extra) ""))
 		  (cons "h" "%s")
 		  (cons "T" (if (string-match "\\S-" text)
 "\n\\frametitle{%s}" ""))
@@ -294,10 +294,10 @@ in org-export-latex-classes."
   (setq have-text (string-match "\\S-" text))
   (setq in (org-fill-template
 		(nth 2 ass)
-		(list (cons "a" (or action ""))
-		  (cons "A" (or defaction ""))
-		  (cons "o" (or option ""))
-		  (cons "x" (if extra (concat "\n" extra) ""))
+		(list (cons "a" (or org-beamer-action ""))
+		  (cons "A" (or org-beamer-defaction ""))
+		  (cons "o" (or org-beamer-option ""))
+		  (cons "x" (if org-beamer-extra (concat "\n" org-beamer-extra) ""))
 		  (cons "h" "%s")
 		  (cons "H" (if have-text (concat "{" text "}") ""))
 		  (cons "U" (if have-text (concat "[" text "]") ""
@@ -321,31 +321,31 @@ in org-export-latex-classes."
   (cons text (cdr (assoc level default
  (t nil
 
-(defvar extra)
-(defvar option)
-(defvar action)
-(defvar defaction)
-(defvar environment)
+(defvar org-beamer-extra)
+(defvar org-beamer-option)
+(defvar org-beamer-action)
+(defvar org-beamer-defaction)
+(defvar org-beamer-environment)
 (defun org-beamer-get-special (props)
   "Extract an option, action, and default action string from text.
-The variables option, action, defaction, extra are all scoped into
-this function dynamically."
+The variables org-beamer-option, org-beamer-action, org-beamer-defaction,
+org-beamer-extra are all scoped into this function dynamically."
   (let (tmp)
-(setq environment (org-beamer-assoc-not-empty "BEAMER_env" props))
-(setq extra (org-beamer-assoc-not-empty "BEAMER_extra" props))
-(when extra
-  (setq extra (replace-regexp-in-string "n" "\n" extra)))
+(setq org-beamer-environment (org-beamer-assoc-not-empty "BEAMER_env" props))
+(setq org-beamer-extra (org-beamer-assoc-not-empty "BEAME

Re: [O] problems with LaTex/BibTex

2012-03-30 Thread Alan E. Davis
I would have a use for this.  I am curious, though...

Suppose I use this as a standard init-file declaration for
org-latex-to-pdf-process .  Does that mean that bibtex will always be run,
every time, during the generation of PDFs via LaTex export?

Alan

On Fri, Mar 30, 2012 at 4:54 AM, Julian Burgos  wrote:

> Yes! That was it.  Thanks!!
>
>
> On fös 30.mar 2012 08:05, suvayu ali wrote:
>
>> Hey Julian,
>>
>> On Fri, Mar 30, 2012 at 03:41, Julian Burgos  wrote:
>>
>>> The "References.bib" is a BibTex file in the same folder as the test
>>> file.
>>>  The citations were entered using RefTex with no problem.  But when
>>> exporting to pdf, I get the following message in the minibuffer:
>>> "Exporting to PDF...done, with some errors: [undefined citations]".  The
>>> pdf produced had, of course, question marks where the citations should
>>> be.
>>>
>> Did you customise your org-latex-to-pdf-process to include bibtex? I use
>> something like this:
>>
>> (setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode %b"
>> "/usr/bin/bibtex %b"
>> "pdflatex -interaction nonstopmode %b"
>> "pdflatex -interaction nonstopmode %b"))
>>
>>
>
> --
> Julian Mariano Burgos, PhD
> Hafrannsóknastofnunin/Marine Research Institute
> Skúlagata 4, 121 Reykjavík, Iceland
> Sími/Telephone : +354-5752037
> Bréfsími/Telefax:  +354-5752001
> Netfang/Email: jul...@hafro.is
>
>
>


[O] [PATCH] Time specifications: Allow specifying relative times

2012-03-30 Thread Ilya Shlyakhter
When specifying times in the tags/properties matcher you can use 
relative time notation, such as  or <-1w>.  This patch

allows this to be used in other places, such as the :tstart and :tend
parameters of clocktable.

Btw, I couldn't quite understand the exact meaning of :block, :tstart 
and :tend as decribed in the manual.  Is there a better explanation

somewhere?

thanks,

ilya
>From d19778b3fc624e14237d69cc76a4aa9cb8450697 Mon Sep 17 00:00:00 2001
From: Ilya Shlyakhter 
Date: Fri, 30 Mar 2012 21:19:12 -0400
Subject: [PATCH] Time specifications: Allow specifying relative times

* org.el (org-parse-time-string): Allow strings supported by tags/properties
matcher (eg , , <-7d>) if the time starts with < and ends
with >.  This means that e.g. in the clocktable parameters you can specify
:tstart "<-1w>" :tend "".

TINYCHANGE
---
 lisp/org.el |   23 +--
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/lisp/org.el b/lisp/org.el
index 4d2ae87..995dffd 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -16016,16 +16016,19 @@ When SHOW-ALL is nil, only return the current 
occurrence of a time stamp."
 This should be a lot faster than the normal `parse-time-string'.
 If time is not given, defaults to 0:00.  However, with optional NODEFAULT,
 hour and minute fields will be nil if not given."
-  (if (string-match org-ts-regexp0 s)
-  (list 0
-   (if (or (match-beginning 8) (not nodefault))
-   (string-to-number (or (match-string 8 s) "0")))
-   (if (or (match-beginning 7) (not nodefault))
-   (string-to-number (or (match-string 7 s) "0")))
-   (string-to-number (match-string 4 s))
-   (string-to-number (match-string 3 s))
-   (string-to-number (match-string 2 s))
-   nil nil nil)
+  (cond
+   ((string-match "^<.+>$" s)
+(decode-time (seconds-to-time (org-matcher-time s
+   ((string-match org-ts-regexp0 s)
+(list 0
+ (if (or (match-beginning 8) (not nodefault))
+ (string-to-number (or (match-string 8 s) "0")))
+ (if (or (match-beginning 7) (not nodefault))
+ (string-to-number (or (match-string 7 s) "0")))
+ (string-to-number (match-string 4 s))
+ (string-to-number (match-string 3 s))
+ (string-to-number (match-string 2 s))
+ nil nil nil))
 (error "Not a standard Org-mode time string: %s" s)))
 
 (defun org-timestamp-up (&optional arg)
-- 
1.7.9.3



[O] [PATCH] Testing: Corrected the command to run batch tests given in testing/README

2012-03-30 Thread Ilya Shlyakhter

Added some details for how to run the test suite in batch mode.
>From 2cf6b6f529748a2a39927ccfdfa583d7f00cc9df Mon Sep 17 00:00:00 2001
From: Ilya Shlyakhter 
Date: Fri, 30 Mar 2012 22:11:22 -0400
Subject: [PATCH] Testing: Corrected the command to run batch tests given in
 README

testing/README (running batch tests): Added missing paths to the command.
   Make sure to load the org-mode code from the git checkout rather than
   whatever Org is installed in Emacs directories.

TINYCHANGE
---
 testing/README |   11 +++
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/testing/README b/testing/README
index 4a68174..f4253c7 100644
--- a/testing/README
+++ b/testing/README
@@ -12,10 +12,13 @@ repository]].
 The simplest way to run the Org-mode test suite is from the command
 line with the following invocation.  Note that the paths below are
 relative to the base of the Org-mode directory.
-#+BEGIN_SRC sh
-  emacs -Q --batch -l lisp/org.el -l testing/org-test.el \
-  --eval "(progn (org-reload) (setq org-confirm-babel-evaluate nil))" \
-  -f org-test-run-batch-tests
+#+BEGIN_SRC sh :dir (expand-file-name "..")
+  # For Emacs earlier than 24, add -L /path/to/ert
+  emacs -Q --batch \
+-L lisp/ -L testing/ -L testing/lisp -l lisp/org.el \
+-l lisp/org-id.el -l testing/org-test.el \
+--eval "(progn (org-reload) (setq org-confirm-babel-evaluate nil))" \
+-f org-test-run-batch-tests
 #+END_SRC
 
 The options in the above command are explained below.
-- 
1.7.9.3



Re: [O] problems with LaTex/BibTex

2012-03-30 Thread Nick Dokos
Alan E. Davis  wrote:

> I would have a use for this.  I am curious, though...
> 
> Suppose I use this as a standard init-file declaration for 
> org-latex-to-pdf-process .  Does that
> mean that bibtex will always be run, every time, during the generation of 
> PDFs via LaTex export?  
> 

I believe so.

I think the best way to deal with the mess of programs that you have to
run for complicated latex productions (at least on linux) is to use
texi2dvi, which is supposed to figure out these dependencies and run the
"correct" sequence of programs the "correct" number of times (it does
this by parsing error messages in the log file, I believe).

The trouble is that, as currently distributed, texi2dvi has a bug that
causes an error with recent versions of egrep.  That's why the
default value of org-latex-to-pdf-process is not texi2dvi. C-h v
org-latex-to-pdf-process RET for more details.

You might try it and see if you get the error: try ``texi2dvi --pdf 
somefile.tex''
The symptom is the message

egrep: Invalid range end

If you get the error, then you can forget about texi2dvi for now.

OTOH, if you are willing to live with the consequences of actually
fixing the bug in your version of texi2dvi, that's pretty easy. The
danger is that you are going to pull an update which might revert
texi2dvi to its unpatched state. But if you have patched it once, it's
easy to patch it again.

The change is around line 1713 of /usr/bin/texi2dvi. The original says

  echo "$command_line_filename" | $EGREP '^(/|[A-z]:/)' >&6 \
  || command_line_filename="./$command_line_filename"

and the fixed version is

  echo "$command_line_filename" | $EGREP '^(/|[A-Za-z]:/)' >&6 \
  || command_line_filename="./$command_line_filename"

just changing the egrep pattern.

The fixed version is not exactly equivalent to the original version
but the difference is academic, unless you run Windows and you have
lots of drives.

FWIW, I've fixed my texi2dvi as above, and have set org-latex-to-pdf-process
to a custom shell command: texi2dvi --pdf --batch %f.

Org provides a texi2dvi customize option for org-latex-to-pdf-process
that also sets the build mode to ``clean'' which gets rid of the extra
files that a latex run produces, but I prefer leaving all the "junk"
files around and clean them up once at the end.

Nick

> Alan
> 
> On Fri, Mar 30, 2012 at 4:54 AM, Julian Burgos  wrote:
> 
> Yes! That was it.  Thanks!!
> 
> On fös 30.mar 2012 08:05, suvayu ali wrote:
>
> Hey Julian,
>
> On Fri, Mar 30, 2012 at 03:41, Julian Burgos  wrote:
>
> The "References.bib" is a BibTex file in the same folder as the 
> test file.
>  The citations were entered using RefTex with no problem.  But 
> when
> exporting to pdf, I get the following message in the minibuffer:
> "Exporting to PDF...done, with some errors: [undefined 
> citations]".  The
> pdf produced had, of course, question marks where the citations 
> should be.
>
> Did you customise your org-latex-to-pdf-process to include bibtex? I 
> use
> something like this:
>
> (setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode 
> %b"
>                                 "/usr/bin/bibtex %b"
>                                 "pdflatex -interaction nonstopmode %b"
>                                 "pdflatex -interaction nonstopmode 
> %b"))
> 
> --
> Julian Mariano Burgos, PhD
> Hafrannsóknastofnunin/Marine Research Institute
> Skúlagata 4, 121 Reykjavík, Iceland
> Sími/Telephone : +354-5752037
> Bréfsími/Telefax:  +354-5752001
> Netfang/Email: jul...@hafro.is
> 
> 
> 
> Alternatives:
> 
> 



Re: [O] About org-babel menu

2012-03-30 Thread Torsten Wagner
My menus are hidden too. However,  if I need them for some reasons there is
some key mouse combo.
Can't remember exactly. Shift right click or C- right click.. something
along this.  The menu will pop up as a context menu close to the mouse
cursor  location. Be aware there is a customization menu too.

Just in case you look for a quick way to use the menu.

Torsten
On Mar 19, 2012 11:53 PM, "Eric Schulte"  wrote:

> Rainer M Krug  writes:
>
> > On 19/03/12 15:22, Eric Schulte wrote:
> >> Hi FengShu,
> >>
> >> I don't know much about the Emacs customization interface, but it is
> certainly the solution to
> >> this issue.  There does currently exist a Babel specific customization
> group, the nesting is
> >> org>babel.  Through this interface there are menus like the one you
> mention below available.
> >>
> >> One way to access these menus is through the help interface, with M-x
> describe-variable RET
> >> org-babel-load-languages RET and then select the "customize" link.
> >
> > Agreed on this point, but I am with FengShu regarding a babel menu. I
> likely would not use it that
> > often (I know the shortcuts relevant to me right now), but
> >
> > 1) it would advertise the babel functionality a little bit more if it is
> shown in the org menu
> >
> > 2) for a beginner, it would be much easier to use org-babel if commands
> like execute source block
> > or section, tangle, un-tangle, ... would be in the menu.
> >
> >
> > So I would see it as a useful way of promoting babel (and therefore
> org-mode) and also as a nice
> > reminder of less frequently (but nevertheless usefull) functionality.
> >
>
> I've had (setq menu-bar-mode nil) in my .emacs for years now and forget
> that Emacs even has support for menus.  I don't know anything about how
> Emacs implements menus, but if anyone is interested in taking on this
> development I'm very happy to consult in the development of and to apply
> contributed patches which add Babel menu support.
>
> Best,
>
> >
> > Cheers,
> >
> > Rainer
> >
> >
> >>
> >> Best,
> >>
> >> FengShu  writes:
> >>
> >>> Hi: Could we add  some org-babel menu items ,so using them we can
> enable and disable the
> >>> computer languages ?
> >>>
> >>> for example: #+begin_example org => org-babel =>  * emacs-lisp sh * R
> ... * screen
> >>>
> >>> #+end_example
> >>
>
> --
> Eric Schulte
> http://cs.unm.edu/~eschulte/
>
>


Re: [O] [PATCH] Allow org-collector to display heading indentation

2012-03-30 Thread Sebastien Vauban
Hi Nicolas,

Nicolas Girard wrote:
> From eaf9e5f06279069ed1072425fd020d8f0442d04f Mon Sep 17 00:00:00 2001
> From: Nicolas Girard 
> Date: Fri, 30 Mar 2012 22:53:13 +0200
> Subject: [PATCH] Allow org-collector to display heading indentation
>
> ---
>  contrib/lisp/org-collector.el |   12 +---
>  1 files changed, 9 insertions(+), 3 deletions(-)
>
> diff --git a/contrib/lisp/org-collector.el b/contrib/lisp/org-collector.el
> index da612e9..2476d62 100644
> --- a/contrib/lisp/org-collector.el
> +++ b/contrib/lisp/org-collector.el
> @@ -121,6 +121,7 @@ preceeding the dblock, then update the contents of
> the dblock."
>   (scope (plist-get params :scope))
>   (noquote (plist-get params :noquote))
>   (colnames (plist-get params :colnames))
> + (indent (plist-get params :indent))
>   (content-lines (org-split-string (plist-get params :content) "\n"))
>   id table line pos)
>   (save-excursion
> @@ -135,7 +136,7 @@ preceeding the dblock, then update the contents of
> the dblock."
> (setq stringformat (if noquote "%s" "%S"))
> (setq table (org-propview-to-table
>  (org-propview-collect cols stringformat conds match 
> scope inherit
> -  (if colnames colnames cols)) 
> stringformat))
> +  (if colnames colnames cols) 
> indent) stringformat))
> (widen))
>   (setq pos (point))
>   (when content-lines
> @@ -171,13 +172,18 @@ variables and values specified in props"
>(when p (cons n p
>inherit
>
> -(defun org-propview-collect (cols stringformat &optional conds match
> scope inherit colnames)
> +(defun org-propview-collect (cols stringformat &optional conds match
> scope inherit colnames indent)
>(interactive)
>;; collect the properties from every header
>(let* ((header-props
> (let ((org-trust-scanner-tags t) alst)
>   (org-map-entries
> -  (quote (cons (cons "ITEM" (org-get-heading t))
> +  (quote (cons (cons "ITEM"
> + (let ((item (org-get-heading t))
> +   (level (- (org-current-level) 1)))
> +   (if (and indent (> level 0))
> +   (format "\\%s %s"
> +   (make-string level ?- ) item) 
> item)))

You may want to follow the "indent" convention used for clockview: "\__"
string.

Have a look at (or reuse?) the function `org-clocktable-indent-string'...

> (org-propview-get-with-inherited inherit)))
>match scope)))
>;; read property values

Best regards,
  Seb

-- 
Sebastien Vauban