[Orgmode] include value of single table cell in text?

2010-07-27 Thread Austin Frank
Hello!

Is it possible to include the value of a single cell from an org-mode
table in the body of an org-mode document? That is, given

#+TBLNAME:  test-table
| key | value |
|-+---|
| a   | 1 |
| b   | 2 |

Is there any way to refer to cell @2$2 within the text of an org-mode
document, and have that reference converted to the value "2" during
export?

I believe one approach would be to use babel's in-line source evaluation
capabilities along with the remote() function from the org spreadsheet
editor.  But I haven't yet been able to identify the right combination
of those functions to get the desired result.  This, for example,
doesn't work for me:

--8<---cut here---start->8---
#+TBLNAME:  test-table
| key | value |
|-+---|
| a   | 1 |
| b   | 2 |

I'm testing to see whether
src_emacs-lisp{(org-table-eval-formula "remote(test-table @2$2)")}
works.
--8<---cut here---end--->8---

It throws an error during export, because I'm not in a table data field.


Additionally, if there's not already a built-in way to do this, I'd
nominate this functionality for some special syntax.  Following babel's
inlining and remote reference conventions, maybe

  table{test-table @2$2}

or

  <>

This would make it very easy to refer to specific elements the tabular
output of babel blocks, adding to the utility of babel as a
meta-programming language for org-mode.


Thanks for any help!
/au

-- 
Austin Frank
http://aufrank.net
GPG Public Key (D7398C2F): http://aufrank.net/personal.asc


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[Orgmode] Re: .ods opens file in Emacs, not OpenOffice

2010-07-27 Thread Shelagh Manton
On Mon, 26 Jul 2010 17:54:00 -0700, C64 Whiz wrote:

> Hello,
> 
> I've searched for an answer but can't find a simple one.  I have an
> OpenOffice document (.ods) I'd like to link to in my .org files.  So I
> have the following syntax:
> 
>   [[file:c:/mydata/myfile.ods][File Description]]
> 
> When I click on the link in OrgMode, Emacs opens the file and not
> OpenOffice.  Yet, when I'm in file explorer (yes, Windows), double
> clicking the file does open up Open Office.  So I know the association
> is there.
> 
> I know there is a variable called 'org-file-apps, but I thought the file
> system was supposed to handle any extension not known my OrgMode?  If I
> do need 'org-file-apps, please provide an example where I may *add* to
> the list rather then re-defining the existing list.  I'd hate to re-do
> "associations" OrgMode already made.
> 
> Thanks!
> 
> --C64Whiz
There are possible a couple of ways of dealing with this. 

One that I have used in the past is to make a new link type and use that 
for opening your .odt files

#+LINK: ooo shell:oowriter

and then use [[ooo:"/path/to/ooo-file" &][name of file]] 



I have no doubt that there are other ways of doing this.

Shelagh
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Re: [Orgmode] [ANN] List improvement v.2

2010-07-27 Thread Scot Becker
Nicolas and list friends

This sounds great.  And it seems you've made it easy to try by putting in in
git.  Since my git usage consists almost exclusively of pulling from the
org-mode repository, and I've never dealt with testing branches, would one
of you be so kind as to feed me the commands necessary to try this out in
the  easiest way possible.  I keep current on the org 'master' repo.

Should I pull a separate repo, or make a branch on the one I have?  Assuming
I find no reason to undo the changes, and assuming they are merged into the
core after some weeks, and assuming that I want keep current on the main org
repository, will I need to do anything if and when these changes get added
to the core if I'm already testing them on the branch?  I'm sure all of this
is blissfully easy (git seems so clever), but I'd be glad to have someone
explain how to do it in the easiest way.

Scot


On Thu, Jul 22, 2010 at 10:08 PM, Nicolas Goaziou wrote:

> Hello,
>
> Here is a new, and probably final feature-wise, suggestion of list
> improvement in Org Mode.
>
> Table of Contents
> =
> 1 What is it about again ?
> 2 Is that all ?
>2.1 Preserving blank lines
>2.2 Timer lists
>2.3 Automatic rules
>2.4 `org-apply-on-list'
> 3 Where can it be tried ?
>
>
> 1 What is it about again ?
> ~~~
>
>  I redefined lists in Org Mode. Lists start, as before, at a bullet
>  (whose true regexp is at `org-item-beginning-re'), and end at either
>  `org-list-end-regexp', a new headline, or, obviously, end of buffer.
>
>  `org-list-end-regexp' is customizable and defaults to 2 blank lines,
>  but `org-empty-line-terminates-plain-lists' has precedence over it.
>  Moreover, any `org-list-end-regexp' found in special blocks does not
>  end list. Here are two examples of valid lists:
>
>  Case 1: `org-list-end-regexp' is at default value
>
>
>  - First item
>
>- Sub item
>
>  #+BEGIN_EXAMPLE
>  Two blank lines below
>
>
>  Two blank lines above
>  #+END_SRC
>
>- Last sub item
>
>
>  List has ended at the beginning of this line.
>
>  Case 2: `org-list-end-regexp' is "^[ \t]*___[ \t]*\n"
>
>
>  - item 1
>  - item 2
>- sub-item
>- sub-item 2
>  - item 3
>  __
>  List has ended at the beginning of this line.
>
>  Now, Org Mode knows when a list has ended and how to indent line
>  accordingly. In other words, you can `org-return-indent' three times
>  to exit a list and be at the right column to go on with the text.
>
>  This new definition is also understood by exporters (LaTeX, DocBook,
>  HTML or ASCII) and `org-list-end-regexp' will appear in source as a
>  blank line, whatever its value is (as long as it starts with a caret
>  and ends with a newline character, as specified in doc-string).
>
>  Another advantage is that you can have two lists of different types
>  in a row like in the example below:
>
>
>  - item
>  - item
>
>
>  1. item
>  2. item
>
>  In this example, you can move (or cycle, or indent) items in the
>  second list without worrying about changing the first one.
>
> 2 Is that all ?
> 
>
>  Yes and no. I tried as much as possible to keep compatibility with
>  previous implementation. But, as I was at it, I made a number of
>  minor improvements I am now going to describe.
>
> 2.1 Preserving blank lines
> ===
>
>   `org-move-item-up' and `org-move-item-down' will not eat blank
>   lines anymore. You can move an item up and down and stay assured
>   list will keep its integrity.
>
>   The same is true for `org-sort-list' that would previously collapse
>   the list being sorted. Sorting is now safe.
>
>   `org-insert-item', when 'plain-list-item is set to 'auto in
>   `org-blank-before-new-entry' (the default, I think), will work hard
>   to guess the appropriate number of blank lines to insert before the
>   item to come. The function is also much more predictable (in
>   previous version, trying to insert an item with point on a blank
>   line between 2 items would create a new headline).
>
> 2.2 Timer lists
> 
>
>   There are three improvements in timer lists (C-c C-x -).
>
>   1. When a new item is created, it should be properly indented and
>  not sticked to column 0 anymore,
>
>   2. When an item is inserted in a pre-existing timer list, it will
>  take profit of what has been done to `org-insert-item',
>
>   3. `org-sort-list' can now sort timer lists with the t and T
>  commands.
>
>   /Note/: in order to preserve lists integrity, Org Mode will send an
>   error if you try to insert a timer list inside a list of another
>   type.
>
> 2.3 Automatic rules
> 
>
>   I've added sets of rules (applied by default) that can improve
>   lists experience. You can deactivate them individually by
>   customizing `org-list-automatic-rules'.
>
>   Bullet rule: Some may have noticed that you couldn't obtain *
>as a bullet when cycling a list a

[Orgmode] [BABEL] org-babel-post-tangle-hook problems

2010-07-27 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Eric

I relized the following problems today:

After setting the org-babel-post-tangle-hook (e.g.
(add-hook 'org-babel-post-tangle-hook
(lambda () (message "I'm in %s" (buffer-file-name)) ))
)

the .org file closes, and the .R file is opened.
If I tangle a second time, emacs tells me that the .R file has changed
on disk, and if it should be re-read.
I don't know what happened, but it would be nice to have the working
behavior back.

I haven't used org for a few days, so I don't know when it happened.

Cheers,

Rainer

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

Centre of Excellence for Invasion Biology
Natural Sciences Building
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Main Campus, Merriman Avenue
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email:  rai...@krugs.de

Skype:  RMkrug
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Re: [Orgmode] include value of single table cell in text?

2010-07-27 Thread Eric Schulte
The following should work.  It uses an inline code block

--8<---cut here---start->8---
#+TBLNAME:  test-table
| key | value |
|-+---|
| a   | 1 |
| b   | 2 |

Is there any way to refer to cell @2$2 within the text of an org-mode
document, and have that reference converted to the value
src_emacs-lisp[:var d=test-table[3,1]]{d} during export?
--8<---cut here---end--->8---

Best -- Eric

Austin Frank  writes:

> Hello!
>
> Is it possible to include the value of a single cell from an org-mode
> table in the body of an org-mode document? That is, given
>
> #+TBLNAME:  test-table
> | key | value |
> |-+---|
> | a   | 1 |
> | b   | 2 |
>
> Is there any way to refer to cell @2$2 within the text of an org-mode
> document, and have that reference converted to the value "2" during
> export?
>
> I believe one approach would be to use babel's in-line source evaluation
> capabilities along with the remote() function from the org spreadsheet
> editor.  But I haven't yet been able to identify the right combination
> of those functions to get the desired result.  This, for example,
> doesn't work for me:
>
> #+TBLNAME:  test-table
> | key | value |
> |-+---|
> | a   | 1 |
> | b   | 2 |
>
> I'm testing to see whether
> src_emacs-lisp{(org-table-eval-formula "remote(test-table @2$2)")}
> works.
>
> It throws an error during export, because I'm not in a table data field.
>
>
> Additionally, if there's not already a built-in way to do this, I'd
> nominate this functionality for some special syntax.  Following babel's
> inlining and remote reference conventions, maybe
>
>   table{test-table @2$2}
>
> or
>
>   <>
>
> This would make it very easy to refer to specific elements the tabular
> output of babel blocks, adding to the utility of babel as a
> meta-programming language for org-mode.
>
>
> Thanks for any help!
> /au

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Re: [Orgmode] [ANN] List improvement v.2

2010-07-27 Thread Daniel Martins
I am on the same level as Scot and with the same doubts.

Anyway one more vote to include these improvements to the core repository of
org-mode ASAP.

Daniel

2010/7/27 Scot Becker 

> Nicolas and list friends
>
> This sounds great.  And it seems you've made it easy to try by putting in
> in git.  Since my git usage consists almost exclusively of pulling from the
> org-mode repository, and I've never dealt with testing branches, would one
> of you be so kind as to feed me the commands necessary to try this out in
> the  easiest way possible.  I keep current on the org 'master' repo.
>
> Should I pull a separate repo, or make a branch on the one I have?
> Assuming I find no reason to undo the changes, and assuming they are merged
> into the core after some weeks, and assuming that I want keep current on the
> main org repository, will I need to do anything if and when these changes
> get added to the core if I'm already testing them on the branch?  I'm sure
> all of this is blissfully easy (git seems so clever), but I'd be glad to
> have someone explain how to do it in the easiest way.
>
> Scot
>
>
>
> On Thu, Jul 22, 2010 at 10:08 PM, Nicolas Goaziou wrote:
>
>> Hello,
>>
>> Here is a new, and probably final feature-wise, suggestion of list
>> improvement in Org Mode.
>>
>> Table of Contents
>> =
>> 1 What is it about again ?
>> 2 Is that all ?
>>2.1 Preserving blank lines
>>2.2 Timer lists
>>2.3 Automatic rules
>>2.4 `org-apply-on-list'
>> 3 Where can it be tried ?
>>
>>
>> 1 What is it about again ?
>> ~~~
>>
>>  I redefined lists in Org Mode. Lists start, as before, at a bullet
>>  (whose true regexp is at `org-item-beginning-re'), and end at either
>>  `org-list-end-regexp', a new headline, or, obviously, end of buffer.
>>
>>  `org-list-end-regexp' is customizable and defaults to 2 blank lines,
>>  but `org-empty-line-terminates-plain-lists' has precedence over it.
>>  Moreover, any `org-list-end-regexp' found in special blocks does not
>>  end list. Here are two examples of valid lists:
>>
>>  Case 1: `org-list-end-regexp' is at default value
>>
>>
>>  - First item
>>
>>- Sub item
>>
>>  #+BEGIN_EXAMPLE
>>  Two blank lines below
>>
>>
>>  Two blank lines above
>>  #+END_SRC
>>
>>- Last sub item
>>
>>
>>  List has ended at the beginning of this line.
>>
>>  Case 2: `org-list-end-regexp' is "^[ \t]*___[ \t]*\n"
>>
>>
>>  - item 1
>>  - item 2
>>- sub-item
>>- sub-item 2
>>  - item 3
>>  __
>>  List has ended at the beginning of this line.
>>
>>  Now, Org Mode knows when a list has ended and how to indent line
>>  accordingly. In other words, you can `org-return-indent' three times
>>  to exit a list and be at the right column to go on with the text.
>>
>>  This new definition is also understood by exporters (LaTeX, DocBook,
>>  HTML or ASCII) and `org-list-end-regexp' will appear in source as a
>>  blank line, whatever its value is (as long as it starts with a caret
>>  and ends with a newline character, as specified in doc-string).
>>
>>  Another advantage is that you can have two lists of different types
>>  in a row like in the example below:
>>
>>
>>  - item
>>  - item
>>
>>
>>  1. item
>>  2. item
>>
>>  In this example, you can move (or cycle, or indent) items in the
>>  second list without worrying about changing the first one.
>>
>> 2 Is that all ?
>> 
>>
>>  Yes and no. I tried as much as possible to keep compatibility with
>>  previous implementation. But, as I was at it, I made a number of
>>  minor improvements I am now going to describe.
>>
>> 2.1 Preserving blank lines
>> ===
>>
>>   `org-move-item-up' and `org-move-item-down' will not eat blank
>>   lines anymore. You can move an item up and down and stay assured
>>   list will keep its integrity.
>>
>>   The same is true for `org-sort-list' that would previously collapse
>>   the list being sorted. Sorting is now safe.
>>
>>   `org-insert-item', when 'plain-list-item is set to 'auto in
>>   `org-blank-before-new-entry' (the default, I think), will work hard
>>   to guess the appropriate number of blank lines to insert before the
>>   item to come. The function is also much more predictable (in
>>   previous version, trying to insert an item with point on a blank
>>   line between 2 items would create a new headline).
>>
>> 2.2 Timer lists
>> 
>>
>>   There are three improvements in timer lists (C-c C-x -).
>>
>>   1. When a new item is created, it should be properly indented and
>>  not sticked to column 0 anymore,
>>
>>   2. When an item is inserted in a pre-existing timer list, it will
>>  take profit of what has been done to `org-insert-item',
>>
>>   3. `org-sort-list' can now sort timer lists with the t and T
>>  commands.
>>
>>   /Note/: in order to preserve lists integrity, Org Mode will send an
>>   error if you try to insert a timer list inside a list of another
>>   type.
>>

Re: [Orgmode] Bug: possible bug in latex export [7.01trans (release_6.36.735.g15ca.dirty)]

2010-07-27 Thread Stephen Eglen
> FYI: This is a know limitation of the LaTeX exporter[1] and the
> current state of this issue (dealing with skipped levels) is that
> patches for the problem are welcome.  I agree that even if
> skipped-level-headlines are not allowed, they shouldn't be silently
> droped neither.
> 
> Best,
>   -- David
> 
> [1] http://thread.gmane.org/gmane.emacs.orgmode/26413

I think I have a patch for this, see below.  I've tested it briefly to
see that it works with both oddeven and odd level headings, but I would
appreciate other people taking a closer look/checking that it doesn't
break other things.  I think I found the problem, in that if you have a
structure like

* A 

*** B

(i.e. a level one and a level 3)

after it has found the level 1 content, it expects to find a level 2
subtree, whereas in fact there could be a level 2+ tree.  See the
comment in the code for the change I made.

Stephen

diff --git a/lisp/org-latex.el b/lisp/org-latex.el
index 24dd8c1..8530723 100644
--- a/lisp/org-latex.el
+++ b/lisp/org-latex.el
@@ -937,13 +937,28 @@ Return a list reflecting the document structure."
 (defun org-export-latex-parse-subcontent (level odd)
   "Extract the subcontent of a section at LEVEL.
 If ODD Is non-nil, assume subcontent only contains odd sections."
-  (if (not (org-re-search-forward-unprotected
-   (concat "^\\(\\(?:\\*\\)\\{"
-   (number-to-string (+ (if odd 4 2) level))
-   "\\}\\) \\(.*\\)$")
-   nil t))
-  nil ; subcontent is nil
-(org-export-latex-parse-global (+ (if odd 2 1) level) odd)))
+
+  (let (nstars new-level)
+;; In the search, we should not assume there will be exactly
+;; LEVEL+1 stars in the next heading, as there may be more than
+;; that number of stars.  hence the regexp should be \\*{N,}
+;; rather than just \\*{N} (i.e. no upper bound, but N is minimum
+;; number of stars to expect.)
+;; We then have to check how many stars were found, rather than
+;; assuming there were exactly N.
+(when (org-re-search-forward-unprotected
+  (concat "^\\(\\(?:\\*\\)\\{"
+  (number-to-string (+ (if odd 4 2) level))
+  ",\\}\\) \\(.*\\)$")
+  nil t)
+  (setq nstars (1- (- (match-end 1) (match-beginning 1
+  (setq new-level (if odd 
+ (/ (+ 3 nstars) 2);; not entirely sure why +3!
+   nstars)))
+(if nstars
+   (org-export-latex-parse-global new-level odd)
+  nil) ; subcontent is nil
+  ))
 
 ;;; Rendering functions:
 (defun org-export-latex-global (content)

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Re: [Orgmode] firefox problem with org-protocol

2010-07-27 Thread Daniel Martins
Daniel

A few weeks ago I had similar problems and gave up of using org-protocol.
Could you give us a step-by-step procedure?

Daniel


2010/7/25 Daniel Goldin 

> Thanks. Got me almost there. This is the link that solved the problem in
> the end:
>
>
> http://support.mozilla.com/en-US/kb/The+protocol+is+not+associated+with+any+program
>
> d.
>
> Excerpts from David Maus's message of Sun Jul 25 09:16:52 -0700 2010:
> > Daniel Goldin wrote:
> > >I don't seem to be able to add emacsclient as a handler for
> > >org-capture in firefox 3.6.7. When I click on the bookmark, I simply
> > >get a message telling me that there is no helper app associated with
> > >the file -- with no option to add my own. Anybody know a way to work
> > >around this?
> >
> > There was recently a thread that discuessed this:
> >
> > http://thread.gmane.org/gmane.emacs.orgmode/27362
> >
> > Does one of the solutions there solve the problem for you?
> >
> > HTH,
> >   -- David
> --
> Daniel Goldin
> 213.926.1960
>
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Re: [Orgmode] .ods opens file in Emacs, not OpenOffice

2010-07-27 Thread Anthony Lander


On 10-Jul-26, at 8:54 PM, C64 Whiz wrote:


Hello,

I've searched for an answer but can't find a simple one.  I have an  
OpenOffice document (.ods) I'd like to link to in my .org files.  So  
I have the following syntax:


  [[file:c:/mydata/myfile.ods][File Description]]

When I click on the link in OrgMode, Emacs opens the file and not  
OpenOffice.  Yet, when I'm in file explorer (yes, Windows), double  
clicking the file does open up Open Office.  So I know the  
association is there.


Try C-u C-c C-o. On my mac, that switches whether the link opens in  
emacs or through the operating system file association (although mine  
is the reverse. With the prefix it opens in emacs. Not sure why). From  
the doc-string for org-open-at-point:


(org-open-at-point &optional IN-EMACS REFERENCE-BUFFER)

Open link at or after point.
If there is no link at point, this function will search forward up to
the end of the current line.
Normally, files will be opened by an appropriate application.  If the
optional argument IN-EMACS is non-nil, Emacs will visit the file.
With a double prefix argument, try to open outside of Emacs, in the
application the system uses for this file type.

Hope this helps,

  -Anthony


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Re: [Orgmode] firefox problem with org-protocol

2010-07-27 Thread Daniel Goldin

Below are the relevant instructions, with the correct changes. I
modified instructions from this link:
http://support.mozilla.com/en-US/kb/The+protocol+is+not+associated+with+any+program


Register the protocol in Firefox

Firefox gets its protocol information from its hidden settings.

   1. In the Location bar, type about:config and press EnterReturn.  *
   The about:config "This might void your warranty!" warning page may
   appear. Click I'll be careful, I promise!, to continue to the
   about:config page.

   2. Right-click anywhere in the grid, choose New, then String.

   3. In the Enter the preference name prompt, type in
   "network.protocol-handler.app.org-protocol" and press OK.

   4. In the Enter string value prompt, type "emacsclient" and press
   OK.

Now that the protocol has been registered, try the link again. You may
get an External Protocol Request dialog. Click Launch Application. The
program you chose should now start.

* Make sure that the path you put in the preference is
  correct. Due to a bug in Firefox, entering an incorrect path
  will give you the same error message.


Hope this helps,

d.






Excerpts from Daniel Martins's message of Tue Jul 27 07:56:49 -0700 2010:
> Daniel
> 
> A few weeks ago I had similar problems and gave up of using org-protocol.
> Could you give us a step-by-step procedure?
> 
> Daniel
> 
> 
> 2010/7/25 Daniel Goldin 
> 
> > Thanks. Got me almost there. This is the link that solved the problem in
> > the end:
> >
> >
> > http://support.mozilla.com/en-US/kb/The+protocol+is+not+associated+with+any+program
> >
> > d.
> >
> > Excerpts from David Maus's message of Sun Jul 25 09:16:52 -0700 2010:
> > > Daniel Goldin wrote:
> > > >I don't seem to be able to add emacsclient as a handler for
> > > >org-capture in firefox 3.6.7. When I click on the bookmark, I simply
> > > >get a message telling me that there is no helper app associated with
> > > >the file -- with no option to add my own. Anybody know a way to work
> > > >around this?
> > >
> > > There was recently a thread that discuessed this:
> > >
> > > http://thread.gmane.org/gmane.emacs.orgmode/27362
> > >
> > > Does one of the solutions there solve the problem for you?
> > >
> > > HTH,
> > >   -- David
> > --
> > Daniel Goldin
> > 213.926.1960
> >
> > ___
> > Emacs-orgmode mailing list
> > Please use `Reply All' to send replies to the list.
> > Emacs-orgmode@gnu.org
> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >
-- 
Daniel Goldin 
213.926.1960

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Re: [Orgmode] [ANN] List improvement v.2

2010-07-27 Thread Nicolas Goaziou
Hello,

> Scot Becker writes:
> Should I pull a separate repo, or make a branch on the one I have?

Both options are possible. In order to make a specific branch in your
current repo, it's a two steps move (and one optional):

  git checkout -b new-lists

  git remote add ngz http://github.com/ngz/org-mode-lists.git (optional
step, it avoids typing the whole url everytime you want to update)

Then, to keep up-to-date:

  git pull ngz end-lists

Don't forget to M-x org-reload.

> Assuming I find no reason to undo the changes, and assuming they are
> merged into the core after some weeks, and assuming that I want keep
> current on the main org repository, will I need to do anything if
> and when these changes get added to the core if I'm already testing
> them on the branch?

You will then switch to master branch, delete new-lists branch (and
ngz remote repository), then reload org-mode.

  git checkout master

  git pull

  git branch -D new-lists

  git remote rm ngz (optional)

  M-x org-reload

I'm no specialist of git, there might be even quicker way to do all of
this.

Thanks for testing.

Regards,

-- Nicolas

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Re: [Orgmode] .ods opens file in Emacs, not OpenOffice

2010-07-27 Thread C64 Whiz
Though I love the command line, I was hoping for a mouse-click solution.
I.e. I click on the link and it properly opens up in OO.

On Tue, Jul 27, 2010 at 8:28 AM, Anthony Lander wrote:

>
> On 10-Jul-26, at 8:54 PM, C64 Whiz wrote:
>
>  Hello,
>>
>> I've searched for an answer but can't find a simple one.  I have an
>> OpenOffice document (.ods) I'd like to link to in my .org files.  So I have
>> the following syntax:
>>
>>  [[file:c:/mydata/myfile.ods][File Description]]
>>
>> When I click on the link in OrgMode, Emacs opens the file and not
>> OpenOffice.  Yet, when I'm in file explorer (yes, Windows), double clicking
>> the file does open up Open Office.  So I know the association is there.
>>
>
> Try C-u C-c C-o. On my mac, that switches whether the link opens in emacs
> or through the operating system file association (although mine is the
> reverse. With the prefix it opens in emacs. Not sure why). From the
> doc-string for org-open-at-point:
>
>(org-open-at-point &optional IN-EMACS REFERENCE-BUFFER)
>
>Open link at or after point.
>If there is no link at point, this function will search forward up
> to
>the end of the current line.
>Normally, files will be opened by an appropriate application.  If
> the
>optional argument IN-EMACS is non-nil, Emacs will visit the file.
>With a double prefix argument, try to open outside of Emacs, in the
>application the system uses for this file type.
>
> Hope this helps,
>
>  -Anthony
>
>
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Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Eric Schulte
Hi Charles,

I just pushed up a fix for the extra prompts in your output.  You will
still have a blank line (the output from "x <- rnorm(1)"), however you
can suppress that line by placing the "x <- rnorm(1)" command in a
previous code block in the same session.

Best -- Eric

"Charles C. Berry"  writes:

> I think this is a new feature or perhaps a bug, which I noticed when
> upgrading to version 7.01.
>
> The newline and the two prompts '> >' in the results block below did
> not show up in the earlier versions I used.
>
> If this is a 'feature', is there a clean way to change this behavior?
>
> If this is a bug, is there a simple patch to fix it?
>
> #+begin_src R :session :results output
> ### create x
> x <- rnorm(1)
> ### now print the result
> x
> #+end_src
>
> #+results:
> :
> : > > [1] 2.186783
>
>
> What I would have liked is to have something that looks like this:
>
> #+results:
> : [1] 2.186783
>
> Thanks,
>
> Chuck
>
>
> Charles C. Berry(858) 534-2098
> Dept of Family/Preventive Medicine
> E mailto:cbe...@tajo.ucsd.edu UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>
>
>
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Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry

On Tue, 27 Jul 2010, Eric Schulte wrote:


Hi Charles,

I just pushed up a fix for the extra prompts in your output.  You will
still have a blank line (the output from "x <- rnorm(1)"), however you
can suppress that line by placing the "x <- rnorm(1)" command in a
previous code block in the same session.


Eric,

Thanks. That works for me.

Chuck



Best -- Eric

"Charles C. Berry"  writes:


I think this is a new feature or perhaps a bug, which I noticed when
upgrading to version 7.01.

The newline and the two prompts '> >' in the results block below did
not show up in the earlier versions I used.

If this is a 'feature', is there a clean way to change this behavior?

If this is a bug, is there a simple patch to fix it?

#+begin_src R :session :results output
### create x
x <- rnorm(1)
### now print the result
x
#+end_src

#+results:
:
: > > [1] 2.186783


What I would have liked is to have something that looks like this:

#+results:
: [1] 2.186783

Thanks,

Chuck


Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Prompts again WAS Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry


Eric,

I spoke too soon.

Have a look at the following. You'll see that the 
prompts show up there. :-(


Chuck

#+begin_src R :session :results output
### create x
x <- data.frame(a=rnorm(2),b=rnorm(2))
### now print the result
x
#+end_src

#+results:
:
: > >   a  b
: 1 0.2702748 -0.2938296
: 2 1.1095136  0.1769425



On Tue, 27 Jul 2010, Charles C. Berry wrote:


On Tue, 27 Jul 2010, Eric Schulte wrote:


 Hi Charles,

 I just pushed up a fix for the extra prompts in your output.  You will
 still have a blank line (the output from "x <- rnorm(1)"), however you
 can suppress that line by placing the "x <- rnorm(1)" command in a
 previous code block in the same session.


Eric,

Thanks. That works for me.

Chuck



 Best -- Eric

 "Charles C. Berry"  writes:

>  I think this is a new feature or perhaps a bug, which I noticed when
>  upgrading to version 7.01.
> 
>  The newline and the two prompts '> >' in the results block below did

>  not show up in the earlier versions I used.
> 
>  If this is a 'feature', is there a clean way to change this behavior?
> 
>  If this is a bug, is there a simple patch to fix it?
> 
>  #+begin_src R :session :results output

>  ### create x
>  x <- rnorm(1)
>  ### now print the result
>  x
>  #+end_src
> 
>  #+results:

>  :
> : > >  [1] 2.186783
> 
> 
>  What I would have liked is to have something that looks like this:
> 
>  #+results:

> :  [1] 2.186783
> 
>  Thanks,
> 
>  Chuck
> 
> 
>  Charles C. Berry(858) 534-2098
>  Dept of Family/Preventive 
>  Medicine

>  E mailto:cbe...@tajo.ucsd.edu UC San Diego
>  http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 
>  92093-0901
> 
> 
> 
>  ___

>  Emacs-orgmode mailing list
>  Please use `Reply All' to send replies to the list.
>  Emacs-orgmode@gnu.org
>  http://lists.gnu.org/mailman/listinfo/emacs-orgmode



Charles C. Berry(858) 534-2098
   Dept of Family/Preventive 
Medicine

E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Re: [Orgmode] Fixing slowness of following Gnus links to IMAP articles (was: Behavior of Gnus when called from an hyperlink)

2010-07-27 Thread David Maus
Tassilo Horn wrote:
>Hi Sébastien,

>I'm trying to add a workaround to org-gnus.el which should save the
>slowness of querying the IMAP server by looking up the article number in
>the group's .overview file.  But since I don't have nnimap groups, we
>have to play some question & answer game. ;-)

>Please apply this patch and set
>`org-gnus-nnimap-query-article-no-from-file' to t.

The patch does not work: It calls `nnimap-retrieve-headers-from-file'
without the required arguments (group server) and the headers are not
fetched because `nnimap-retrieve-headers-from-file' looks for a NOV
cache file, not .overview.

Alas: I couldn't figure out how to enable NOV cache for my nnimap
group.  Setting `nnimap-nov-is-evil' to nil didn't help.

Best,
  -- David
-- 
OpenPGP... 0x99ADB83B5A4478E6
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Email. dm...@ictsoc.de


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[Orgmode] Nice links bookmarks

2010-07-27 Thread Andrea Crotti
I was wondering how many people add nice links in the footnotes like [1]

I use "turn-on-orgstruct" and "turn-on-orgtbl" when I write messages and
I suspect that it could be an orgmode feature, but I could not find it.

If I add a footnote I get a similar result but not exactly the same...
Thansk a lot

[1] www.fakelink.com





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[Orgmode] Re: word count checklist?

2010-07-27 Thread Andrea Crotti
I feel that maybe a minor mode would be a good choice for this.
You could set a file variable (something like
// -*- compile-command: "gcc -Wall -o dest file" -*-
)
where you set the max and the minor mode with a hook on every key could
update a value in the modeline.

I'm not sure I can do it but I might try if I don't get asleep :D


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[Orgmode] Re: Installation - no way

2010-07-27 Thread Andrea Crotti
Have a look also here
http://www.ourcomments.org/Emacs/EmacsW32Util.html
It looks a bit old and I'm not sure it contains org-mode but it should
be a bit easier for beginners.

It will be quite hard anyway if you don't use it every day for some time
to grasp the main concepts.



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Re: [Orgmode] Nice links bookmarks

2010-07-27 Thread Eric Schulte
Hi Andrea,

I use `footnote-mode' (which is not related to Org-mode) for footnoting
my emails.  It is provided by footnote.el which I believe is part of
recent Emacses.

Best -- Eric

Andrea Crotti  writes:

> I was wondering how many people add nice links in the footnotes like [1]
>
> I use "turn-on-orgstruct" and "turn-on-orgtbl" when I write messages and
> I suspect that it could be an orgmode feature, but I could not find it.
>
> If I add a footnote I get a similar result but not exactly the same...
> Thansk a lot
>
> [1] www.fakelink.com
>
>
>
>
>
> ___
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[Orgmode] Re: Nice links bookmarks

2010-07-27 Thread Matt Lundin
Hi Andrea,

Andrea Crotti  writes:

> I was wondering how many people add nice links in the footnotes like [1]
>
> I use "turn-on-orgstruct" and "turn-on-orgtbl" when I write messages and
> I suspect that it could be an orgmode feature, but I could not find it.
>
> If I add a footnote I get a similar result but not exactly the same...
> Thansk a lot
>
> [1] www.fakelink.com
>

Could you please clarify your question? I'm not quite sure what you are
trying to accomplish.

Are you perhaps inquiring how to use org-footnote in message-mode? You
can do so with "M-x org-footnote-action".

But that may not be what you are looking for

Best,
Matt

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Re: [Orgmode] Fixing slowness of following Gnus links to IMAP articles (was: Behavior of Gnus when called from an hyperlink)

2010-07-27 Thread Nick Dokos
David Maus  wrote:

> ...
> Alas: I couldn't figure out how to enable NOV cache for my nnimap
> group.  Setting `nnimap-nov-is-evil' to nil didn't help.
> 

[Warning: I know very little about gnus, perhaps just enough
 to be dangerous and you probably already know all this, but just
 in case... The bit that caught my attention is the slowness of
 the uid search command on some versions of Courier, which seems...
 related.]

Perhaps this bit from the Gnus docs might help?

,
| `nnimap-nov-is-evil'
|  Never generate or use a local NOV database. Defaults to the value
|  of `gnus-agent'.
| 
|  Using a NOV database usually makes header fetching much faster,
|  but it uses the `UID SEARCH UID' command, which is very slow on
|  some servers (notably some versions of Courier). Since the Gnus
|  Agent caches the information in the NOV database without using the
|  slow command, this variable defaults to true if the Agent is in
|  use, and false otherwise.
`

Seems to have something to do with the agent? In my case, both

  gnus-agent
and
  gnus-agent-cache

are t, but I have no idea how to set up nnimap, so I can't check
any of this.

One-of-these-days-I'll-really-understand-gnus-but-not-soon-ly yours,
Nick

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[Orgmode] Re: Nice links bookmarks

2010-07-27 Thread Andrea Crotti
I meant exactly what Eric said, footnote.el is quite cool in fact.
But we can achieve the same result with org-mode (even in his minor-mode
version), so why don't use it?

With this variable moreover we get the same style:
(setq org-footnote-auto-label 'plain)

The only thing that puzzles me is the fact that with C-c I should go
back in the text while in message-mode it will try to send it, BUT
looking at what the command does we get:

--8<---cut here---start->8---
C-c C-c runs the command orgtbl-ctrl-c-ctrl-c
--8<---cut here---end--->8---

Does that mean that in the minor mode it passes the control on the major
mode for keys?

Could it not be possible to execute the footnote command with C-c if
we're on a footnote and message-mode command otherwise?
Thanks


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Re: Prompts again WAS Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry


Eric,

In ob-R.el, changing this

  (if (string-match "^\\([ >]+\\)\\[[0-9]+\\]" line)

to this

  (if (string-match "^\\([ ]*[>+][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)

seems to fix things (note I added plus sign which is the continuation 
prompt in R).


I tried it on a bunch of varied source blocks and it seems to work OK, but 
I worry that there may be case where it will fail.


Chuck


On Tue, 27 Jul 2010, Charles C. Berry wrote:



Eric,

I spoke too soon.

Have a look at the following. You'll see that the prompts show up there. :-(

Chuck

#+begin_src R :session :results output
### create x
x <- data.frame(a=rnorm(2),b=rnorm(2))
### now print the result
x
#+end_src

#+results:
:
: > >a  b
:  1 0.2702748 -0.2938296
:  2 1.1095136  0.1769425



On Tue, 27 Jul 2010, Charles C. Berry wrote:


 On Tue, 27 Jul 2010, Eric Schulte wrote:

>   Hi Charles,
> 
>   I just pushed up a fix for the extra prompts in your output.  You will

>   still have a blank line (the output from "x <- rnorm(1)"), however you
>   can suppress that line by placing the "x <- rnorm(1)" command in a
>   previous code block in the same session.

 Eric,

 Thanks. That works for me.

 Chuck

> 
>   Best -- Eric
> 
>   "Charles C. Berry"  writes:
> 
> >   I think this is a new feature or perhaps a bug, which I noticed when

> >   upgrading to version 7.01.
> > 
> >   The newline and the two prompts '> >' in the results block below did

> >   not show up in the earlier versions I used.
> > 
> >   If this is a 'feature', is there a clean way to change this behavior?
> > 
> >   If this is a bug, is there a simple patch to fix it?
> > 
> >   #+begin_src R :session :results output

> >   ### create x
> >   x <- rnorm(1)
> >   ### now print the result
> >   x
> >   #+end_src
> > 
> >   #+results:

> >   :
> > : > >   [1] 2.186783
> > 
> > 
> >   What I would have liked is to have something that looks like this:
> > 
> >   #+results:

> > :   [1] 2.186783
> > 
> >   Thanks,
> > 
> >   Chuck
> > 
> > 
> >   Charles C. Berry(858) 534-2098
> >   Dept of Family/Preventive 
> >   Medicine

> >   E mailto:cbe...@tajo.ucsd.edu   UC San Diego
> >   http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 
> >   92093-0901
> > 
> > 
> > 
> >   ___

> >   Emacs-orgmode mailing list
> >   Please use `Reply All' to send replies to the list.
> >   Emacs-orgmode@gnu.org
> >   http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> 


 Charles C. Berry(858) 534-2098
Dept of Family/Preventive
 Medicine
 E mailto:cbe...@tajo.ucsd.edu  UC San Diego
 http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Charles C. Berry(858) 534-2098
   Dept of Family/Preventive 
Medicine

E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901



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[Orgmode] R Babel Example

2010-07-27 Thread Russell Adams
I just did a sample of R with Babel in dual formats, png for viewing
inline and PDF for latex importing of smooth graphics.

Nothing official, but open to all. I borrowed a free sample graph with
credit to the original URL, thanks Paul Murrel!

http://adamsinfoserv.com/RExample/RBabelExample.org
http://adamsinfoserv.com/RExample/RBabelExample_screenshot.png
http://adamsinfoserv.com/RExample/RBabelExample.pdf

I was trying to demonstrate why its so easy to write complex reports
in Org, with viewing my R code results inline, and publishing to great
PDF output.

Enjoy.


--
Russell Adamsrlad...@adamsinfoserv.com

PGP Key ID: 0x1160DCB3   http://www.adamsinfoserv.com/

Fingerprint:1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3

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[Orgmode] Eliminate line breaks in html

2010-07-27 Thread John Hendy
Hi,


I use org for exporting to html and then pasting into blogger... but every
time I do I need to delete line breaks. Is there a way to get org to just
publish the blob without breaking lines every time? I'm guessing it has to
do with my minor fill mode as the line breaks tend to be the same as they
are in org.

In typical export, everything is surrounded by  tags but in blogger on
doesn't have these and thus line breaks are line breaks. I could resort to
explicit html every time I post (requiring  for every line break) but
this would also require fixing all pre-existing posts which is pretty much
not an option.

Any idea what I could do?


Thanks,
John
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[Orgmode] Migrating from zim to org-mode ?

2010-07-27 Thread Olivier Berger
Hi.

Is there docs already compiled by someone having "migrated" from Zim, a
desktop wiki [0], to Emacs + org-mode ?

Zim also uses text files, so I guess a few conversion scripts wouldn't
be so hard, but of course if someone already tried it, it would save me
time and effort.

Some useability / convenience comparison betw Zim and Org-Mode would be
interesting to me too.

Thanks in advance.

Best regards,

[0] http://zim-wiki.org/
-- 
Olivier BERGER 
http://www-public.it-sudparis.eu/~berger_o/ - OpenPGP-Id: 2048R/5819D7E8
Ingénieur Recherche - Dept INF
Institut TELECOM, SudParis (http://www.it-sudparis.eu/), Evry (France)


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[Orgmode] Re: Fixing slowness of following Gnus links to IMAP articles

2010-07-27 Thread Tassilo Horn
David Maus  writes:

Hi David,

>>I'm trying to add a workaround to org-gnus.el which should save the
>>slowness of querying the IMAP server by looking up the article number
>>in the group's .overview file.  But since I don't have nnimap groups,
>>we have to play some question & answer game. ;-)
>
>>Please apply this patch and set
>>`org-gnus-nnimap-query-article-no-from-file' to t.
>
> The patch does not work: It calls `nnimap-retrieve-headers-from-file'
> without the required arguments (group server)

Argh, stupid me!  Here's a corrected patch.

--8<---cut here---start->8---
diff --git a/lisp/org-gnus.el b/lisp/org-gnus.el
index 7ec305b..7a339cd 100644
--- a/lisp/org-gnus.el
+++ b/lisp/org-gnus.el
@@ -55,6 +55,16 @@ negates this setting for the duration of the command."
   :group 'org-link-store
   :type 'boolean)
 
+(defcustom org-gnus-nnimap-query-article-no-from-file nil
+  "If non-nil, `org-gnus-follow-link' will try to translate
+Message-Ids to article numbers by querying the .overview file.
+Normally, this translation is done by querying the IMAP server,
+which is usually very fast.  Unfortunately, some (maybe badly
+configured) IMAP servers don't support this operation quickly.
+So if following a link to a Gnus article takes ages, try setting
+this variable to `t'."
+  :group 'org-link-store
+  :type 'boolean)
 
 ;; Install the link type
 (org-add-link-type "gnus" 'org-gnus-open)
@@ -173,7 +183,11 @@ If `org-store-link' was called with a prefix arg the 
meaning of
   (cond ((and group article)
 (gnus-activate-group group t)
 (condition-case nil
-(let ((backend (car (gnus-find-method-for-group group
+(let* ((method (gnus-find-method-for-group group))
+   (backend (car method))
+   (server (cadr method)))
+  (message "method = %s\ngroup = %s\nbackend = %s\nserver = %s"
+   method group backend server)
   (cond
((eq backend 'nndoc)
 (if (gnus-group-read-group t nil group)
@@ -183,6 +197,12 @@ If `org-store-link' was called with a prefix arg the 
meaning of
(t
 (let ((articles 1)
   group-opened)
+  ;; work arround IMAP servers that perform badly in
+  ;; SEARCH commands.
+  (when (and (eq backend 'nnimap)
+ org-gnus-nnimap-query-article-no-from-file)
+(let ((headers (nnimap-retrieve-headers-from-file group 
server)))
+  (message "headers = %s" headers)))
   (while (and (not group-opened)
   ;; stop on integer overflows
   (> articles 0))
--8<---cut here---end--->8---


> and the headers are not fetched because
> `nnimap-retrieve-headers-from-file' looks for a NOV cache file, not
> .overview.

Aren't overview file and NOV file synonyms?

Hm, anyway.  In the Gnus docs I've found this paragraph:

,[ (info "(gnus)IMAP") ]
| `nnimap-nov-is-evil'
|  Never generate or use a local NOV database. Defaults to the value
|  of `gnus-agent'.
| 
|  Using a NOV database usually makes header fetching much faster,
|  but it uses the `UID SEARCH UID' command, which is very slow on
|  some servers (notably some versions of Courier). Since the Gnus
|  Agent caches the information in the NOV database without using the
|  slow command, this variable defaults to true if the Agent is in
|  use, and false otherwise.
`

So maybe we're trying to replace one slow command with another slow
command.  Especially, the fact that Courier is explicitly mentioned is a
bit frustrating.  Well, let's try it out and see if it helps a bit.

> Alas: I couldn't figure out how to enable NOV cache for my nnimap
> group.  Setting `nnimap-nov-is-evil' to nil didn't help.

This variable defaults to the value of `gnus-agent', so I assume the
agent has to be enabled (which is default), and most probably the IMAP
server has to be agentized as well.  That can be done in the server
buffer (`^' in *Group*), and then:

,[ (info "(gnus)Server Agent Commands") ]
| `J a'
|  Add the current server to the list of servers covered by the Gnus
|  Agent (`gnus-agent-add-server').
`

Bye,
Tassilo


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[Orgmode] Re: Fixing slowness of following Gnus links to IMAP articles

2010-07-27 Thread Tassilo Horn
Nick Dokos  writes:

Hi Nick,

> [Warning: I know very little about gnus, perhaps just enough
>  to be dangerous and you probably already know all this, but just
>  in case... The bit that caught my attention is the slowness of
>  the uid search command on some versions of Courier, which seems...
>  related.]

Yeah, just a minute ago when replying to David I also stumbled across
that paragraph.  So maybe we are trying to replace one extremely long
running command which only occurs when following links (or searching for
Message-Ids) with a constant slowness in normal operation.  But let's
try it out.

> Perhaps this bit from the Gnus docs might help?
>
> ,
> | `nnimap-nov-is-evil'
> |  Never generate or use a local NOV database. Defaults to the value
> |  of `gnus-agent'.
> | 
> |  Using a NOV database usually makes header fetching much faster,
> |  but it uses the `UID SEARCH UID' command, which is very slow on
> |  some servers (notably some versions of Courier). Since the Gnus
> |  Agent caches the information in the NOV database without using the
> |  slow command, this variable defaults to true if the Agent is in
> |  use, and false otherwise.
> `
>
> Seems to have something to do with the agent? In my case, both
>
>   gnus-agent
> and
>   gnus-agent-cache
>
> are t, but I have no idea how to set up nnimap, so I can't check any
> of this.

It should be as easy as:

(add-to-list 'gnus-secondary-select-methods
 '(nnimap "MyAccount"
  (nnimap-address "my-imap.server.com")))

and putting your user/password for my-imap.server.com into your
~/.authinfo.  You might want to put a (nnimap-stream tls) into the
method spec above if the server supports TLS (or ssl for SSL).

> One-of-these-days-I'll-really-understand-gnus-but-not-soon-ly yours,

Nobody understands Gnus. ;-)

Bye,
Tassilo


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