Re: [O] Organizing and taming hectic Academia work (faculty viewpoint)? Tips or a good guides sought after :)

2015-06-15 Thread Bob Newell
"Julian Burgos"  writes:

> b) I write the manuscript in org-mode.  Then I send the org-mode file to
> my coauthor.  Because the org-mode file is just a text file, my coauthor
> can use Word to edit it.  I ask him/her *not* to use "track changes" and
> to save the edited version also as a text file.  Then, when I receive it I
> use ediff in emacs to compare both documents and incorporate the edits I
> want.

Simple is best, and I wish I had thought of this simple idea before I
took an 87,000 word novel that I wrote in org-mode, output as ODT,
converted to DOCX, and then sent to an editor. I got back all the track
changes stuff and even worse, margin notes, and punctuation (like quotes
and ellipses) changed over to Word-ish characters.

It wasn't utterly useless but it created a lot of extra work, which
still isn't over. Next time I'll do as per above, tell her to just edit
the thing directly, write her notes in-line, and keep it as pure ASCII.

I really believe she thinks I was going to use Word to publish the
novel. Failure to communicate on my part. I could say lack of judgment
on her part but that's unfair; in her world, most everyone uses Word at
some stage in the process.

-- 
Bob Newell
Honolulu, Hawai`i
* Sent via Ma Gnus 0.12-Emacs 24.3-Linux Mint 17 *



Re: [O] How to make footnotes be fnlocal by default?

2015-06-15 Thread William Denton

Thanks, Kyle and Rasmus.

Attached is a tiny patch to add mention of this variable in the section of the 
docs where all those options are listed.


Bill


On 16 June 2015, Rasmus wrote:


William Denton  writes:


I'm writing something with a bunch of footnotes and instead of doing
them by hand I'm using C-c C-x f, which in the usual Emacs/Org way
strikes me as a more difficult at first but then turns into magic.

By default, adding a footnote puts it at the bottom of the document.
This is because of org-footnote-define-inline:

'Non-nil means define footnotes inline, at reference location. When
nil, footnotes will be defined in a special section near the end of
the document. When t, the [fn:label:definition] notation will be used
to define the footnote at the reference position."

However, there are three (not two) possible options available in
STARTUP options:


fninlinedefine footnotes inline
fnnoinline  define footnotes in separate section
fnlocal define footnotes near first reference, but not inline


I found I like fnlocal, which puts the footnotes at the bottom of the
paragraph or section, where they are nearby and easy to see.

I'd like to make this the default in all Org files by setting
org-footnote-define-inline, but it seems I can't---all I can definte
that way are the fninline and fnnoinline options.  Am I correct?  Is
there some way around this, or perhaps a (setq
org-footnote-define-inline 'fnlocal) setting could be added?


How about:
   (setq org-footnote-section nil)

Rasmus




--
William Denton ↔  Toronto, Canada ↔  https://www.miskatonic.org/*** org.texi	2015-05-31 13:00:44.415430490 -0400
--- org.texi.new	2015-06-15 21:17:30.771751673 -0400
***
*** 17155,17161 
  @vindex org-footnote-auto-adjust
  To influence footnote settings, use the following keywords.  The
  corresponding variables are @code{org-footnote-define-inline},
! @code{org-footnote-auto-label}, and @code{org-footnote-auto-adjust}.
  @cindex @code{fninline}, STARTUP keyword
  @cindex @code{nofninline}, STARTUP keyword
  @cindex @code{fnlocal}, STARTUP keyword
--- 17155,17162 
  @vindex org-footnote-auto-adjust
  To influence footnote settings, use the following keywords.  The
  corresponding variables are @code{org-footnote-define-inline},
! @code{org-footnote-auto-label}, @code{org-footnote-auto-adjust},
! and @code{org-footnote-section}.
  @cindex @code{fninline}, STARTUP keyword
  @cindex @code{nofninline}, STARTUP keyword
  @cindex @code{fnlocal}, STARTUP keyword


Re: [O] How to make footnotes be fnlocal by default?

2015-06-15 Thread Rasmus
William Denton  writes:

> I'm writing something with a bunch of footnotes and instead of doing
> them by hand I'm using C-c C-x f, which in the usual Emacs/Org way
> strikes me as a more difficult at first but then turns into magic.
>
> By default, adding a footnote puts it at the bottom of the document.
> This is because of org-footnote-define-inline:
>
> 'Non-nil means define footnotes inline, at reference location. When
> nil, footnotes will be defined in a special section near the end of
> the document. When t, the [fn:label:definition] notation will be used
> to define the footnote at the reference position."
>
> However, there are three (not two) possible options available in
> STARTUP options:
>
>> fninlinedefine footnotes inline
>> fnnoinline  define footnotes in separate section
>> fnlocal define footnotes near first reference, but not inline
>
> I found I like fnlocal, which puts the footnotes at the bottom of the
> paragraph or section, where they are nearby and easy to see.
>
> I'd like to make this the default in all Org files by setting
> org-footnote-define-inline, but it seems I can't---all I can definte
> that way are the fninline and fnnoinline options.  Am I correct?  Is
> there some way around this, or perhaps a (setq
> org-footnote-define-inline 'fnlocal) setting could be added?

How about:
(setq org-footnote-section nil) 

Rasmus

-- 
Send from my Emacs




Re: [O] How to make footnotes be fnlocal by default?

2015-06-15 Thread Kyle Meyer
William Denton  wrote:
[...]
> However, there are three (not two) possible options available in
> STARTUP options:
>
>> fninlinedefine footnotes inline
>> fnnoinline  define footnotes in separate section
>> fnlocal define footnotes near first reference, but not inline
>
> I found I like fnlocal, which puts the footnotes at the bottom of the
> paragraph or section, where they are nearby and easy to see.
>
> I'd like to make this the default in all Org files by setting
> org-footnote-define-inline, but it seems I can't---all I can definte
> that way are the fninline and fnnoinline options.  Am I correct?  Is
> there some way around this, or perhaps a (setq
> org-footnote-define-inline 'fnlocal) setting could be added?

I think you can get this by setting org-footnote-section to nil.  (I
haven't tried this but am guessing based off of org-startup-options.)

-- 
Kyle



[O] How to make footnotes be fnlocal by default?

2015-06-15 Thread William Denton

I'm writing something with a bunch of footnotes and instead of doing them by 
hand I'm using C-c C-x f, which in the usual Emacs/Org way strikes me as a more 
difficult at first but then turns into magic.

By default, adding a footnote puts it at the bottom of the document.  This is 
because of org-footnote-define-inline:


'Non-nil means define footnotes inline, at reference location. When nil, 
footnotes will be defined in a special section near the end of the document. 
When t, the [fn:label:definition] notation will be used to define the footnote 
at the reference position."


However, there are three (not two) possible options available in STARTUP 
options:



fninlinedefine footnotes inline
fnnoinline  define footnotes in separate section
fnlocal define footnotes near first reference, but not inline


I found I like fnlocal, which puts the footnotes at the bottom of the paragraph 
or section, where they are nearby and easy to see.


I'd like to make this the default in all Org files by setting 
org-footnote-define-inline, but it seems I can't---all I can definte that way 
are the fninline and fnnoinline options.  Am I correct?  Is there some way 
around this, or perhaps a (setq org-footnote-define-inline 'fnlocal) setting 
could be added?


Bill
--
William Denton ↔  Toronto, Canada ↔  https://www.miskatonic.org/

Re: [O] Custom column environment in beamer export

2015-06-15 Thread Rasmus
Suvayu Ali  writes:

> * Fitting technique:B_minipage:
>   :PROPERTIES:
>   :BEAMER_env: minipage
>   :BEAMER_arg: 0.1\linewidth
>   :END:
> +/cFit/+

The closest would probably be something like

(add-to-list 'org-beamer-environments-extra
 '("minipage"
   "m"
   "\\begin{minipage}%o%a\n\\structure{%h}"
   "\\end{minipage}"))

Which would afford you something like

* slide
** Fitting technique:B_minipage:
  :PROPERTIES:
  :BEAMER_env: minipage
  :BEAMER_OPT: [t]{0.1\linewidth}
  :BEAMER_ACT: <5>
  :END:
  /cFit/

Unfortunately, BEAMER_OPTs are wrapped in square brackets thanks to
org-beamer--normalize-argument, so the above won't actually work (see
org-beamer--format-block).  From the looks of it I'd be willing to call it
a bug, but Nicolas may have had something in mind.

Perhaps these days it would be nice to allow the third element of
org-beamer-environments-extra to be a λ taking either the object or so.
Then again, perhaps this is an overkill and too low-level.

Personally, I'd use a block, e.g.

#+attr_latex: :options [t]{.1\textwidth}
#+begin_minipage
Cfit
#+end_minipage

Rasmus

-- 
This space is left intentionally blank




[O] Custom column environment in beamer export

2015-06-15 Thread Suvayu Ali
Hi,

Is it possible to define a custom column like environment?  At the
moment I'm hacking around the need with this:

(add-to-list 'org-beamer-environments-extra
 '("minipage" "m" "\\begin{minipage}%H" "\\end{minipage}%"))

With the above I can export the following

* 0.1\linewidth  :B_minipage:
  :PROPERTIES:
  :BEAMER_env: minipage
  :END:
+/cFit/+

to

\begin{minipage}{0.1\linewidth}
\structure{\emph{cFit}}
\end{minipage}%

However within Org, not being able to specify a descriptive headline
sacrifices readability.  It would be great if I could write something
like this:

* Fitting technique  :B_minipage:
  :PROPERTIES:
  :BEAMER_env: minipage
  :BEAMER_arg: 0.1\linewidth
  :END:
+/cFit/+

I seem to recall this was possible in the past.  Is there any chance to
get something like this going?

Thanks for any thoughts.

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] Specifying ATTR_LATEX document wide?

2015-06-15 Thread Nicolas Goaziou
Rainer M Krug  writes:

> Thanks for the clarification. Is there a technical or security reason
> for this? because especially for export, file local variables would make
> sense to avoid the #+BIND keywords?

ISTR there is a technical reason for this. Under some circumstances,
local variables are not activated during export. I cannot remember which
ones, unfortunately.

Also, unlike to local variables, BIND keywords can be set through
SETUPFILE keywords.


Regards,



Re: [O] Tangling takes long - profiling and calling R

2015-06-15 Thread Nicolas Goaziou
Hello,

Rainer M Krug  writes:

> I have a relatively large file with
> about 200 =source blocks (R) to be tangled to get an R package. But the
> tangling takes about 20 seconds.
>
> Profiling the tangling showed that the call to ~mapcar~ in
> ~org-babel-params-from-properties~ takes about 40% of the execution time
> (see profiler excerpt below). Is there anything one can do to make this
> faster?

In this function, there is

 ;; DEPRECATED header arguments specified as separate property at
 ;; point of definition
 (let (val sym)
   (org-babel-parse-multiple-vars
(delq nil
  (mapcar
   (lambda (header-arg)
 (and (setq val (org-entry-get (point) header-arg t))
  (cons (intern (concat ":" header-arg))
(org-babel-read val
   (mapcar
#'symbol-name
(mapcar
 #'car
 (org-babel-combine-header-arg-lists
  org-babel-common-header-args-w-values
  (progn
(setq sym (intern (concat "org-babel-header-args:" lang)))
(and (boundp sym) (eval sym))

While the 3 `mapcar' calls could be turned into a single one, I wonder
if this snippet could be removed altogether instead. It has been
deprecated for 2 years already.

WDYT?

Regards,

-- 
Nicolas Goaziou



[O] current status of citation syntax discussion

2015-06-15 Thread Matt Price
Hi folks,

Am just wondering what the current status is of the work that was being
done earlier this year on improved citation support in org.  Has an
official syntax been settled on? Are there blessed citation managers and
export solutions? I would like to figure out a personal system over the
summer, and would prefer to adhere to whatever stand(s) others have settled
on.

Thanks,
Matt


[O] remedial elisp: treating result of plist-get as a string

2015-06-15 Thread Matt Price
Hi,

I'm looking at some old code Erik Hetzner wrote for me in January.

I have an html string stored in a plist cell, and a function that converts
an html string to org-mode syntax.  I want to do something like this:

 (org-zotxt-htmlstring2org (plist-get item :citation-html))


But for whatever reason this doesn't produce a string.  It might help to
give a little context -- this is a very dirty hack intended to get
zotero-beased bibliographies to display in ODT documents. I have no doubt
there are better methods for this, but I am currently trying this:

;; zotxt
(org-add-link-type "zotero"
   (lambda (rest)
 (zotxt-select-key (substring rest 15)))
   (lambda (path desc format)
 (if (string-match "^@\\(.*\\)$" desc)
 (cond ((eq format 'latex)
(format "\\cite{%s}" (match-string 1 desc)))
   ((eq format 'md)
desc)
   ((eq format 'html)
(deferred:$
  (zotxt-get-item-bibliography-deferred
`(:key , (substring path 15)))
  (deferred:nextc it
(lambda (item)
  (plist-get item :citation-html)))
  (deferred:sync! it)))
   ((eq format 'odt)
(deferred:$
  (zotxt-get-item-bibliography-deferred
`(:key , (substring path 15)))
  (deferred:nextc it
(lambda (item)
  (org-zotxt-htmlstring2org (plist-get
item :citation-html)) ))
  (deferred:sync! it)))
   (t nil)
   nil
---

The html export is working perfectly well, but I am trying to get
/something/ to display in odt export, and failing. (I realize that a
further step will be required, namely, sending the org-mode string
generated by org-zotxt-htmlstring2org through the odt export filter -- I
don't have the faintest idea how to do that but am assuming it's
possible).

Hints appreciated, as always.

Matt


Re: [O] Tangling takes long - profiling and calling R

2015-06-15 Thread Charles C. Berry

On Mon, 15 Jun 2015, Rainer M Krug wrote:


Hi

I have a relatively large file with
about 200 =source blocks (R) to be tangled to get an R package. But the
tangling takes about 20 seconds.

Profiling the tangling showed that the call to ~mapcar~ in
~org-babel-params-from-properties~ takes about 40% of the execution time
(see profiler excerpt below). Is there anything one can do to make this
faster?

In addition to this, I observed there is some interaction with ESS when
tangling, which in my understanding is not necessary. I get messages
like

,
| ...
| Wrote /Users/rainerkrug/Documents/Projects/EnergyBalance/.Rbuildignore
| Wrote /Users/rainerkrug/Documents/Projects/EnergyBalance/tests/wpLELTest.R
| You are developing: (EnergyBalance)
| Wrote 
/Users/rainerkrug/Documents/Projects/EnergyBalance/R/plotwpLELFitListParDistr.R
| You are developing: (EnergyBalance)
| ...
`

where the messages "You are developing: (EnergyBalance)" come from
ESS. Is this to be expected that R is called for some blocks, but not
for others, when tangling?


The major mode is invoked when tangling, if possible.

This enables comments to be rendered. See the docstring for 
`org-babel-spec-to-string'.


HTH,

Chuck



Re: [O] clocktables output in hours and minutes only

2015-06-15 Thread Sharon Kimble
Sebastien Vauban  writes:

> Sharon Kimble  writes:
>> Still on about clocktables, how can I have the time output show just
>> in "hours.minutes" and not in "days.hours.minutes" please?
>
> IIRC, customizing `org-time-clocksum-format' should help.
>
Thanks Seb.

Its worked extremely well and done the job :)

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.0, fluxbox 1.3.7, emacs 24.5.50.1


signature.asc
Description: PGP signature


Re: [O] Add LaTeX to SVG support to org-mode

2015-06-15 Thread Suvayu Ali
Hi Adam,

As others mentioned, diffs are easier to work with.  Please see the
instructions on the how to contribute page on Worg.

That said, if you do not want to checkout the latest Org (the version
you sent looks like a version that was shipped with Emacs).  You can
still generate a diff.  Copy the original somewhere, and then edit the
copy.  Once done editing, you can generate a diff like this:

$ diff -u /path/to/original/org.el /path/to/edited/org.el > org.el.diff

If you then send the org.el.diff file, people would be happy to look at
it and help you get to a good solution.

Hope this email ecourages you to put in the extra effort :).

Cheers,


On Sat, Jun 13, 2015 at 06:45:51PM +0200, Adam Sneller wrote:
> 
> Out of the box, emacs supports two methods for rendering LaTeX previews in 
> orgmode: dvipng and imagemagick. I want to add a third method, using dvisvgm. 
> I have modified the org.el file to add org-create-formula-image-with-dvisvg. 
> Everything seems to work fine, except that orgmode is unable to find the SVG 
> file and errors "Failed to create svg file from ...". But the file it is 
> looking for does exist.
> 
> Any ideas?

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] Organizing and taming hectic Academia work (faculty viewpoint)? Tips or a good guides sought after :)

2015-06-15 Thread Julian Burgos
Hi Ken,

This is a good idea! I will give it a try.  Thanks!

Julian

> Hi Julian,
>
> On 2015-06-10 at 10:16, Julian Burgos  wrote:
>> a) I first write in org-mode. Export to Word, either exporting first
>> to ODT and then to Word, or to LaTex and then use pandoc to convert
>> LaTex to Word. My coauthor can edit the document as he wishes, using
>> the "Track changes" option. Then, I transcribe their edits back into
>> the org-mode document. Advantage of this approach: your coauthor
>> receives a clean word file, that could include figures, references,
>> etc., and he/she uses the tools she likes to edit the file.
>> Disadvantage: you have to manually incorporate the changes to the
>> org-mode file each time there are edits.
>>
>> b) I write the manuscript in org-mode. Then I send the org-mode file
>> to my coauthor. Because the org-mode file is just a text file, my
>> coauthor can use Word to edit it. I ask him/her *not* to use "track
>> changes" and to save the edited version also as a text file. Then,
>> when I receive it I use ediff in emacs to compare both documents and
>> incorporate the edits I want. Advantage of this approach: the merging
>> of the documents is easy using ediff. Disadvantage: your coauthor has
>> to edit a weird-looking document, with markup, code blocks, etc.
>
> It seems like with a bit of extra (scriptable?) work you could remove both
> disadvantages.
>
> Why can't you use method (a) above, and then DOCX -> Org via pandoc (with
> --accept-all option)?
>
> I know pandoc introduce some of its own changes to the Org syntax but not
> the document itself. You can get around this. You can remove the
> pandoc-generated changes automagically so that only co-author changes
> appear in Org format, which you can then use with your (b) above and emacs
> ediff.
>
> Original: Your Org source
> A: Org -> DOCX for co-authors (using pandoc)
> B: Org -> DOCX -> Org (using pandoc).
> C: A -> Org (using pandoc and --accept-all-changes)
> D: B-Original
>
> The difference between B and Original are pandoc-introduced changes that
> you do not want. Ignore/remove these changes from C, call it D and then
> the difference between D and the Original are your co-author comments. Now
> your authors can edit DOCX with Track Changes and you can work on those
> edits with Emacs ediff.
>
>   -k.
>





[O] org-babel-load-file fails with (wrong-type-argument stringp nil)

2015-06-15 Thread Marcelo de Moraes Serpa
Hi list,

I'm using Org-mode version 8.2.10 (8.2.10-dist @
/Users/fullofcaffeine/.emacs.d/vendor/org-mode/lisp/) -- which as you can
see was installed in a custom location, with emacs GNU Emacs 24.3.1
(x86_64-apple-darwin11.4.2, Carbon Version 1.6.0 AppKit 1138.51) of
2014-04-03 on Yukikaze.local.

After updating to org 8.2.10, I started getting some cryptic (for me)
errors with org-babel. My main conf file is an org file which gets
processed by babel to .el. It used to work fine, but now I get this
(stacktrace follows):

`
Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  expand-file-name(nil)
  load-file(nil)
  org-babel-load-file("/Users/fullofcaffeine/.emacs.d/fullofcaffeine.org")
  mapc(org-babel-load-file ("/Users/fullofcaffeine/.emacs.d/
fullofcaffeine.org"))
  eval-buffer(# nil
"/Users/fullofcaffeine/.emacs.d/init.el" nil t)  ; Reading at buffer
position 1458
  load-with-code-conversion("/Users/fullofcaffeine/.emacs.d/init.el"
"/Users/fullofcaffeine/.emacs.d/init.el" t t)
  load("/Users/fullofcaffeine/.emacs.d/init" t t)
  #[nil "^H\205\276^@   \306=\203^Q^@\307^H\310Q\202A^@
\311=\2033^@\312\307\313\314#\203#^@\315\202A^@\312\307\313\316#\203/^@\317\202A^@\315\202A^@
  \320=\203=^@\321\202A^@\307^H\322Q^Z\323^S\324\n\$
  command-line()
  normal-top-level()
`

Here's my init.el file: http://pastie.org/private/1eajm9mkmqfjbpr0z3ska

Does anyone know what is the issue?

Thanks,

-- Marcelo.


Re: [O] bug in ox-koma-letter

2015-06-15 Thread Nicolas Goaziou
Hello,

Rasmus  writes:

> Thomas Holst  writes:
>
>> when I try to export an subtree with koma letter I get the following
>> error:
>>
>>   cond: Symbol's value as variable is void: with-title
>>
>> This seems to be related to the following commit:
>>
>>   d3196f0 * ox-koma-letter: Fix missing \begin{document}
>>
>> because if I switch to the commit prior to this one (6463b6c *
>> ox-koma-letter: Fix typo in docstring) everything works
>> fine and I don't get an error.
>>
>> Emacs Version: 24.3.1 on Ubuntu 12.04
>> org-version: most recent git
>
> Can you please provide a minimal example that triggers the bug from
> emacs -q? I'm unable to produce it with the example from org (with one
> extra outer level).

My bad. Fixed in bfe1b2fbe2baa62cd26bf9a76077e56a9c243075.

Thank you.

Regards,

-- 
Nicolas Goaziou



Re: [O] bug in ox-koma-letter

2015-06-15 Thread Rasmus
Hi,

Thomas Holst  writes:

> when I try to export an subtree with koma letter I get the following
> error:
>
>   cond: Symbol's value as variable is void: with-title
>
> This seems to be related to the following commit:
>
>   d3196f0 * ox-koma-letter: Fix missing \begin{document}
>
> because if I switch to the commit prior to this one (6463b6c *
> ox-koma-letter: Fix typo in docstring) everything works
> fine and I don't get an error.
>
> Emacs Version: 24.3.1 on Ubuntu 12.04
> org-version: most recent git

Can you please provide a minimal example that triggers the bug from
emacs -q? I'm unable to produce it with the example from org (with one
extra outer level).

Rasmus

-- 
C is for Cookie




[O] bug in ox-koma-letter

2015-06-15 Thread Thomas Holst
Hello all,

when I try to export an subtree with koma letter I get the following
error:

  cond: Symbol's value as variable is void: with-title

This seems to be related to the following commit:

  d3196f0 * ox-koma-letter: Fix missing \begin{document}

because if I switch to the commit prior to this one (6463b6c *
ox-koma-letter: Fix typo in docstring) everything works
fine and I don't get an error.

Emacs Version: 24.3.1 on Ubuntu 12.04
org-version: most recent git

Thanks for looking into this.

-- 
Bis neulich ...
  Thomas



[O] allow italic quote marks? org-emphasis-regexp-components

2015-06-15 Thread Myles English
Hello,

Can anyone tell me what to set org-emphasis-regexp-components to in
order to allow italic quote marks?

i.e. /"like this"/

I don't understand the documentation and am just not in the mood to
spend the next hour or so working it out.  (That is a rule of thumb for
me; if it involves a regular expression, it will take at least an hour,
and three cups of tea.)

Thanks,
Myles




[O] Tangling takes long - profiling and calling R

2015-06-15 Thread Rainer M Krug
Hi

I have a relatively large file with
about 200 =source blocks (R) to be tangled to get an R package. But the
tangling takes about 20 seconds.

Profiling the tangling showed that the call to ~mapcar~ in
~org-babel-params-from-properties~ takes about 40% of the execution time
(see profiler excerpt below). Is there anything one can do to make this
faster?

In addition to this, I observed there is some interaction with ESS when
tangling, which in my understanding is not necessary. I get messages
like

,
| ...
| Wrote /Users/rainerkrug/Documents/Projects/EnergyBalance/.Rbuildignore
| Wrote /Users/rainerkrug/Documents/Projects/EnergyBalance/tests/wpLELTest.R
| You are developing: (EnergyBalance)
| Wrote 
/Users/rainerkrug/Documents/Projects/EnergyBalance/R/plotwpLELFitListParDistr.R
| You are developing: (EnergyBalance)
| ...
`

where the messages "You are developing: (EnergyBalance)" come from
ESS. Is this to be expected that R is called for some blocks, but not
for others, when tangling?

Version info:
,
| Org-mode version 8.3beta (release_8.3beta-1209-gc532ff @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
| GNU Emacs 24.5.1 (x86_64-apple-darwin14.3.0, Carbon Version 157 AppKit 
1347.57) of 2015-04-13 on Rainers-MacBook-Pro.local
`

Cheers,

Rainer

,
| - time-execute4950  84%
|  - call-interactively4950  84%
|   - org-babel-tangle 4828  82%
|- org-babel-tangle-collect-blocks 2728  46%
| - org-babel-tangle-single-block  1363  23%
|  - org-babel-get-src-block-info  1304  22%
|   - org-babel-parse-src-block-match  1210  20%
|### - org-babel-params-from-properties1193  20%
| + mapcar 1144  19%
| + org-entry-get33   0%
| + org-babel-parse-header-arguments 12   0%
| + org-babel-combine-header-arg-lists4   0%
|+ org-babel-parse-header-arguments   3   0%
|+ apply  2   0%
|  generate-new-buffer1   0%
|+ org-unescape-code-in-string1   0%
|  byte-code  1   0%
|   + org-babel-generate-file-param  86   1%
|   + org-babel-process-params2   0%
| org-babel-where-is-src-block-head   1   0%
|  + org-store-link  36   0%
|line-number-at-pos  17   0%
|  + byte-code2   0%
|generate-new-buffer  1   0%
| - org-babel-get-src-block-info   1334  22%
|  - org-babel-parse-src-block-match   1235  21%
|   - org-babel-params-from-properties 1212  20%
|+ mapcar  1163  19%
|+ org-entry-get 30   0%
|+ org-babel-parse-header-arguments  12   0%
|+ org-babel-combine-header-arg-lists 7   0%
|   + org-babel-parse-header-arguments7   0%
|   + apply   4   0%
|   + org-unescape-code-in-string 2   0%
| generate-new-buffer 1   0%
|  + org-babel-generate-file-param   89   1%
|org-babel-where-is-src-block-head2   0%
| + org-in-commented-heading-p8   0%
| + org-babel-active-location-p   4   0%
| + byte-code 2   0%
|+ mapc2098  35%
|+ run-hooks  1   0%
|   + smex  122   2%
| + ... 912  15%
| + flyspell-post-command-hook4   0%
| + redisplay_internal (C function)   3   0%
| + timer-event-handler   3   0%
`


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT)

Re: [O] clocktables output in hours and minutes only

2015-06-15 Thread Sebastien Vauban
Sharon Kimble  writes:
> Still on about clocktables, how can I have the time output show just
> in "hours.minutes" and not in "days.hours.minutes" please?

IIRC, customizing `org-time-clocksum-format' should help.

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] Trouble passing variables into shell blocks on windows

2015-06-15 Thread Rainer M Krug
Johan W. Klüwer  writes:

> I'm having difficulties passing org variables into shell source blocks.
> This is using Windows 7 and Cygwin with bash shell. For instance, the
> following
>
> #+BEGIN_SRC sh :var x="."
>   ls $x
> #+END_SRC
>
> fails with the error message (as displayed in emacs)

Works on OS X Yosemite,

,
| Org-mode version 8.3beta (release_8.3beta-1209-gc532ff @ 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
| GNU Emacs 24.5.1 (x86_64-apple-darwin14.3.0, Carbon Version 157 AppKit 
1347.57) of 2015-04-13 on Rainers-MacBook-Pro.local
`

Cheers,

Rainer

>
>   ls: cannot access .^M^M : No such file or directory
>
>
> As far as I can see, the first ^M stems from org-babel-sh-var-quote-fmt,
> and the second from org-babel-expand-body:generic, but I haven't been able
> to figure out a solution. Any suggestions?

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

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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

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

email:  rai...@krugs.de

Skype:  RMkrug

PGP: 0x0F52F982


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