[O] Is it possible to run shell script src blocks as root or to export individual blocks?

[Leo Alekseyev]

I was wondering if there was an easy way to execute some shell
commands contained in a src block as root.  Alternatively, is there a
quick way to export _just_ that one source block to a temp file so
that I could run it as root manually?

Re: [O] Size and placement of images in table in PDF export

[Nick Dokos]

Michael Hannon  wrote:

> Greetings.  I've got another export question.  If I put two small images into
> an Org-mode table and export the containing document to HTML, I see the two
> images displayed side-by-side in an area of the page that is at least roughly
> the actual size of the concatenated images.
> 
> If I export the same document to PDF, the two images are again displayed
> side-by-side, but image on the left is magnified to take up most of the
> horizontal space on the page; the image on the right is also magnified and
> runs off the page to the right.
> 
> I'm not sure how to provide a simple, self-contained example of this.  The
> structure of the table is:
> 
>     | [[./x1.jpg]] | [[./x2.jpg]] |
> 
> The images themselves are "small":
> 
>   $ identify x*.jpg
>   x1.jpg JPEG 189x142 189x142+0+0 8-bit DirectClass 9.56KB 0.000u 0:00.000
>   x2.jpg[1] JPEG 190x160 190x160+0+0 8-bit DirectClass 55.6KB 0.000u 0:00.000
> 
> If I just print the images from an image viewer, each of them comes out on
> paper at about 2.5in (~64 mm) in width.
> 
> Is there some way to override the default size/placement of the images in PDF
> export?
> 

The trouble is that the default option says "width=.9\\linewidth" so
if you try to put two of them on the same "line", they end up overflowing
the page. For an image not inside a table, you could reset that with

#+ATTR_LaTeX: width=.4\\linewidth

but this is a rather blunt instrument: for images inside a table, it
applies not only to the images but also to the table (and it ends up
producing a syntactically incorrect latex program - that's probably
a bug in the latex exporter.)

The following variation does work however:

--8<---cut here---start->8---
#+BIND: org-export-latex-image-default-option "width=.4\\linewidth"

* foo

| col1 | col2 |
|--+--|
| [[./x1.jpg]] | [[./x2.jpg]] |
|  |  |
--8<---cut here---end--->8---

Of course, if you try to put three images on the line, you'll have to
recalibrate the factor (you can also use absolute dimensions: width=3cm).

There is also this second variation, which uses height, rather than width: the
latex exporter thinks height is not relevant to tables, so it does not
try to give that attribute to the table, just to the images:

--8<---cut here---start->8---
* foo

#+ATTR_LaTeX: height=2cm

| col1 | col2 |
|--+--|
| [[./x1.jpg]] | [[./x2.jpg]] |
|  |  |
--8<---cut here---end--->8---

but you can also use the BIND form too:

#+BIND: org-export-latex-image-default-option "height=2cm"


Note btw, that the width in the first case (and the height in the
second case) is the same for both images. AFAICT, there is no way
to give different dimensions to the two images - except for the
following variation.

The third variation allows the two images to have their "natural"
dimensions:

--8<---cut here---start->8---
#+BIND: org-export-latex-image-default-option ""

* foo

| col1 | col2 |
|--+--|
| [[./x1.jpg]] | [[./x2.jpg]] |
|  |  |
--8<---cut here---end--->8---

Nick

Re: [O] Agenda TODO sorting by date

[Bernt Hansen]

James Harkins  writes:

> Given this:
>
> * Category 1
> ** TODO First todo in file <2012-03-30 Fri>   :Tag:
> ** TODO Second todo in file <2012-03-29 Thu>  :Tag:
> * Category 2
> ** TODO Third todo in file <2012-03-28 Wed>   :Tag:
> ** TODO Fourth todo in file <2012-03-31 Sat>  :Tag:
>
> I do C-c a < M Tag  and get:
>
> Headlines with TAGS match: Tag
> Press `C-u r' to search again with new search string
>   todo_sort:  TODO First todo in file <2012-03-30 Fri> 
> :Tag:
>   todo_sort:  TODO Second todo in file <2012-03-29 Thu>
> :Tag:
>   todo_sort:  TODO Third todo in file <2012-03-28 Wed> 
> :Tag:
>   todo_sort:  TODO Fourth todo in file <2012-03-31 Sat>
> :Tag:
>
> I want to configure a custom agenda command so that I get:
>
> Headlines with TAGS match: Tag
> Press `C-u r' to search again with new search string
>   todo_sort:  TODO Third todo in file <2012-03-28 Wed> 
> :Tag:
>   todo_sort:  TODO Second todo in file <2012-03-29 Thu>
> :Tag:
>   todo_sort:  TODO First todo in file <2012-03-30 Fri> 
> :Tag:
>   todo_sort:  TODO Fourth todo in file <2012-03-31 Sat>
> :Tag:
>
> How do I do this?

You could write a custom sorting function that parses out the date from
the heading and compares them.  There may be a better way to do this
that I'm not aware of for this.

Set this function up in org-agenda-cmp-user-defined and
org-agenda-sorting-strategy to get the results you want.

HTH,
Bernt

[O] Agenda TODO sorting by date

[James Harkins]

Given this:

* Category 1
** TODO First todo in file <2012-03-30 Fri> :Tag:
** TODO Second todo in file <2012-03-29 Thu>:Tag:
* Category 2
** TODO Third todo in file <2012-03-28 Wed> :Tag:
** TODO Fourth todo in file <2012-03-31 Sat>:Tag:

I do C-c a < M Tag  and get:

Headlines with TAGS match: Tag
Press `C-u r' to search again with new search string
  todo_sort:  TODO First todo in file <2012-03-30 Fri> :Tag:
  todo_sort:  TODO Second todo in file <2012-03-29 Thu>:Tag:
  todo_sort:  TODO Third todo in file <2012-03-28 Wed> :Tag:
  todo_sort:  TODO Fourth todo in file <2012-03-31 Sat>:Tag:

I want to configure a custom agenda command so that I get:

Headlines with TAGS match: Tag
Press `C-u r' to search again with new search string
  todo_sort:  TODO Third todo in file <2012-03-28 Wed> :Tag:
  todo_sort:  TODO Second todo in file <2012-03-29 Thu>:Tag:
  todo_sort:  TODO First todo in file <2012-03-30 Fri> :Tag:
  todo_sort:  TODO Fourth todo in file <2012-03-31 Sat>:Tag:

How do I do this?

James


--
James Harkins /// dewdrop world
jamshar...@dewdrop-world.net
http://www.dewdrop-world.net

"Come said the Muse,
Sing me a song no poet has yet chanted,
Sing me the universal."  -- Whitman

blog: http://www.dewdrop-world.net/words
audio clips: http://www.dewdrop-world.net/audio
more audio: http://soundcloud.com/dewdrop_world/tracks

Re: [O] Include TOC in PDF export?

[suvayu ali]

On Sat, Mar 3, 2012 at 00:44, Michael Hannon  wrote:
>> I think the only way to get a TOC is to set num:t. You can probably
>> rewrite a chunk of latex code so that unnumbered sections etc end up in
>> the .toc file, but I think it would be a fairly major undertaking.
>
> Thanks, Nick.  I think I'll learn to love the current arrangement.

There is a slightly hacky solution. With "num:nil", you can put a line
like the following line after every heading you want to see in the
TOC.

\addcontentsline{toc}{subsection}{\nameref{}}

Hope this helps.

-- 
Suvayu

Open source is the future. It sets us free.

[O] Size and placement of images in table in PDF export

[Michael Hannon]

Greetings.  I've got another export question.  If I put two small images into
an Org-mode table and export the containing document to HTML, I see the two
images displayed side-by-side in an area of the page that is at least roughly
the actual size of the concatenated images.

If I export the same document to PDF, the two images are again displayed
side-by-side, but image on the left is magnified to take up most of the
horizontal space on the page; the image on the right is also magnified and
runs off the page to the right.

I'm not sure how to provide a simple, self-contained example of this.  The
structure of the table is:

    | [[./x1.jpg]] | [[./x2.jpg]] |

The images themselves are "small":

  $ identify x*.jpg
  x1.jpg JPEG 189x142 189x142+0+0 8-bit DirectClass 9.56KB 0.000u 0:00.000
  x2.jpg[1] JPEG 190x160 190x160+0+0 8-bit DirectClass 55.6KB 0.000u 0:00.000

If I just print the images from an image viewer, each of them comes out on
paper at about 2.5in (~64 mm) in width.

Is there some way to override the default size/placement of the images in PDF
export?

BTW, this is:

    Org-mode version 7.8.03 (release_7.8.03.324.gc4b233)

in Fedora 16, 64-bit.

Thanks,

-- Mike

Re: [O] Include TOC in PDF export?

[Michael Hannon]

> From: Nick Dokos 
>> Greetings.  I'm exporting a document to both HTML and PDF.  In the
>> HTML version, I get a table of contents.  In the PDF version, I do NOT
>> get a table of contents.  The appended text illustrates the problem. 
>> I'd like to get the TOC in both.
>>

> num:nil causes unnumbered sections in latex (\section*{...})  which are
> not entered into the .toc file (that's a latex limitation, not an
> org-mode one), so the latex exporter wants both num: and toc: to be
> enabled before it produces a table of contents.

> I think the only way to get a TOC is to set num:t. You can probably
> rewrite a chunk of latex code so that unnumbered sections etc end up in
> the .toc file, but I think it would be a fairly major undertaking.

Thanks, Nick.  I think I'll learn to love the current arrangement.

-- Mike

Re: [O] Include TOC in PDF export?

[Nick Dokos]

Nick Dokos  wrote:

> Michael Hannon  wrote:
> 
> > Greetings.  I'm exporting a document to both HTML and PDF.  In the
> > HTML version, I get a table of contents.  In the PDF version, I do NOT
> > get a table of contents.  The appended text illustrates the problem. 
> > I'd like to get the TOC in both.
> > 
> 
> num:nil causes unnumbered sections in latex (\section*{...})  which are
> not entered into the .toc file (that's a latex limitation, not an
> org-mode one), so the latex exporter wants both num: and toc: to be
> enabled before it produces a table of contents.
> 
> I think the only way to get a TOC is to set num:t. You can probably
> rewrite a chunk of latex code so that unnumbered sections etc end up in
> the .toc file, but I think it would be a fairly major undertaking.
> 

There is a trick (I found it in the titlesec doc) that allows you
to get unnumbered sections without using the \section* forms:

--8<---cut here---start->8---
#+TITLE:
#+OPTIONS: num:t ^:{} toc:5
#+LaTeX_HEADER: \setcounter{secnumdepth}{0}
--8<---cut here---end--->8---

Since num: is t, the latex exporter will produce a TOC and the \setcounter
will suppress section numbers. Unfortunately, that won't work with HTML
though: the sections will be numbered (unless some other trick can be found
there - maybe some CSS magic, although I wouldn't know where to start with 
that).

Nick

Re: [O] Include TOC in PDF export?

[Nick Dokos]

Michael Hannon  wrote:

> Greetings.  I'm exporting a document to both HTML and PDF.  In the
> HTML version, I get a table of contents.  In the PDF version, I do NOT
> get a table of contents.  The appended text illustrates the problem. 
> I'd like to get the TOC in both.
> 

num:nil causes unnumbered sections in latex (\section*{...})  which are
not entered into the .toc file (that's a latex limitation, not an
org-mode one), so the latex exporter wants both num: and toc: to be
enabled before it produces a table of contents.

I think the only way to get a TOC is to set num:t. You can probably
rewrite a chunk of latex code so that unnumbered sections etc end up in
the .toc file, but I think it would be a fairly major undertaking.

Nick

> 
> I'm running:
> 
>     Org-mode version 7.8.03 (release_7.8.03.324.gc4b233)
> 
> in Fedora 16, 64-bit.
> 
> What am I missing?
> 
> Thanks,
> 
> -- Mike
> 
> 
> 
> #+TITLE:
> #+OPTIONS: num:nil ^:{} toc:t
> 
> * Tale of Two Cities
> 
> *It was the best of times, it was the worst of times*
> 
> It was the best of times, it was the worst of times, it was the age of
> wisdom, it was the age of foolishness, it was the epoch of belief, it
> was the epoch of incredulity, it was the season of Light, it was the
> season of Darkness, it was the spring of hope, it was the winter of
> despair, we had everything before us, we had nothing before us, we
> were all going direct to heaven, we were all going direct the other
> way - in short, the period was so far like the present period, that
> some of its noisiest authorities insisted on its being received, for
> good or for evil, in the superlative degree of comparison only.
> 
> * David Copperfield
> 
> *Barkis is willin*
> 
> As he repudiated this suggestion, however, with a jerk of his head,
> and once more confirmed his previous request by saying, with profound
> gravity, 'Barkis is willin'. That's the message,' I readily undertook
> its transmission. While I was waiting for the coach in the hotel at
> Yarmouth that very afternoon, I procured a sheet of paper and an
> inkstand, and wrote a note to Peggotty, which ran thus: 'My dear
> Peggotty. I have come here safe. Barkis is willing. My love to
> mama. Yours affectionately. P.S. He says he particularly wants you to
> know - BARKIS IS WILLING.'
> 

Re: [O] How to include pre-existing pdf files/pages into orgmode pdf or other export output

[Martin Weigele]

Hey Skip and Suvayu,

this is so cool. Thank you!
says Martin

Re: [O] Selectively export RESULTS

[Nick Dokos]

cbe...@tajo.ucsd.edu wrote:

> 
> I've been bitten by the 'no C-c C-c' after changing a #+property line so
> many times, you would think I'd learn. :-(
> 

Yup - I don't know why, but for some reason I can see it more easily
when others do it than when I do it: I sometimes spend *minutes*
bewildered ("*how can that be?!?!*").  At some point, I get into
"Terminator" mode, go down the list for the appropriate response,
remember the C-c C-c problem, whack my head on my desk a few times, and
go on.  But when next time comes, it's as if it never happened before
(well, perhaps things are improving: I generally go into "Terminator"
mode much more quickly nowadays - a couple of times in the more distant
past, I gave up in disgust, went to bed and didn't think of C-c C-c
until the next day.)

It would be so nice if org did the org-mode-restart bit automatically
after a change to a #+KEYWORD line: in some cases (e.g. TBLFM lines) you
have direct feedback so it doesn't matter too much, but in other cases,
that feedback is just nowhere to be found. I don't know how difficult it
would be to implement such a facility[fn:1], but maybe it can be added
to the GSoC list if somebody has a bright idea on how to do it.

Nick

Footnotes:

[fn:1] ... without making it too expensive to run: I wonder how
expensive it would be running org-mode-restart from an idle timer -
probably prohibitive if the file is large enough. And I can imagine
situations where that would be even *more* confusing: changing behavior
apparently without any other change - can you say magic?

[O] Include TOC in PDF export?

[Michael Hannon]

Greetings.  I'm exporting a document to both HTML and PDF.  In the HTML 
version, I get a table of contents.  In the PDF version, I do NOT get a table 
of contents.  The appended text illustrates the problem.  I'd like to get the 
TOC in both.


I'm running:

    Org-mode version 7.8.03 (release_7.8.03.324.gc4b233)

in Fedora 16, 64-bit.

What am I missing?

Thanks,

-- Mike



#+TITLE:
#+OPTIONS: num:nil ^:{} toc:t

* Tale of Two Cities

*It was the best of times, it was the worst of times*

It was the best of times, it was the worst of times, it was the age of
wisdom, it was the age of foolishness, it was the epoch of belief, it
was the epoch of incredulity, it was the season of Light, it was the
season of Darkness, it was the spring of hope, it was the winter of
despair, we had everything before us, we had nothing before us, we
were all going direct to heaven, we were all going direct the other
way - in short, the period was so far like the present period, that
some of its noisiest authorities insisted on its being received, for
good or for evil, in the superlative degree of comparison only.

* David Copperfield

*Barkis is willin*

As he repudiated this suggestion, however, with a jerk of his head,
and once more confirmed his previous request by saying, with profound
gravity, 'Barkis is willin'. That's the message,' I readily undertook
its transmission. While I was waiting for the coach in the hotel at
Yarmouth that very afternoon, I procured a sheet of paper and an
inkstand, and wrote a note to Peggotty, which ran thus: 'My dear
Peggotty. I have come here safe. Barkis is willing. My love to
mama. Yours affectionately. P.S. He says he particularly wants you to
know - BARKIS IS WILLING.'

Re: [O] Export <> to latex

[Markus Grebenstein]

Dear Nick,

that is even more than enough ;-)

Thanks a lot! That solves quite a bit of preoblems for me.

I tried to put the anchor in the line of the headline itself and it 
worked in orgmode but was not exported as I expected.


Best,

Markus

Am 02.03.2012 21:23, schrieb Nick Dokos:

Markus Grebenstein  wrote:


Dear List,

I am regularly running into problems with internal links to headings,
since my document meanwhile is 200pp+ long and I tend to change
headings.

Since I loose the ability to jump to the heading, I do not like to use
the classic latex approach using \label.

I am wondering why anchors are not exported as a label. Alternatively
having an "option" for headings would be nice like:
* Heading [label:anchor]

Is there a possibility to tweak orgmode to export anchors?

Thanks in advance,


I may be misunderstanding what you mean, but when I try exporting to latex
the following org file:

--8<---cut here---start->8---

* foo
#<>

foo text

* bar
#<>

bar text
--8<---cut here---end--->8---

I get the following latex code:

,
| ...
| \section{foo}
| \label{sec-1}
| \label{fooanchor}
|
|
| foo text
| \section{bar}
| \label{sec-2}
| \label{baranchor}
|
|
| bar text
| ...
`

Isn't that enough?

Nick

Re: [O] footnote doc not clear

[Nicolas Goaziou]

Hello,

Samuel Wales  writes:

> Export of inline footnotes breaks if you do (setf org-footnote-section
> nil).  The footnote section goes in a single place but not at the end.
>
> *** test
> a
> * b
> b[fn::one]
> * c
> c[fn::two]
> * d
> d
> * e
> e
>
> The docstring says "before export" which implies that it will not
> affect export.  Or it seems to.
>
> Perhaps it should say "before export and for export" or something.  Or
> perhaps there should be two variables.
>
> And the behavior is a bug, although it isn't an important one.
>
> b032a6d51bbd0c8e1be4f20dd68abfe52b328e25 is the first bad commit

I have pushed a patch to fix that behaviour, although, I didn't fix the
variable doc-string. Can you confirm that it is working as expected?


Regards,

-- 
Nicolas Goaziou

Re: [O] Selectively export RESULTS

[cberry]

Nick Dokos  writes:

> cbe...@tajo.ucsd.edu wrote:
>
>> cbe...@tajo.ucsd.edu writes:
>> 
>> inline correction below.
>> 
>> > Eric Schulte  writes:
>> >
>> >> Matthew Landis  writes:
>> >>
>> >>>   tajo.ucsd.edu> writes:
>> >>>
>>  
>>  Eric Schulte  gmx.com> writes:
>>  
>>  >>> Does this do what you want?
>> >>>
>>  >
>>  > Have you looked at the :cache header argument [1], from my 
>>  > understanding
>>  > of your use case it should be exactly what you are after.
>>  >
>>  
>>  Its a step in the right direction.
>>  
>>  It seems I have to set :cache yes on every block I use before I invoke
>>  it. My attempt to use a buffer-wide PROPERTY setting for cache did not
>>  pan out. 
>>  
>> >>
>> >> Were these technical problems with the implementation of :cache, or
>> >> logistical problems specific to your organization of code blocks?
>> >>
>> > [rest deleted]
>> >
>> > Eric,
>> >
>> > your response is threaded as a reply to Matthew, but here you have
>> > replied to my comment about buffer wide PROPERTY setting of :cache.
>> >
>> > Here is an example of the difficulty I face:
>> >
>> > ,
>> > | #+property: :cache yes
>> > | 
>> 
>> Of course that should have been 
>> 
>> 
>> #+property: cache yes
>> 
>> but the result below is the same.
>> 
>
> Did you C-c C-c on the #+property: line after changing it?
> I think it works as expected.
>

You are right. It reports the cache'd value of the date.

I've been bitten by the 'no C-c C-c' after changing a #+property line so
many times, you would think I'd learn. :-(

Thanks.

Chuck

> Nick
>
>> Chuck
>> 
>> > | 
>> > | #+name: Ablock
>> > | #+begin_src emacs-lisp :results value :exports both 
>> > |   (current-time-string)
>> > | #+end_src
>> > | 
>> > | #+results[2ca40f0dc0f23e5743133e229d9e8f31b31830c5]: Ablock
>> > | : Wed Feb 29 11:57:19 2012
>> > | 
>> > | 
>> > | * headline 1
>> > |   :PROPERTIES:
>> > |   :cache:   no
>> > |   :END:
>> > | 
>> > | #+CALL: Ablock() :exports results
>> > | 
>> > `
>> >
>> > When I place point under the headline and issue 
>> >
>> >  C-c @ C-c C-e a
>> >
>> > I get 
>> >
>> > ,
>> > |   headline 1
>> > |   ==
>> > | 
>> > | Author: 
>> > | Date: 2012-03-02 11:28:54 PST
>> > | 
>> > | 
>> > | 
>> > | 
>> > | Fri Mar  2 11:28:52 2012
>> > | 
>> > `
>> >
>> > showing that Ablock() actually was executed.
>> >
>> > If the :cache setting under 'headline 1' is omitted then no update of
>> > the time string is performed.
>> >
>> > I understand that this behavior might be considered a *feature*, not a
>> > *bug*. 
>> >
>> > Either way, having an easy way to copy results into other parts of a
>> > document would help me out.
>> >
>> > Best,
>> >
>> > Chuck
>> 
>> -- 
>> Charles C. BerryDept of Family/Preventive 
>> Medicine
>> cberry at ucsd edu   UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>> 
>> 
>
>

-- 
Charles C. BerryDept of Family/Preventive Medicine
cberry at ucsd edu  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

[Nick Dokos]

cbe...@tajo.ucsd.edu wrote:

> cbe...@tajo.ucsd.edu writes:
> 
> inline correction below.
> 
> > Eric Schulte  writes:
> >
> >> Matthew Landis  writes:
> >>
> >>>   tajo.ucsd.edu> writes:
> >>>
>  
>  Eric Schulte  gmx.com> writes:
>  
>  >>> Does this do what you want?
> >>>
>  >
>  > Have you looked at the :cache header argument [1], from my 
>  > understanding
>  > of your use case it should be exactly what you are after.
>  >
>  
>  Its a step in the right direction.
>  
>  It seems I have to set :cache yes on every block I use before I invoke
>  it. My attempt to use a buffer-wide PROPERTY setting for cache did not
>  pan out. 
>  
> >>
> >> Were these technical problems with the implementation of :cache, or
> >> logistical problems specific to your organization of code blocks?
> >>
> > [rest deleted]
> >
> > Eric,
> >
> > your response is threaded as a reply to Matthew, but here you have
> > replied to my comment about buffer wide PROPERTY setting of :cache.
> >
> > Here is an example of the difficulty I face:
> >
> > ,
> > | #+property: :cache yes
> > | 
> 
> Of course that should have been 
> 
> 
> #+property: cache yes
> 
> but the result below is the same.
> 

Did you C-c C-c on the #+property: line after changing it?
I think it works as expected.

Nick

> Chuck
> 
> > | 
> > | #+name: Ablock
> > | #+begin_src emacs-lisp :results value :exports both 
> > |   (current-time-string)
> > | #+end_src
> > | 
> > | #+results[2ca40f0dc0f23e5743133e229d9e8f31b31830c5]: Ablock
> > | : Wed Feb 29 11:57:19 2012
> > | 
> > | 
> > | * headline 1
> > |   :PROPERTIES:
> > |   :cache:   no
> > |   :END:
> > | 
> > | #+CALL: Ablock() :exports results
> > | 
> > `
> >
> > When I place point under the headline and issue 
> >
> >  C-c @ C-c C-e a
> >
> > I get 
> >
> > ,
> > |   headline 1
> > |   ==
> > | 
> > | Author: 
> > | Date: 2012-03-02 11:28:54 PST
> > | 
> > | 
> > | 
> > | 
> > | Fri Mar  2 11:28:52 2012
> > | 
> > `
> >
> > showing that Ablock() actually was executed.
> >
> > If the :cache setting under 'headline 1' is omitted then no update of
> > the time string is performed.
> >
> > I understand that this behavior might be considered a *feature*, not a
> > *bug*. 
> >
> > Either way, having an easy way to copy results into other parts of a
> > document would help me out.
> >
> > Best,
> >
> > Chuck
> 
> -- 
> Charles C. BerryDept of Family/Preventive Medicine
> cberry at ucsd eduUC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
> 
> 

Re: [O] Selectively export RESULTS

[Eric Schulte]

>
> Eric,
>
> your response is threaded as a reply to Matthew, but here you have
> replied to my comment about buffer wide PROPERTY setting of :cache.
>
> Here is an example of the difficulty I face:
>
> ,
> | #+property: :cache yes
> | 
> | 
> | #+name: Ablock
> | #+begin_src emacs-lisp :results value :exports both 
> |   (current-time-string)
> | #+end_src
> | 
> | #+results[2ca40f0dc0f23e5743133e229d9e8f31b31830c5]: Ablock
> | : Wed Feb 29 11:57:19 2012
> | 
> | 
> | * headline 1
> |   :PROPERTIES:
> |   :cache:   no
> |   :END:
> | 
> | #+CALL: Ablock() :exports results
> | 
> `
>
> When I place point under the headline and issue 
>
>  C-c @ C-c C-e a
>
> I get 
>
> ,
> |   headline 1
> |   ==
> | 
> | Author: 
> | Date: 2012-03-02 11:28:54 PST
> | 
> | 
> | 
> | 
> | Fri Mar  2 11:28:52 2012
> | 
> `
>
> showing that Ablock() actually was executed.
>
> If the :cache setting under 'headline 1' is omitted then no update of
> the time string is performed.
>
> I understand that this behavior might be considered a *feature*, not a
> *bug*. 
>
> Either way, having an easy way to copy results into other parts of a
> document would help me out.
>

Hi Chuck,

You have a simple syntax error at the top of the file.  Replace 

> | #+property: :cache yes

with

> | #+property:  cache yes
^
(delete a colon | right there)

and you will get the behavior you are seeking.

Best,

>
> Best,
>
> Chuck

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] Selectively export RESULTS

[cberry]

cbe...@tajo.ucsd.edu writes:

inline correction below.

> Eric Schulte  writes:
>
>> Matthew Landis  writes:
>>
>>>   tajo.ucsd.edu> writes:
>>>
 
 Eric Schulte  gmx.com> writes:
 
 >>> Does this do what you want?
>>>
 >
 > Have you looked at the :cache header argument [1], from my understanding
 > of your use case it should be exactly what you are after.
 >
 
 Its a step in the right direction.
 
 It seems I have to set :cache yes on every block I use before I invoke
 it. My attempt to use a buffer-wide PROPERTY setting for cache did not
 pan out. 
 
>>
>> Were these technical problems with the implementation of :cache, or
>> logistical problems specific to your organization of code blocks?
>>
> [rest deleted]
>
> Eric,
>
> your response is threaded as a reply to Matthew, but here you have
> replied to my comment about buffer wide PROPERTY setting of :cache.
>
> Here is an example of the difficulty I face:
>
> ,
> | #+property: :cache yes
> | 

Of course that should have been 


#+property: cache yes

but the result below is the same.

Chuck

> | 
> | #+name: Ablock
> | #+begin_src emacs-lisp :results value :exports both 
> |   (current-time-string)
> | #+end_src
> | 
> | #+results[2ca40f0dc0f23e5743133e229d9e8f31b31830c5]: Ablock
> | : Wed Feb 29 11:57:19 2012
> | 
> | 
> | * headline 1
> |   :PROPERTIES:
> |   :cache:   no
> |   :END:
> | 
> | #+CALL: Ablock() :exports results
> | 
> `
>
> When I place point under the headline and issue 
>
>  C-c @ C-c C-e a
>
> I get 
>
> ,
> |   headline 1
> |   ==
> | 
> | Author: 
> | Date: 2012-03-02 11:28:54 PST
> | 
> | 
> | 
> | 
> | Fri Mar  2 11:28:52 2012
> | 
> `
>
> showing that Ablock() actually was executed.
>
> If the :cache setting under 'headline 1' is omitted then no update of
> the time string is performed.
>
> I understand that this behavior might be considered a *feature*, not a
> *bug*. 
>
> Either way, having an easy way to copy results into other parts of a
> document would help me out.
>
> Best,
>
> Chuck

-- 
Charles C. BerryDept of Family/Preventive Medicine
cberry at ucsd edu  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

Re: [O] How to build a project from org files using ant/make?

[Eric Schulte]

Robert McIntyre  writes:

> Hi,
>
> I use org-babel to produce the source and html documentation for my projects.
>
> My projects generally look like this:
>
> [~/tmp/org-project] $ tree
> .
> |-- html
> |   `-- proj.html
> |-- org
> |   `-- proj.org
> `-- src
> `-- namesace
> |-- prog_1.clj
> `-- prog_2.clj
>
> Here prog_1.clj, prog_2.clj, and proj.html are all generated from the
> proj.org file.
>
> Because the source and html files are generated files, I don't include
> them in source control.
>
> When I download my project on another computer, I want to be able to
> generate all these files again, preferably from a makefile/build.xml,
> etc.
>
> What is the best practice for doing this?  Right now, I maintain two
> shell scripts called "tangle" and "weave" that invoke emacs on the
> project, but these rely on my specific emacs setup.  How can I make it
> possible for someone to build my project if they have emacs and
> make/ant?  What are other people doing when it comes to automatically
> building a project whose source files are generated from org files?
>

I've attached the Makefile I use to build a pdf of my proposal from the
Org-mode source.  Notice the EMACS, BATCH_EMACS, and proposal.tex lines.
You should be able to adopt proposal.tex to export source code by
replacing org-export-as-latex with org-babel-tangle.  This setup has
worked very reliably for me and should extend naturally.

I use an init.el file to holds project-specific customization.  If you
can assume that the user has Emacs24 installed, then you need not do
anything special and can omit init.el entirely, otherwise you will have
to ensure that a recent version of Org-mode is installed and loaded.

Hope this helps -- Eric



Makefile
Description: Binary data

>
> sincerely,
> --Robert McIntyre
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] org-odt: cannot find factory styles

[Jambunathan K]

Jambunathan K  writes:

>> But I do see C:/emacs-23.4/etc/org/styles, which has
>> OrgOdtStyles.xml,

I didn't see this in your earlier message.

This is how it is on my Emacs-24.0.94. There is no "styles" subdir. The
XML files are directly under etc/org.

,
|   c:/Program Files/emacs-24.0.94/etc/org:
|   total used in directory 78 available 33663996
|   drwxrwxrwx  1 kjambunathan None 0 02-26 22:35 .
|   drwxrwxrwx  1 kjambunathan None 0 02-26 22:35 ..
|   -rw-rw-rw-  1 kjambunathan None 17036 02-26 22:35 OrgOdtContentTemplate.xml
|   -rw-rw-rw-  1 kjambunathan None 61383 02-26 22:35 OrgOdtStyles.xml
|   -rw-rw-rw-  1 kjambunathan None  1352 02-26 22:35 README
`

[O] How to build a project from org files using ant/make?

[Robert McIntyre]

Hi,

I use org-babel to produce the source and html documentation for my projects.

My projects generally look like this:

[~/tmp/org-project] $ tree
.
|-- html
|   `-- proj.html
|-- org
|   `-- proj.org
`-- src
`-- namesace
|-- prog_1.clj
`-- prog_2.clj

Here prog_1.clj, prog_2.clj, and proj.html are all generated from the
proj.org file.

Because the source and html files are generated files, I don't include
them in source control.

When I download my project on another computer, I want to be able to
generate all these files again, preferably from a makefile/build.xml,
etc.

What is the best practice for doing this?  Right now, I maintain two
shell scripts called "tangle" and "weave" that invoke emacs on the
project, but these rely on my specific emacs setup.  How can I make it
possible for someone to build my project if they have emacs and
make/ant?  What are other people doing when it comes to automatically
building a project whose source files are generated from org files?

sincerely,
--Robert McIntyre

Re: [O] org-odt: cannot find factory styles

[Jambunathan K]

The easiest solution is to use ELPA. There is some instruction on how to
use ELPA here:

http://orgmode.org/worg/org-faq.html#installing-via-elpa

If you are installing through ELPA for the first time, make sure that
you have no installation of org in your load-path. M-x locate-library
RET org RET will show where the current Org is located. Rename the
parent dir to someother name, so that it is removed out of load
path. Repeat this process until there is no more Org in your
load-path. Then proceed with ELPA installation.

Another solution is to download the tar and use

$ make install

More specifically, use of "byte-compile-directory" to compile and
install Org will definitely *break* the ODT exporter. Copying the .elc
files by hand will also break the exporter. The only solution to have a
working installation is to use "make install" to install the Org >= 7.8.

,
| # Where local software is found
| prefix=/usr/local
| 
| # Where local lisp files go
| lispdir   = $(prefix)/share/emacs/site-lisp
| 
| # Where data files go
| # $(datadir) contains auxiliary files for use with ODT exporter.
| # See comments under DATAFILES.
| datadir = $(prefix)/share/emacs/etc
`

> Debug (org-odt): Trying c:/emacs-23.4/site-lisp/etc/styles/...
> Debug (org-odt): Trying c:/emacs-23.4/site-lisp/org/etc/styles/...
> Debug (org-odt): Trying c:/emacs-23.4/etc/org/...

The above two messages suggests that whoever built the binaries had the
following setting for lispdir.

lispdir = c:/emacs-23.4/site-lisp/org

and *didn't* use 'make install'.

If the Org is meant for a global distribution (as opposed to personal
installation), the distributor has to specifically ask the users to copy
the styles file to <>/etc/org.

C-h v data-directory

In your case, the data-directory is c:/emacs-23.4/etc/org/.

Emacs-24.1 (pretest) users will not see this problem because the styles
files are already part of the emacs tree. See
http://bzr.savannah.gnu.org/lh/emacs/trunk/files/head:/etc/org/.


Style files from the git repo is here:
http://orgmode.org/w/?p=org-mode.git;a=tree;f=etc/styles;hb=HEAD

Schema files form the git repo is here:
http://orgmode.org/w/?p=org-mode.git;a=tree;f=contrib/odt/etc/schema;hb=HEAD

Remember to download the raw files if you are downloading from git repo.


> Hello all,
>
> I've been googling this problem and searching the archives, but I
> can't seem to find a solution.  When I try to export to ODT, I get
>
> Error (org-odt): Cannot find factory styles files. Aborting.
>
> Looking in my *Messages* buffer, I see at startup:
>
> Debug (org-odt): Searching for OpenDocument schema files...
> Debug (org-odt): Trying
> c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/schema/...
> Debug (org-odt): Trying c:/emacs-23.4/site-lisp/contrib/odt/etc/schema/...
> Debug (org-odt): No OpenDocument schema files installed
> Debug (org-odt): Searching for OpenDocument styles files...
> Debug (org-odt): Trying
> c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/styles/...
> Debug (org-odt): Trying c:/emacs-23.4/site-lisp/etc/styles/...
> Debug (org-odt): Trying c:/emacs-23.4/site-lisp/org/etc/styles/...
> Debug (org-odt): Trying c:/emacs-23.4/etc/org/...
> Problems while trying to load feature `org-odt'
>
> So you can see that i am using Windows (Win 7 64 bit).  In fact, I am
> using Vincent Goulet's Windows installer (modified-2, FWIW), and I
> directed it to install into C:/emacs-23.4 instead of the default
> C:/Program Files (x86) directory.
>
> Looking in the site-lisp directories for the folders org-odt is
> searching, I don't see contrib, org, or etc directories.
>
> But I do see C:/emacs-23.4/etc/org/styles, which has OrgOdtStyles.xml,
> and C:/emacs-23.4/etc/schema, which doesn't obviously have any files
> to do with ODT.
>
> Is there a workaround or alternative installation to fix it?  It would
> be really cool to export to ODT!
>
> M

-- 

Re: [O] [BABEL] Redirect stderr to stdout?

[Eric Schulte]

Viktor Rosenfeld  writes:

> Hi Eric,
>
> Eric Schulte wrote:
>
>> Currently the only action Babel takes with STDERR is to display it in a
>> pop-up buffer when code block evaluation fails.  
>
> On my system (OS X) the buffer does not popup. I just tried
>
> #+BEGIN_SRC sh
> echo foo 1>&2
> #+END_SRC
>

That is because the evaluation did not fail, try

#+BEGIN_SRC sh
echo foo 1>&2
exit 1
#+END_SRC

>
> in Aquamacs and Cocoa Emacs. Strangely, the output seems to be lost
> entirely.

I don't pretend to understand the many oddities of Aquamacs, and I don't
know what Cocoa Emacs is.

> Normally, stderr is captured in another buffer which I have to open
> manually.
>
>> It would certainly be
>> possible to add :results header argument to incorporate STDERR into
>> results (and this desire has been expressed previously).  Reasonable
>> combination options would likely include (at least) the following.
>> 
>> | stderr-only | return stderr instead of stdout|
>> | 2>&1| interleave stderr and stdout   |
>> | concat  | add stderr to the end of stdout|
>> | list| return a list of stderr and stdotu |
>> 
>> The best (read simple and extensible) implementation and syntax for this
>> behavior is not obvious to me (and I simply don't have time).  If you
>> (or anyone on the list) have any interest in hacking elisp code the
>> place to start would be `org-babel-eval' for a serious implementation,
>> or an quick hack may be possible through customization of the
>> `org-babel-eval-error-notify' function.
>> 
>> Hope this helps.
>
> Okay, thanks. My elisp skills are very rudimentary and this is beyond
> me. Maybe somebody else will pick it up if the interest is big enough.
>

This feature has been requested previously on the mailing list, so there
is certainly demand.  As always demand outstrips development resources.

Best,

>
> Cheers,
> Viktor
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] Selectively export RESULTS

[Eric Schulte]

Matthew Landis  writes:

> On 3/2/2012 2:33 PM, Eric Schulte wrote:
>>
>> The above line should be #+PROPERTY: singular.  That explains why
>> file-wide settings aren't working for you.
> THANK YOU.  That makes it work,

Good to hear.

> especially once I realized that the Property has to be set when the
> buffer is loaded.

You can also press C-c C-c on the #+Property line to apply it's effects.

> Now I have #+PROPERTY: eval no-export
>
>> I would suggest either fixing the properties issue above, which will 
>> allow you to set eval to "no" before export when you are content with 
>> your current results, 
> This is exactly what I did, and it does exactly what I want.  org-babel 
> totally rocks.

Great, happy this was resolved successfully.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] Export <> to latex

[Nick Dokos]

Markus Grebenstein  wrote:

> Dear List,
> 
> I am regularly running into problems with internal links to headings,
> since my document meanwhile is 200pp+ long and I tend to change
> headings.
> 
> Since I loose the ability to jump to the heading, I do not like to use
> the classic latex approach using \label.
> 
> I am wondering why anchors are not exported as a label. Alternatively
> having an "option" for headings would be nice like:
> * Heading [label:anchor]
> 
> Is there a possibility to tweak orgmode to export anchors?
> 
> Thanks in advance,
> 

I may be misunderstanding what you mean, but when I try exporting to latex
the following org file:

--8<---cut here---start->8---

* foo
# <>

foo text

* bar
# <>

bar text
--8<---cut here---end--->8---

I get the following latex code:

,
| ...
| \section{foo}
| \label{sec-1}
| \label{fooanchor}
| 
| 
| foo text
| \section{bar}
| \label{sec-2}
| \label{baranchor}
| 
| 
| bar text
| ...
`

Isn't that enough?

Nick

Re: [O] Selectively export RESULTS

[Matthew Landis]

On 3/2/2012 2:33 PM, Eric Schulte wrote:


The above line should be #+PROPERTY: singular.  That explains why
file-wide settings aren't working for you.
THANK YOU.  That makes it work, especially once I realized that the 
Property has to be set when the buffer is loaded.  Now I have

#+PROPERTY: eval no-export

I would suggest either fixing the properties issue above, which will 
allow you to set eval to "no" before export when you are content with 
your current results, 
This is exactly what I did, and it does exactly what I want.  org-babel 
totally rocks.



--
~~
Matthew Landis, Ph.D.
Research Scientist
ISciences, LLC
61 Main St. Suite 200
Burlington VT 05401
802.864.2999
www.isciences.com
~~

[O] ConTeXt export

[Markus Grebenstein]

Dear List,

Since the name of ConTeXt makes it almost impossible to search for that 
topic I'd like to ask you:


Is there an ConTeXt exporter (planned??). I am getting more and more fed 
up with all the package trouble...


Thanks in advance,

Markus

[O] Export <> to latex

[Markus Grebenstein]

Dear List,

I am regularly running into problems with internal links to headings, 
since my document meanwhile is 200pp+ long and I tend to change headings.


Since I loose the ability to jump to the heading, I do not like to use 
the classic latex approach using \label.


I am wondering why anchors are not exported as a label. Alternatively 
having an "option" for headings would be nice like:

* Heading [label:anchor]

Is there a possibility to tweak orgmode to export anchors?

Thanks in advance,

Markus

Re: [O] How to include pre-existing pdf files/pages into orgmode pdf or other export output

[Skip Collins]

On Fri, Mar 2, 2012 at 10:57 AM, Martin Weigele  wrote:
> Hi, is there an easy way to do this (rather than to fiddle around with
> resulting pdfs)?

I think the LaTeX package pdfpages is what you are looking for.

Re: [O] [BABEL] Redirect stderr to stdout?

[Viktor Rosenfeld]

Hi Eric,

Eric Schulte wrote:

> Currently the only action Babel takes with STDERR is to display it in a
> pop-up buffer when code block evaluation fails.  

On my system (OS X) the buffer does not popup. I just tried

#+BEGIN_SRC sh
echo foo 1>&2
#+END_SRC

in Aquamacs and Cocoa Emacs. Strangely, the output seems to be lost
entirely. Normally, stderr is captured in another buffer which I have to
open manually.

> It would certainly be
> possible to add :results header argument to incorporate STDERR into
> results (and this desire has been expressed previously).  Reasonable
> combination options would likely include (at least) the following.
> 
> | stderr-only | return stderr instead of stdout|
> | 2>&1| interleave stderr and stdout   |
> | concat  | add stderr to the end of stdout|
> | list| return a list of stderr and stdotu |
> 
> The best (read simple and extensible) implementation and syntax for this
> behavior is not obvious to me (and I simply don't have time).  If you
> (or anyone on the list) have any interest in hacking elisp code the
> place to start would be `org-babel-eval' for a serious implementation,
> or an quick hack may be possible through customization of the
> `org-babel-eval-error-notify' function.
> 
> Hope this helps.

Okay, thanks. My elisp skills are very rudimentary and this is beyond
me. Maybe somebody else will pick it up if the interest is big enough.

Cheers,
Viktor

Re: [O] Selectively export RESULTS

[cberry]

Eric Schulte  writes:

> Matthew Landis  writes:
>
>>   tajo.ucsd.edu> writes:
>>
>>> 
>>> Eric Schulte  gmx.com> writes:
>>> 
>>> >>> Does this do what you want?
>>
>>> >
>>> > Have you looked at the :cache header argument [1], from my understanding
>>> > of your use case it should be exactly what you are after.
>>> >
>>> 
>>> Its a step in the right direction.
>>> 
>>> It seems I have to set :cache yes on every block I use before I invoke
>>> it. My attempt to use a buffer-wide PROPERTY setting for cache did not
>>> pan out. 
>>> 
>
> Were these technical problems with the implementation of :cache, or
> logistical problems specific to your organization of code blocks?
>
[rest deleted]

Eric,

your response is threaded as a reply to Matthew, but here you have
replied to my comment about buffer wide PROPERTY setting of :cache.

Here is an example of the difficulty I face:

,
| #+property: :cache yes
| 
| 
| #+name: Ablock
| #+begin_src emacs-lisp :results value :exports both 
|   (current-time-string)
| #+end_src
| 
| #+results[2ca40f0dc0f23e5743133e229d9e8f31b31830c5]: Ablock
| : Wed Feb 29 11:57:19 2012
| 
| 
| * headline 1
|   :PROPERTIES:
|   :cache:   no
|   :END:
| 
| #+CALL: Ablock() :exports results
| 
`

When I place point under the headline and issue 

 C-c @ C-c C-e a

I get 

,
|   headline 1
|   ==
| 
| Author: 
| Date: 2012-03-02 11:28:54 PST
| 
| 
| 
| 
| Fri Mar  2 11:28:52 2012
| 
`

showing that Ablock() actually was executed.

If the :cache setting under 'headline 1' is omitted then no update of
the time string is performed.

I understand that this behavior might be considered a *feature*, not a
*bug*. 

Either way, having an easy way to copy results into other parts of a
document would help me out.

Best,

Chuck

-- 
Charles C. BerryDept of Family/Preventive Medicine
cberry at ucsd edu  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

[Eric Schulte]

Matthew Landis  writes:

> Eric Schulte  gmx.com> writes:
>
>> 
>> Matthew Landis  isciences.com> writes:
>> 
>> Have you tried this?  The cache header argument has special handling of
>> code blocks with sessions to handle such cases.
>
> Fair enough!  I hadn't tried it.  But I did just try this example:
>
> -
> #+TITLE: Super simple example using cache header arguments
> #+PROPERTIES: eval no
>

The above line should be #+PROPERTY: singular.  That explains why
file-wide settings aren't working for you.

>
> Here is a really simple example.
>
> #+begin_src R :session :results silent :exports code :cache yes
> x <- rnorm(100)
> cat('ran this code block')
> #+end_src
>
> here is code block two.
>
> #+begin_src R :session :results graphics :exports both :file hist.png :cache 
> yes
> hist(x, main = 'A new title' )
> #+end_src
>
> #+results[1987d49b46ffd8b7263dc04e7c7b5d25f90342aa]:
> [[file:hist.png]]
> -
>

Thanks for the example, after working through it I now know what is
causing this issue.  The first code block will always be run for two
reasons.
1. it is run in a session, which means that Babel can not guess at to
   what state it could be changing internal to the session, so it
   defaults to the safest option which is allowing the code block to run
2. since this code block returns no results, there is no place for Babel
   to store the hash key holding the information on the code block and
   arguments used to produce the results.  Remember that Org-mode is
   nothing more than the text in the file, so without this stored hash,
   there is no way for Babel to know that the code block was previously
   run, or that it may have results.

For these reasons I would suggest either fixing the properties issue
above, which will allow you to set eval to "no" before export when you
are content with your current results, or I would suggest that you
switch from session based evaluation to explicitly passing the values
through Org-mode, which will allow babel to cache results.

I will update the ":cache" section of the manual so that it mentions the
issues around mixing ":session" and ":cache" header arguments.

Best,

>
> RESULTS:
> On 1st export to html, both code blocks are run, and #+results block is *not* 
> created.  
>
> On 2nd export, both code blocks are run again, counter to my desires.
>
> IF I run the code blocks interactively first using C-c C-c, the #+results 
> block 
> is created for the code block 2.  After that, subsequent exports run code 
> block 
> 1 but not code block 2.  Again, this is counter to my desires because I want 
> code block 1 to be ignored as well.  I understand why code block 1 is rerun, 
> because I have :results silent, but I'd rather not have to change that.  
> Generally, code block 1 is producing large R data.frames which don't need to 
> be 
> viewed anywhere.
>
>> Are you requesting a new option to :cache, such that even if the code
>> block has changes the old results are used anyway?
>
> Sort of.  I think I'm asking for a file wide option to decide whether to run 
> any 
> code blocks, or just do the export based on whatever is currently existing in 
> the #+results blocks.
>
> As in this example, I tried #+PROPERTIES: eval no but it is ignored.  It 
> would 
> be great if I could set an eval argument at the top of the file to be either 
> 'no' (don't run any code blocks) 'yes' (run all code blocks) or 'block' 
> respect 
> block level eval settings 
>
> Maybe such functionality exists in some other way - I claim only beginners 
> knowledge of org-babel.
>
>
>
>
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

[O] org-odt: cannot find factory styles

[Matthew Landis]

Hello all,

I've been googling this problem and searching the archives, but I can't 
seem to find a solution.  When I try to export to ODT, I get


Error (org-odt): Cannot find factory styles files. Aborting.

Looking in my *Messages* buffer, I see at startup:

Debug (org-odt): Searching for OpenDocument schema files...
Debug (org-odt): Trying 
c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/schema/...

Debug (org-odt): Trying c:/emacs-23.4/site-lisp/contrib/odt/etc/schema/...
Debug (org-odt): No OpenDocument schema files installed
Debug (org-odt): Searching for OpenDocument styles files...
Debug (org-odt): Trying 
c:/c/Emacs-modified/tmpdir/emacs-23.4/etc/org/styles/...

Debug (org-odt): Trying c:/emacs-23.4/site-lisp/etc/styles/...
Debug (org-odt): Trying c:/emacs-23.4/site-lisp/org/etc/styles/...
Debug (org-odt): Trying c:/emacs-23.4/etc/org/...
Problems while trying to load feature `org-odt'

So you can see that i am using Windows (Win 7 64 bit).  In fact, I am 
using Vincent Goulet's Windows installer (modified-2, FWIW), and I 
directed it to install into C:/emacs-23.4 instead of the default 
C:/Program Files (x86) directory.


Looking in the site-lisp directories for the folders org-odt is 
searching, I don't see contrib, org, or etc directories.


But I do see C:/emacs-23.4/etc/org/styles, which has OrgOdtStyles.xml, 
and C:/emacs-23.4/etc/schema, which doesn't obviously have any files to 
do with ODT.


Is there a workaround or alternative installation to fix it?  It would 
be really cool to export to ODT!


M


--
~~
Matthew Landis, Ph.D.
Research Scientist
ISciences, LLC
61 Main St. Suite 200
Burlington VT 05401
802.864.2999
www.isciences.com
~~

Re: [O] Selectively export RESULTS

[Matthew Landis]

On 3/2/2012 12:59 PM, Christophe Pouzat wrote:


Matthew,

I think that you're wrongly expecting babel's cache header argument to
behave like the argument of the same name in Sweave code chunks. Babel
will cache, in your case, the value of your code block evaluation and
there is none in your first code block, therefore nothing gets cached by
babel, try that instead:

#+name: my-random-vector
#+begin_src R :session :cache yes
rnorm(100)
#+end_src

#+headers: :var x=my-random-vector
#+headers: :results graphics :exports results :file hist.png
#+begin_src R :session  :cache yes
hist(x)
#+end_src

Does it work better? In that case you don't even need a session.

Christophe
Christophe - thanks for the suggestion.  I haven't messed around much 
with variables passed between code blocks.  When I try this, R tells me 
that 'x' must be numeric.  When I query x in the R buffer, x is a 
data.frame.  So the second code block reads x in as a data.frame instead 
of a numeric vector.


For most purposes this would be OK (since a data.frame is the most usual 
outcome), but I'm reluctant to use this approach -- I'd like all of the 
variable passing to be in the R session.  Intuitively this seems 
simpler, less error prone, and more conducive to tangling later.  (Of 
course, I could be totally wrong - since I haven't really tried that 
approach).


M

--
~~
Matthew Landis, Ph.D.
Research Scientist
ISciences, LLC
61 Main St. Suite 200
Burlington VT 05401
802.864.2999
www.isciences.com
~~

Re: [O] Selectively export RESULTS

[Matthew Landis]

Eric Schulte  gmx.com> writes:

> 
> Matthew Landis  isciences.com> writes:
> 
> Have you tried this?  The cache header argument has special handling of
> code blocks with sessions to handle such cases.

Fair enough!  I hadn't tried it.  But I did just try this example:

-
#+TITLE: Super simple example using cache header arguments
#+PROPERTIES: eval no

Here is a really simple example.

#+begin_src R :session :results silent :exports code :cache yes
x <- rnorm(100)
cat('ran this code block')
#+end_src

here is code block two.

#+begin_src R :session :results graphics :exports both :file hist.png :cache yes
hist(x, main = 'A new title' )
#+end_src

#+results[1987d49b46ffd8b7263dc04e7c7b5d25f90342aa]:
[[file:hist.png]]
-

RESULTS:
On 1st export to html, both code blocks are run, and #+results block is *not* 
created.  

On 2nd export, both code blocks are run again, counter to my desires.

IF I run the code blocks interactively first using C-c C-c, the #+results block 
is created for the code block 2.  After that, subsequent exports run code block 
1 but not code block 2.  Again, this is counter to my desires because I want 
code block 1 to be ignored as well.  I understand why code block 1 is rerun, 
because I have :results silent, but I'd rather not have to change that.  
Generally, code block 1 is producing large R data.frames which don't need to be 
viewed anywhere.

> Are you requesting a new option to :cache, such that even if the code
> block has changes the old results are used anyway?

Sort of.  I think I'm asking for a file wide option to decide whether to run 
any 
code blocks, or just do the export based on whatever is currently existing in 
the #+results blocks.

As in this example, I tried #+PROPERTIES: eval no but it is ignored.  It would 
be great if I could set an eval argument at the top of the file to be either 
'no' (don't run any code blocks) 'yes' (run all code blocks) or 'block' respect 
block level eval settings 

Maybe such functionality exists in some other way - I claim only beginners 
knowledge of org-babel.

Re: [O] Double SCHEDULED: problem

[François Pinard]

Bernt Hansen  writes:

> pin...@iro.umontreal.ca (François Pinard) writes:

> Two SCHEDULED: lines on a single entry is not supported by org-mode
> AFAIK.

OK!

> I would create a subtask for each of these

I'll use this, thanks Bernt!

François

Re: [O] Selectively export RESULTS

[Christophe Pouzat]

Matthew Landis  writes:

>   tajo.ucsd.edu> writes:
>
>> 
>> Eric Schulte  gmx.com> writes:
>> 
>> >>> Does this do what you want?
>
>> >
>> > Have you looked at the :cache header argument [1], from my understanding
>> > of your use case it should be exactly what you are after.
>> >
>> 
>> Its a step in the right direction.
>> 
>> It seems I have to set :cache yes on every block I use before I invoke
>> it. My attempt to use a buffer-wide PROPERTY setting for cache did not
>> pan out. 
>> 
>
> I'd like to put in a vote for the kind of functionality that cberry is 
> describing.  I have a very similar situation - a large org file that uses R 
> to 
> do a lot of time consuming data manipulation and model fitting, resulting in 
> statistical tables and graphs.  I run a lot of the code blocks as I'm writing 
> it, resulting in :results in the org file.  
>
> In the end, I'd like to export the org file to html or ODT, but I'd like to 
> be 
> able to choose buffer-wide whether to rerun all of the code blocks or just 
> use 
> the results that are already in the buffer.  I tried setting #+PROPERTY: eval 
> no 
> at the top of the buffer in the hopes that on export, it would ignore all my 
> code blocks and just incorporate the :results, but this was ignored and my 
> code 
> blocks were rerun.
>
> The cache argument only partially deals with the problem, as this example 
> illustrates:
>
> #+begin_src R :session :cache yes
> x <- rnorm(100)
> #+end_src
> #+begin_src R :session :results graphics :exports results :file hist.png 
> :cache 
> yes
> hist(x)
> #+end_src
>
> Now after the first export, I change code block 2, but not code block 1.  If 
> I 
> understand how cache works correctly, code block 2 will be rerun, but it will 
> fail because code block 1 is not rerun, so x doesn't exist in the R session.  
>
> For this reason, I'd prefer to be able to decide whether to re-run on a file-
> wide basis.
>
> Many thanks to all of you who have created such an amazing system.  
>
> M
>

Matthew,

I think that you're wrongly expecting babel's cache header argument to
behave like the argument of the same name in Sweave code chunks. Babel
will cache, in your case, the value of your code block evaluation and
there is none in your first code block, therefore nothing gets cached by
babel, try that instead:

#+name: my-random-vector
#+begin_src R :session :cache yes
rnorm(100)
#+end_src

#+headers: :var x=my-random-vector
#+headers: :results graphics :exports results :file hist.png
#+begin_src R :session  :cache yes
hist(x)
#+end_src

Does it work better? In that case you don't even need a session.

Christophe
-- 

Président, Nicolas Sarkozy représente une sorte de triomphe bouffon de 
l'égalitarisme français ; pour la première fois de notre histoire, nous avons 
un chef de l'État qui se comporte comme s'il ne valait pas mieux que les 
citoyens. C'est en réalité toujours le cas, mais cette vérité doit être cachée 
pour que les institutions et le système social tournent de façon, si ce n'est 
harmonieuse, du moins raisonnable.

E. Todd, Après la démocratie. 
--

Christophe Pouzat
MAP5 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France

tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html

Re: [O] [babel] Is Org Babel an X11 application?

[Thorsten]

Rick Frankel  writes:

Hi Eric, Hi Rick,

> Are you running babel code which generates images (e.g., dot, mscgen,
> etc.)?
> If so, check if =org-display-inline-images= is being executed in the
> =org-babel-after-execute-hook=. It automatically replaces the file link
> results with the inline image, therefore requiring a GUI emacs.

Yes, that was the culprit:
,---
| org-babel-after-execute-hook is a variable defined in `ob.el'.
| Its value is (org-display-inline-images)
`---

thanks for the tip
-- 
cheers,
Thorsten

Re: [O] [BUG?] subtle sequencing error when setting org-bbdb-old in org-bbdb.el

[Nick Dokos]

David Maus  wrote:

> At Mon, 27 Feb 2012 17:21:59 -0500,
> Nick Dokos wrote:
> > 
> > David Maus  wrote:
> > 
> > > > The problem was that org-bbdb is part of org-modules by default and that
> > > > was loading org-bbdb way too early, certainly before bbdb itself was
> > > > loaded.  That would set the value to nil and nothing I would do could
> > > > change it (short of whacking it with a setq).
> > > 
> > > I pushed a patch that should fix this problem. I wrapped a
> > > `eval-after-load' around the `defvar', this should make sure that the
> > > variable is set after bbdb was loaded.
> > > 
> > 
> > I still have a problem with one configuration (but not with another),
> > but I haven't drilled down to figure out what the problem is. I was
> > wondering however if the eval-after-load should be predicated on
> > bbdb-com rather than bbdb[fn:1]: with this change, both of my tested
> > configurations work (hardly a definitive test but perhaps better than
> > nothing).
> 
> Thanks for the feedback. Eval after load 'bbdb-com would have been
> better -- I just replaced the entire defvar by a check in
> `org-bbdb-open' and `org-bbdb-store-link' for the required functions.
> 
> So this should really work now.
> 

It does, at least in the two configurations I've tested: my full-blown one
and a minimal org one with bbdb loaded after the fact.

I'll be trying it with bbdb 3.x some time soon, I hope.

Thanks very much!
Nick

Re: [O] Selectively export RESULTS

[Eric Schulte]

Matthew Landis  writes:

>   tajo.ucsd.edu> writes:
>
>> 
>> Eric Schulte  gmx.com> writes:
>> 
>> >>> Does this do what you want?
>
>> >
>> > Have you looked at the :cache header argument [1], from my understanding
>> > of your use case it should be exactly what you are after.
>> >
>> 
>> Its a step in the right direction.
>> 
>> It seems I have to set :cache yes on every block I use before I invoke
>> it. My attempt to use a buffer-wide PROPERTY setting for cache did not
>> pan out. 
>> 

Were these technical problems with the implementation of :cache, or
logistical problems specific to your organization of code blocks?

>
> I'd like to put in a vote for the kind of functionality that cberry is 
> describing.  I have a very similar situation - a large org file that uses R 
> to 
> do a lot of time consuming data manipulation and model fitting, resulting in 
> statistical tables and graphs.  I run a lot of the code blocks as I'm writing 
> it, resulting in :results in the org file.  
>
> In the end, I'd like to export the org file to html or ODT, but I'd like to 
> be 
> able to choose buffer-wide whether to rerun all of the code blocks or just 
> use 
> the results that are already in the buffer.  I tried setting #+PROPERTY: eval 
> no 
> at the top of the buffer in the hopes that on export, it would ignore all my 
> code blocks and just incorporate the :results, but this was ignored and my 
> code 
> blocks were rerun.
>
> The cache argument only partially deals with the problem, as this example 
> illustrates:
>
> #+begin_src R :session :cache yes
> x <- rnorm(100)
> #+end_src
> #+begin_src R :session :results graphics :exports results :file hist.png 
> :cache yes
> hist(x)
> #+end_src
>
> Now after the first export, I change code block 2, but not code block 1.  If 
> I 
> understand how cache works correctly, code block 2 will be rerun, but it will 
> fail because code block 1 is not rerun, so x doesn't exist in the R session.  
>

Have you tried this?  The cache header argument has special handling of
code blocks with sessions to handle such cases.

>
> For this reason, I'd prefer to be able to decide whether to re-run on a file-
> wide basis.
>

I'm not clear on why file-wide setting of cache does not work.

Are you requesting a new option to :cache, such that even if the code
block has changes the old results are used anyway?

>
> Many thanks to all of you who have created such an amazing system.
>

Thanks,

>
> M
>
>
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

[Achim Gratz]

Nicolas Goaziou  writes:
> This should be fixed now. Thank you for reporting it.

I confirm the fix, testing is clean again, thank you very much.


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

SD adaptation for Waldorf microQ V2.22R2:
http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [O] Git repo not cloneable?

[jeremiah . dodds]

suvayu ali  writes:

> Hi Jonathan and Jeremiah,
>
> On Fri, Mar 2, 2012 at 14:29, Jonathan Leech-Pepin
>  wrote:
>> Seems that the URL listed on that page is not correct for cloning.
>> The URL is the correct one for web access.
>>
>
> [...]
>
>>
>> So http cloning is enabled, the URL simply isn't mentioned (And I
>> can't remember where I found it originally)
>
> I updated the page. Please take a look and feel free to edit/comment if
> its still unclear. :)


Thanks for putting the correct url in, that cleared up all the issues I
was having :D

Re: [O] org-export-blocks-preprocess: Marker does not point anywhere

[Matthew Landis]

Nick Dokos  hp.com> writes:

> 
> Matthew Landis  isciences.com> wrote:

> 
> I can't reproduce it either with latest (more or less) or with 7.8.03.
> The html export succeeds and the code is exported, pdf export (with
> minted) succeeds except that the code block is not processed, because
> there is no minted lexer for R (at least in my setup). But I get no
> error.
> 
> Nick

Well, thanks for trying.  In my current work flow, I tend to have an R session 
running before I try to export, so I'm not troubled by this anymore.  I guess 
I'll just wait until it's a problem.

M

Re: [O] Selectively export RESULTS

[Matthew Landis]

  tajo.ucsd.edu> writes:

> 
> Eric Schulte  gmx.com> writes:
> 
> >>> Does this do what you want?

> >
> > Have you looked at the :cache header argument [1], from my understanding
> > of your use case it should be exactly what you are after.
> >
> 
> Its a step in the right direction.
> 
> It seems I have to set :cache yes on every block I use before I invoke
> it. My attempt to use a buffer-wide PROPERTY setting for cache did not
> pan out. 
> 

I'd like to put in a vote for the kind of functionality that cberry is 
describing.  I have a very similar situation - a large org file that uses R to 
do a lot of time consuming data manipulation and model fitting, resulting in 
statistical tables and graphs.  I run a lot of the code blocks as I'm writing 
it, resulting in :results in the org file.  

In the end, I'd like to export the org file to html or ODT, but I'd like to be 
able to choose buffer-wide whether to rerun all of the code blocks or just use 
the results that are already in the buffer.  I tried setting #+PROPERTY: eval 
no 
at the top of the buffer in the hopes that on export, it would ignore all my 
code blocks and just incorporate the :results, but this was ignored and my code 
blocks were rerun.

The cache argument only partially deals with the problem, as this example 
illustrates:

#+begin_src R :session :cache yes
x <- rnorm(100)
#+end_src

#+begin_src R :session :results graphics :exports results :file hist.png :cache 
yes
hist(x)
#+end_src

Now after the first export, I change code block 2, but not code block 1.  If I 
understand how cache works correctly, code block 2 will be rerun, but it will 
fail because code block 1 is not rerun, so x doesn't exist in the R session.  

For this reason, I'd prefer to be able to decide whether to re-run on a file-
wide basis.

Many thanks to all of you who have created such an amazing system.  

M

Re: [O] Double SCHEDULED: problem

[Bernt Hansen]

pin...@iro.umontreal.ca (François Pinard) writes:

> Hi, Org friends!
>
> For my employer, I have to fill a "time form" every two weeks for
> salary, and also every month for customer billing.  So, I have one
> SCHEDULED: line for each of these recurrences.  Last week, the entry
> started like this:
>
>
> ** TODO *Rapport d'heures (Formation):projet:
> SCHEDULED: <2012-02-27 lun ++2w>
> SCHEDULED: <2012-03-01 dim ++1m>
>
>
> Last Monday, turning the entry to DONE produced the following:
>
>
> ** TODO *Rapport d'heures (Formation):projet:
> SCHEDULED: <2012-03-12 lun ++2w>
> SCHEDULED: <2012-04-01 dim ++1m>
>
>
> That is, *both* SCHEDULED: lines were advanced, and so, I missed to be
> remembered to do my little filling duty yesterday, which has not been a
> problem because others and I also received an email to that effect.
>
> I wonder if or how Org could have helped me better.  I would prefer
> keeping a single entry, because there many lines of contents ( the
> recipe details about how to fill the company form, clocktables,
> logbooks, and such things), which I would not like duplicated.
>

Two SCHEDULED: lines on a single entry is not supported by org-mode
AFAIK.  I would create a subtask for each of these



* TODO Parent task with the details
  All your notes and procedures go here
** TODO Subtask 1
   SCHEDULED: <2012-03-12 lun ++2w>
** TODO subtask 2
   <2012-04-01 dim ++1m>

HTH,
Bernt

Re: [O] Participating in Google Summer of Code 2012

[Jambunathan K]

Eric Schulte  writes:

> Jambunathan K  writes:
>
>> "Git merge tool for Org files"
>>
>> http://lists.gnu.org/archive/html/emacs-orgmode/2011-08/msg00601.html
>>
>
> Interesting, along these lines, I know git is able to use custom diffs
> (e.g., there exist sentence rather than line-based diffs for writing
> prose).  I wonder if an outline diff would be useful, so that
> re-ordering subtrees in an Org-mode file was represented as a single
> operation rather than many un-related deletions and insertions.

Caveat: I know practically nothing - technically - about the project
being discussed. I am commenting here as a lay user.

Sometime back while looking at change tracking within OpenDocument
files, I stumbled upon the following two entries.

http://wiki.documentfoundation.org/Track_changes#Google_Summer_of_Code_2009:_Improve_Writer.27s_compare_function

http://gsoc-tzvetelina.blogspot.in/

In the above blog, the author is talking about paragraphs as a unit and
makes a note of the algorithms he uses to narrow down the paragraphs of
interest. I think in Org's context, outline could (also) be considered
as a unit.

Re: [O] Participating in Google Summer of Code 2012

[Eric Schulte]

Jambunathan K  writes:

> "Git merge tool for Org files"
>
> http://lists.gnu.org/archive/html/emacs-orgmode/2011-08/msg00601.html
>

Interesting, along these lines, I know git is able to use custom diffs
(e.g., there exist sentence rather than line-based diffs for writing
prose).  I wonder if an outline diff would be useful, so that
re-ordering subtrees in an Org-mode file was represented as a single
operation rather than many un-related deletions and insertions.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] Participating in Google Summer of Code 2012

[Jambunathan K]

"Git merge tool for Org files"

http://lists.gnu.org/archive/html/emacs-orgmode/2011-08/msg00601.html

Re: [O] Participating in Google Summer of Code 2012

[Eric Schulte]

Hi,

Thanks to Bastien and Thorsten for advancing this opportunity.  I think
this could be a good chance for the community to collect and prioritize
some of our more ambitious development goals, and to widen the pool of
users who are familiar with the Org-mode internals -- a wonderful
journey to take through some of the most hackable code I've ever had the
pleasure of working on [1].

If there is any interest in working on the Babel (source code) elements
of Org-mode I would be happy to serve as a mentor.  Some ideas that come
to mind include;
- implementing a multi-programming-language "notebook" like console
  interface build on top of Org-mode and Babel (with both Emacs and
  HTML interfaces)
- adding support for asynchronous code block execution
- adding support for piping results between code blocks allowing many
  blocks to run concurrently (probably best combined with asynchronous
  execution)
- adding support for handling output written to STDERR

I'm sure there are many more exciting things to be done, the above are
just those that come to mind at the moment.

Best,

Bastien  writes:

> Dear all,
>
> Thorsten wrote a page about the Google Summer of Code on Worg:
>   http://orgmode.org/worg/org-contrib/gsoc2012/
>
> He described his own project on the "ideas" page:
>   http://orgmode.org/worg/org-contrib/gsoc2012/orgmode-gsoc2012-ideas.html
>
> (See "Real webprogramming with Org Mode and PicoLisp".)
>
> If you are a student and want to submit an Org-mode project for the 
> GSoC 2012, please reply in this thread - we will give directions on
> how to edit the Worg page.  When you have the first draft for your
> project, you'll then have to find a mentor for it, which I guess 
> will also happen by discussing it in this list.
>
> The timeline for applications is here:
>
>   http://www.google-melange.com/gsoc/events/google/gsoc2012
>
>   Organization (GNU) should register *before March 9th*.
>
>   Students should register before *April 6th*.
>
> Org-mode related projects are likely to be presented under the GNU
> umbrella, but we are still waiting to know if GNU will apply as an
> Organization this year.
>
> Let's make this happen!  And thanks to Thorsten who paved the way
> for _any_ project, not only his own.


Footnotes: 
[1]  I can't count the number of times I've sat down to implement
 something thinking I had hours of work ahead of me, only to find
 that thanks to well placed hooks, and thoughtfully created and
 exposed variables the task was trivial.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

[O] Double SCHEDULED: problem

[François Pinard]

Hi, Org friends!

For my employer, I have to fill a "time form" every two weeks for
salary, and also every month for customer billing.  So, I have one
SCHEDULED: line for each of these recurrences.  Last week, the entry
started like this:


** TODO *Rapport d'heures (Formation):projet:
SCHEDULED: <2012-02-27 lun ++2w>
SCHEDULED: <2012-03-01 dim ++1m>


Last Monday, turning the entry to DONE produced the following:


** TODO *Rapport d'heures (Formation):projet:
SCHEDULED: <2012-03-12 lun ++2w>
SCHEDULED: <2012-04-01 dim ++1m>


That is, *both* SCHEDULED: lines were advanced, and so, I missed to be
remembered to do my little filling duty yesterday, which has not been a
problem because others and I also received an email to that effect.

I wonder if or how Org could have helped me better.  I would prefer
keeping a single entry, because there many lines of contents ( the
recipe details about how to fill the company form, clocktables,
logbooks, and such things), which I would not like duplicated.

François

Re: [O] [BUG?] subtle sequencing error when setting org-bbdb-old in org-bbdb.el

[David Maus]

At Mon, 27 Feb 2012 17:21:59 -0500,
Nick Dokos wrote:
> 
> David Maus  wrote:
> 
> > > The problem was that org-bbdb is part of org-modules by default and that
> > > was loading org-bbdb way too early, certainly before bbdb itself was
> > > loaded.  That would set the value to nil and nothing I would do could
> > > change it (short of whacking it with a setq).
> > 
> > I pushed a patch that should fix this problem. I wrapped a
> > `eval-after-load' around the `defvar', this should make sure that the
> > variable is set after bbdb was loaded.
> > 
> 
> I still have a problem with one configuration (but not with another),
> but I haven't drilled down to figure out what the problem is. I was
> wondering however if the eval-after-load should be predicated on
> bbdb-com rather than bbdb[fn:1]: with this change, both of my tested
> configurations work (hardly a definitive test but perhaps better than
> nothing).

Thanks for the feedback. Eval after load 'bbdb-com would have been
better -- I just replaced the entire defvar by a check in
`org-bbdb-open' and `org-bbdb-store-link' for the required functions.

So this should really work now.

Best,
  -- David
-- 
OpenPGP... 0x99ADB83B5A4478E6
Jabber dmj...@jabber.org
Email. dm...@ictsoc.de

Re: [O] [BABEL] Redirect stderr to stdout?

[Eric Schulte]

Viktor Rosenfeld  writes:

> Hi,
>
> is there a way to capture stderr output of a babel block and have it
> appear in the results block (instead of being printed in the *Shell
> Command Output* buffer)? On sh blocks I could redirect myself, but I'm
> trying to capture the output of psql (the PostgreSQL client).
>
> Specifically, I have the following code block:
>
> #+BEGIN_SRC sql :noweb yes :results output verbatim
> \timing on
> <>
> #+END_SRC
>
> #+RESULTS:
> : count
> : 95977
>
> The \timing directive causes psql to print the runtime of the query on
> stderr. If I run the query on the psql command line, the following
> output appears:
>
>  count 
>  ---
>  95977
>  (1 row)
>
>  Time: 1895,558 ms
>
> I suppose that duplicating this output in Babel would be difficult,
> because it interferes with the parsing of the result set.
>

Hi Viktor,

Currently the only action Babel takes with STDERR is to display it in a
pop-up buffer when code block evaluation fails.  It would certainly be
possible to add :results header argument to incorporate STDERR into
results (and this desire has been expressed previously).  Reasonable
combination options would likely include (at least) the following.

| stderr-only | return stderr instead of stdout|
| 2>&1| interleave stderr and stdout   |
| concat  | add stderr to the end of stdout|
| list| return a list of stderr and stdotu |

The best (read simple and extensible) implementation and syntax for this
behavior is not obvious to me (and I simply don't have time).  If you
(or anyone on the list) have any interest in hacking elisp code the
place to start would be `org-babel-eval' for a serious implementation,
or an quick hack may be possible through customization of the
`org-babel-eval-error-notify' function.

Hope this helps.

Best,

>
> Cheers,
> Viktor
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] How to include pre-existing pdf files/pages into orgmode pdf or other export output

[suvayu ali]

Hey Martin,

On Fri, Mar 2, 2012 at 16:57, Martin Weigele  wrote:
> Hi, is there an easy way to do this (rather than to fiddle around with
> resulting pdfs)?
>

If you want to include the preexisting pdf as an image, just do

[[file:/path/to/preexisting.pdf]]

and export. I don't think there is any straight forward way to include
it as text though.

> Thanks, Martin
>

HTH

-- 
Suvayu

Open source is the future. It sets us free.

[O] How to include pre-existing pdf files/pages into orgmode pdf or other export output

[Martin Weigele]

Hi, is there an easy way to do this (rather than to fiddle around with 
resulting pdfs)?

Thanks, Martin

Re: [O] [babel] Is Org Babel an X11 application?

[Rick Frankel]

On 02.03.2012 02:11, Thorsten wrote:

Hi List,

results of code block evaluations seem to be inserted as pictures in 
the

org document - and need X11 or there is an error message.

Is that true - Org Babel only works in an X11 session and not on the
console? Or is there some configuration/trick to make it work on a
console too?


Are you running babel code which generates images (e.g., dot, mscgen, 
etc.)?

If so, check if =org-display-inline-images= is being executed in the
=org-babel-after-execute-hook=. It automatically replaces the file link
results with the inline image, therefore requiring a GUI emacs.

rick

Re: [O] [babel] Is Org Babel an X11 application?

[Eric Schulte]

Can you provide a minimal example?  I have a similar usage pattern
(emacs daemon and a mixture of X11 and screen Emacs windows) and I have
never experienced what you describe.

Also, try to reproduce with Emacs -Q, maybe you have some inline-image
configuration set.

Best,

Thorsten  writes:

> Hi List, 
>
> having figured out that it is really nice to have one emacs daemon
> running and then open several emacsclient-windows managed by tmux (a
> modern gnu screen) instead of winring.el e.g (a console session)
> I tried to use Org Babel with that setting. Only to find out that the
> results of code block evaluations seem to be inserted as pictures in the
> org document - and need X11 or there is an error message.
>
> Is that true - Org Babel only works in an X11 session and not on the
> console? Or is there some configuration/trick to make it work on a
> console too? 

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [O] [Bug] Tests for experimental org-features should expect to fail if not activated by the user

[Nicolas Goaziou]

Hello,

Achim Gratz  writes:

> There's another patch by Nicolas that added a few test, one of which
> seems broken:

This should be fixed now. Thank you for reporting it.


Regards,

-- 
Nicolas Goaziou

Re: [O] Git repo not cloneable?

[suvayu ali]

Hi Jonathan and Jeremiah,

On Fri, Mar 2, 2012 at 14:29, Jonathan Leech-Pepin
 wrote:
> Seems that the URL listed on that page is not correct for cloning.
> The URL is the correct one for web access.
>

[...]

>
> So http cloning is enabled, the URL simply isn't mentioned (And I
> can't remember where I found it originally)

I updated the page. Please take a look and feel free to edit/comment if
its still unclear. :)

Cheers,

-- 
Suvayu

Open source is the future. It sets us free.

Re: [O] Git repo not cloneable?

[Jonathan Leech-Pepin]

Seems that the URL listed on that page is not correct for cloning.
The URL is the correct one for web access.

The following works for me (stuck behind a firewall that blocks git://):
,
| [remote "origin"]
| fetch = +refs/heads/*:refs/remotes/origin/*
| url = http://orgmode.org/org-mode.git
`

So http cloning is enabled, the URL simply isn't mentioned (And I
can't remember where I found it originally)

Hope this helps,

Jonathan

On Fri, Mar 2, 2012 at 07:40, suvayu ali  wrote:
>
> On Fri, Mar 2, 2012 at 09:00,   wrote:
> >
> > I was looking to add scala support to org-babel, but the repo linked
> > from http://orgmode.org/worg/org-contribute.html appears to need some
> > server-side love:
> >
> >    $ git --version
> >    git version 1.7.9.2
> >
> >    $ git clone http://orgmode.org/w/org-mode.git
> >    Cloning into 'org-mode'...
> >    fatal: http://orgmode.org/w/org-mode.git/info/refs not found: did
> >    you run git update-server-info on the server?
> >
>
> I believe the url is incorrect (http cloning is not enabled I think).
>
> 
>
> That said, it might be nice to have the clone and push urls mentioned
> on the gitweb summary page as in the repo.or.cz mirror:
> .
>
> --
> Suvayu
>
> Open source is the future. It sets us free.
>

Re: [O] Git repo not cloneable?

[suvayu ali]

On Fri, Mar 2, 2012 at 09:00,   wrote:
>
> I was looking to add scala support to org-babel, but the repo linked
> from http://orgmode.org/worg/org-contribute.html appears to need some
> server-side love:
>
>    $ git --version
>    git version 1.7.9.2
>
>    $ git clone http://orgmode.org/w/org-mode.git
>    Cloning into 'org-mode'...
>    fatal: http://orgmode.org/w/org-mode.git/info/refs not found: did
>    you run git update-server-info on the server?
>

I believe the url is incorrect (http cloning is not enabled I think).



That said, it might be nice to have the clone and push urls mentioned
on the gitweb summary page as in the repo.or.cz mirror:
.

-- 
Suvayu

Open source is the future. It sets us free.

[O] [BABEL] Redirect stderr to stdout?

[Viktor Rosenfeld]

Hi,

is there a way to capture stderr output of a babel block and have it
appear in the results block (instead of being printed in the *Shell
Command Output* buffer)? On sh blocks I could redirect myself, but I'm
trying to capture the output of psql (the PostgreSQL client).

Specifically, I have the following code block:

#+BEGIN_SRC sql :noweb yes :results output verbatim
\timing on
<>
#+END_SRC

#+RESULTS:
: count
: 95977

The \timing directive causes psql to print the runtime of the query on
stderr. If I run the query on the psql command line, the following
output appears:

 count 
 ---
 95977
 (1 row)

 Time: 1895,558 ms

I suppose that duplicating this output in Babel would be difficult,
because it interferes with the parsing of the result set.

Cheers,
Viktor

Re: [O] spot the LaTeX error

[Peter Salazar]

With some help I was able to fix the problem. If anyone is interested in
the template, let me know and I can supply the corrected code.


On Thu, Mar 1, 2012 at 11:26 PM, Peter Salazar wrote:

> Not sure if this is the right forum for this question, so feel free to
> direct me elsewhere...
>
> I'm trying to quit Markdown and switch to org-mode completely. To do that,
> I need to get my LaTeX template working with org-mode.
>
> I had a LaTeX template I cobbled together and successfully used with
> Pandoc for Markdown -> LaTeX -> PDF.
>
> I tried to convert my template to work with org-mode, but I haven't had
> any success. The .tex file it generates looks valid as far as I can tell,
> but when I do org-export to LaTeX and open resulting PDF, it crashes Emacs.
>
> Here's what I added to my .emacs file. Can anyone see what I've done
> wrong? As may be apparent, I don't really know what I'm doing.
>
>
> (add-to-list 'org-export-latex-classes
>   '("salazar"
> "\\documentclass[12pt]{article}
> \\usepackage{float}
> \\usepackage{hyperref}
> \\usepackage{algorithm}
> \\usepackage{amsmath}
> \\usepackage{ifxetex}
> \\ifxetex
>   \\usepackage{fontspec,xltxtra,xunicode}
>   \\defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
>   \\setromanfont{Adobe Garamond Pro}
>   \\setsansfont{Arial}
>   \\setmonofont{Courier}
> \\else
>   \\usepackage[mathletters]{ucs}
>   \\usepackage[utf8x]{inputenc}
> \\fi
> \\usepackage{microtype}
> \\usepackage{fancyhdr}
> \\pagestyle{fancy}
> \\pagenumbering{arabic}
> \\lhead{\\href{mailto:cycleofs...@gmail.com}{Peter Salazar}}
> \\chead{\itshape}
> \\rhead{\\itshape{\\nouppercase{\\@title}: {\\nouppercase\\leftmark}}}
> \\lfoot{}
> \\cfoot{\\thepage}
> \\rfoot{}
> \\usepackage{listings}
>
> \\lstnewenvironment{code}{\\lstset{language=Haskell,basicstyle=\\small\\ttfamily}}{}
> \\setlength{\\parindent}{0pt}
> \\setlength{\\parskip}{12pt plus 2pt minus 1pt}
> \\usepackage{fancyvrb}
> \\usepackage{enumerate}
> \\usepackage{ctable}
> \\setlength{\\paperwidth}{8.5in}
> \\setlength{\\paperheight}{11in}
>  \\usepackage[margin=1.5in,hmargin=1.5in,vmargin=1.5in]{geometry}
>   \\tolerance=1000
> \\usepackage{tocloft}
> \\renewcommand{\\cftsecleader}{\\cftdotfill{\\cftdotsep}}
> \\usepackage[normalem]{ulem}
> \\newcommand{\\textsubscr}[1]{\\ensuremath{_{\\scriptsize\\textrm{#1
>
>
> \\usepackage[breaklinks=true,linktocpage,pdftitle={\\@title},pdfauthor={\\@author},xetex]{hyperref}
>
> \\usepackage{url}
> \\usepackage{graphicx}
> \\hypersetup{ colorlinks,
> citecolor=black,filecolor=black,linkcolor=black,urlcolor=blue}
> \\makeatletter
> \\def\\maketitle{
>   \\thispagestyle{empty}
> \\vfill
>   \\begin{raggedright}
>   \\leavevmode
> \\vskip 1cm
> \{\\fontsize{50}{60}\\selectfont \\@title\\par}
> \\vskip 1cm
> \\normalfont
> \{\\huge {\\@author\\par}}
>   \\vfill
> \{\\Large Peter Salazar}
> \\newline
>   \{\\Large \\href{mailto:cycleofs...@gmail.com}{
> cycleofs...@gmail.com}}
> \\newline
> \{\\Large \\@date\\par}
>\\end{raggedright}
>   \\null
>   \\cleardoublepage
> \}
>   [NO-DEFAULT-PACKAGES]
>   [NO-PACKAGES]"
>  ("\\section{%s}" . "\\section*{%s}")
>  ("\\subsection{%s}" . "\\subsection*{%s}")
>  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>  ("\\paragraph{%s}" . "\\paragraph*{%s}")
>  ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
>
>
> (setq org-latex-to-pdf-process
>   '("xelatex -interaction nonstopmode %f"
>  "xelatex -interaction nonstopmode %f")) ;; for multiple passes
>
>

[O] Participating in Google Summer of Code 2012

[Bastien]

Dear all,

Thorsten wrote a page about the Google Summer of Code on Worg:
  http://orgmode.org/worg/org-contrib/gsoc2012/

He described his own project on the "ideas" page:
  http://orgmode.org/worg/org-contrib/gsoc2012/orgmode-gsoc2012-ideas.html

(See "Real webprogramming with Org Mode and PicoLisp".)

If you are a student and want to submit an Org-mode project for the 
GSoC 2012, please reply in this thread - we will give directions on
how to edit the Worg page.  When you have the first draft for your
project, you'll then have to find a mentor for it, which I guess 
will also happen by discussing it in this list.

The timeline for applications is here:

  http://www.google-melange.com/gsoc/events/google/gsoc2012

  Organization (GNU) should register *before March 9th*.

  Students should register before *April 6th*.

Org-mode related projects are likely to be presented under the GNU
umbrella, but we are still waiting to know if GNU will apply as an
Organization this year.

Let's make this happen!  And thanks to Thorsten who paved the way
for _any_ project, not only his own.

-- 
 Bastien

[O] Git repo not cloneable?

[jeremiah . dodds]

I was looking to add scala support to org-babel, but the repo linked
from http://orgmode.org/worg/org-contribute.html appears to need some
server-side love:

$ git --version
git version 1.7.9.2

$ git clone http://orgmode.org/w/org-mode.git
Cloning into 'org-mode'...
fatal: http://orgmode.org/w/org-mode.git/info/refs not found: did
you run git update-server-info on the server?