How to use ox-bibtex

How to use ox-bibtex

[o.castillo.felisola]

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Dear community,

I'm using org-mode to draft most of my activities, and day after day I get
closer to managing my paper writing. Nonetheless, there is a point still
drives me crazy.

All over the web I find post about using such or what tool to get emacs
org-mode to work with Bibtex... all of them seems complex to execute. I
found the exported ox-bibtex.el [1] (included in my installation from git),
which 'It also introduces "cite" syntax for Org links.', but no examples of
the usage are included in this document.

*Question*

Can anyone provide a minimal example of the use to this tool, including the
configuration (if needed), and the necessary external (non-org) files?

Thank you!

[1]
http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD

-- 
_____________________________________
Oscar Castillo-Felisola.
Grupo de Fisica Teorica.
UTFSM -- CCTVal.
Av. Espana, 1680, Valparaiso-Chile.
______________________________________

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Re: How to use ox-bibtex

[Eric Schulte]

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"o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:

> Dear community,
>
> I'm using org-mode to draft most of my activities, and day after day I get
> closer to managing my paper writing. Nonetheless, there is a point still
> drives me crazy.
>
> All over the web I find post about using such or what tool to get emacs
> org-mode to work with Bibtex... all of them seems complex to execute. I
> found the exported ox-bibtex.el [1] (included in my installation from git),
> which 'It also introduces "cite" syntax for Org links.', but no examples of
> the usage are included in this document.
>
> *Question*
>
> Can anyone provide a minimal example of the use to this tool, including the
> configuration (if needed), and the necessary external (non-org) files?
>

The attached two files (.org and .bib) provide an example of usage.


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[-- Attachment #2: ox-bibtex-example.org --]
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#+Title: An Example Demonstrating ox-bibtex Usage
#+Author: Eric Schulte
#+Options: toc:nil ^:{}

An example document demonstrating generation of bibliographies for
LaTeX, HTML and ASCII export using Org-mode cite:dominik2010org with
the =ox-bibtex= contributed package.  Included code blocks are
executable for reproducibility cite:schulte2012multi.

(taken from the comments at the top of =ox-bibtex.el=)

* Introduction and Requirements
Use =cite= syntax for Org links (e.g., =cite:bibtexid=).  For HTML and
ascii it uses the bibtex2html software from
http://www.lri.fr/~filliatr/bibtex2html/, and for ascii it uses the
pandoc software from http://johnmacfarlane.net/pandoc/.

* Usage
The usage is as follows:

: #+BIBLIOGRAPHY: bibfilebasename stylename optional-options

e.g. given =foo.bib= and using style "plain":

: #+BIBLIOGRAPHY: foo plain option:-d

"stylename" can also be "nil", in which case no style will be used.

Optional options are of the form:

: option:-foobar

pass '-foobar' to bibtex2html

e.g.,

| =option:-d= | sort by date                                 |
| =option:-a= | sort as BibTeX (usually by author) *default* |
| =option:-u= | unsorted i.e. same order as in .bib file     |
| =option:-r= | reverse the sort                             |

See the bibtex2html man page for more.  Multiple options can be
combined like:

: option:-d option:-r

Limiting to only the entries cited in the document:

: limit:t

For LaTeX export this simply inserts the lines

: \bibliographystyle{plain}
: \bibliography{foo}

into the TeX file when exporting.

For HTML export it:
1) converts all =\cite{foo}= and =[[cite:foo=]] to links to the
   bibliography,
2) creates a =foo.html= and =foo_bib.html=,
3) includes the contents of =foo.html= in the exported HTML file.

For ascii export it:
1) converts all =\cite{foo}= and =[[cite:foo=]] to links to the
   bibliography,
2) creates a =foo.txt= and =foo_bib.html=,
3) includes the contents of foo.txt in the exported ascii file.

For LaTeX export it:
1) converts all =[[cite:foo=]] to =\cite{foo}=.

* Emacs Configuration
The =.emacs= configuration is simple.  With path to Org-mode's
=contrib/= repository in your load path, require =ox-bibtex= as in the
following example.

#+begin_src emacs-lisp
(add-to-list 'load-path "~/.emacs.d/src/org-mode/contrib/lisp/")
(require 'ox-bibtex)
#+end_src

#+BIBLIOGRAPHY: ox-bibtex-example plain

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[-- Attachment #3: ox-bibtex-example.bib --]
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@book{dominik2010org,
  title={The Org Mode 7 Reference Manual-Organize your life with GNU Emacs},
  author={Dominik, Carsten},
  year={2010},
  publisher={Network Theory Ltd.}
}

@article{schulte2012multi,
  title={A multi-language computing environment for literate programming and reproducible research},
  author={Schulte, Eric and Davison, Dan and Dye, Thomas and Dominik, Carsten},
  journal={Journal of Statistical Software},
  volume={46},
  number={3},
  pages={1--24},
  year={2012},
  publisher={American Statistical Association}
}

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Best,

>
> Thank you!
>
> [1]
> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: How to use ox-bibtex

[o.castillo.felisola]

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Thank you Eric, I'll try it asap! Cheers!
On Jan 26, 2014 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:

> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:
>
> > Dear community,
> >
> > I'm using org-mode to draft most of my activities, and day after day I
> get
> > closer to managing my paper writing. Nonetheless, there is a point still
> > drives me crazy.
> >
> > All over the web I find post about using such or what tool to get emacs
> > org-mode to work with Bibtex... all of them seems complex to execute. I
> > found the exported ox-bibtex.el [1] (included in my installation from
> git),
> > which 'It also introduces "cite" syntax for Org links.', but no examples
> of
> > the usage are included in this document.
> >
> > *Question*
> >
> > Can anyone provide a minimal example of the use to this tool, including
> the
> > configuration (if needed), and the necessary external (non-org) files?
> >
>
> The attached two files (.org and .bib) provide an example of usage.
>
>
>
> Best,
>
> >
> > Thank you!
> >
> > [1]
> >
> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>
> --
> Eric Schulte
> https://cs.unm.edu/~eschulte
> PGP: 0x614CA05D
>
>

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Re: How to use ox-bibtex

[o.castillo.felisola]

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Hello Eric. I finally try the examples you attached above, and I'm getting
a problem. The file is not imported, because of an error "Wrong type
argument arrayp, nil".

Does anyone know what I am missing?

Cheers


On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com <
o.castillo.felisola@gmail.com> wrote:

> Thank you Eric, I'll try it asap! Cheers!
> On Jan 26, 2014 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
>
>> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:
>>
>> > Dear community,
>> >
>> > I'm using org-mode to draft most of my activities, and day after day I
>> get
>> > closer to managing my paper writing. Nonetheless, there is a point still
>> > drives me crazy.
>> >
>> > All over the web I find post about using such or what tool to get emacs
>> > org-mode to work with Bibtex... all of them seems complex to execute. I
>> > found the exported ox-bibtex.el [1] (included in my installation from
>> git),
>> > which 'It also introduces "cite" syntax for Org links.', but no
>> examples of
>> > the usage are included in this document.
>> >
>> > *Question*
>> >
>> > Can anyone provide a minimal example of the use to this tool, including
>> the
>> > configuration (if needed), and the necessary external (non-org) files?
>> >
>>
>> The attached two files (.org and .bib) provide an example of usage.
>>
>>
>>
>> Best,
>>
>>
>> >
>> > Thank you!
>> >
>> > [1]
>> >
>> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>>
>> --
>> Eric Schulte
>> https://cs.unm.edu/~eschulte
>> PGP: 0x614CA05D
>>
>>


-- 
_____________________________________
Oscar Castillo-Felisola.
Grupo de Fisica Teorica.
UTFSM -- CCTVal.
Av. Espana, 1680, Valparaiso-Chile.
______________________________________

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Re: How to use ox-bibtex

[Eric Schulte]

"o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:

> Hello Eric. I finally try the examples you attached above, and I'm getting
> a problem. The file is not imported, because of an error "Wrong type
> argument arrayp, nil".
>
> Does anyone know what I am missing?
>
> Cheers
>

My guess is that something is messed up in either your version of
Org-mode or your personal config.  Please try the following to
reproduce.

1. launch a version of Emacs with Org-mode loaded but without your
   personal config, this may be conveniently done by running

     make vanilla

   from the base of your Org-mode installation.

2. evaluate the following

   (add-to-list 'load-path "contrib/lisp/")
   (require 'ox-bibtex)

3. open the example .org file attached previously (with the example .bib
   file in the same directory), and export to latex.

You should now see appropriate \cite{ref} and \bibliography elements in
the exported latex.  This all works for me, if you get an error please
send the whole debug trace along with version info for your Org-mode and
Emacs.

Best,

>
>
> On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com <
> o.castillo.felisola@gmail.com> wrote:
>
>> Thank you Eric, I'll try it asap! Cheers!
>> On Jan 26, 2014 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
>>
>>> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:
>>>
>>> > Dear community,
>>> >
>>> > I'm using org-mode to draft most of my activities, and day after day I
>>> get
>>> > closer to managing my paper writing. Nonetheless, there is a point still
>>> > drives me crazy.
>>> >
>>> > All over the web I find post about using such or what tool to get emacs
>>> > org-mode to work with Bibtex... all of them seems complex to execute. I
>>> > found the exported ox-bibtex.el [1] (included in my installation from
>>> git),
>>> > which 'It also introduces "cite" syntax for Org links.', but no
>>> examples of
>>> > the usage are included in this document.
>>> >
>>> > *Question*
>>> >
>>> > Can anyone provide a minimal example of the use to this tool, including
>>> the
>>> > configuration (if needed), and the necessary external (non-org) files?
>>> >
>>>
>>> The attached two files (.org and .bib) provide an example of usage.
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>> >
>>> > Thank you!
>>> >
>>> > [1]
>>> >
>>> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>>>
>>> --
>>> Eric Schulte
>>> https://cs.unm.edu/~eschulte
>>> PGP: 0x614CA05D
>>>
>>>

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: How to use ox-bibtex

[Rainer M Krug]

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On 01/27/14, 15:36 , Eric Schulte wrote:
> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com>
> writes:
> 
>> Hello Eric. I finally try the examples you attached above, and
>> I'm getting a problem. The file is not imported, because of an
>> error "Wrong type argument arrayp, nil".
>> 
>> Does anyone know what I am missing?
>> 
>> Cheers
>> 
> 
> My guess is that something is messed up in either your version of 
> Org-mode or your personal config.  Please try the following to 
> reproduce.
> 
> 1. launch a version of Emacs with Org-mode loaded but without your 
> personal config, this may be conveniently done by running
> 
> make vanilla
> 
> from the base of your Org-mode installation.
> 
> 2. evaluate the following
> 
> (add-to-list 'load-path "contrib/lisp/") (require 'ox-bibtex)
> 
> 3. open the example .org file attached previously (with the example
> .bib file in the same directory), and export to latex.
> 
> You should now see appropriate \cite{ref} and \bibliography
> elements in the exported latex.  This all works for me, if you get
> an error please send the whole debug trace along with version info
> for your Org-mode and Emacs.

Thanks for this thread - very interesting. Just one correction (or is
it a bug?): Even the export to text - ASCII aborts the bibtex2htlm
installation.

But also: I don't get it to work. I evaluated (require 'ox-bibtex)
which worked, but export to te4xt and html gives the following error:

org-babel-exp process emacs-lisp at line 78...
if: Executing bibtex2html failed


but bibtex2html is installed (homebrew)

Export to LaTeX gives the attached .tex file, but the pdf contains
corrupt citations "[?]" and no bibliograhy.

Is this my setup? Bibliographies work in LaTex here.

Cheers,

Rainer

> 
> Best,
> 
>> 
>> 
>> On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com < 
>> o.castillo.felisola@gmail.com> wrote:
>> 
>>> Thank you Eric, I'll try it asap! Cheers! On Jan 26, 2014 4:20
>>> PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
>>> 
>>>> "o.castillo.felisola@gmail.com"
>>>> <o.castillo.felisola@gmail.com> writes:
>>>> 
>>>>> Dear community,
>>>>> 
>>>>> I'm using org-mode to draft most of my activities, and day
>>>>> after day I
>>>> get
>>>>> closer to managing my paper writing. Nonetheless, there is
>>>>> a point still drives me crazy.
>>>>> 
>>>>> All over the web I find post about using such or what tool
>>>>> to get emacs org-mode to work with Bibtex... all of them
>>>>> seems complex to execute. I found the exported ox-bibtex.el
>>>>> [1] (included in my installation from
>>>> git),
>>>>> which 'It also introduces "cite" syntax for Org links.',
>>>>> but no
>>>> examples of
>>>>> the usage are included in this document.
>>>>> 
>>>>> *Question*
>>>>> 
>>>>> Can anyone provide a minimal example of the use to this
>>>>> tool, including
>>>> the
>>>>> configuration (if needed), and the necessary external
>>>>> (non-org) files?
>>>>> 
>>>> 
>>>> The attached two files (.org and .bib) provide an example of
>>>> usage.
>>>> 
>>>> 
>>>> 
>>>> Best,
>>>> 
>>>> 
>>>>> 
>>>>> Thank you!
>>>>> 
>>>>> [1]
>>>>> 
>>>> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>>>>
>>>>
>>>> 
- --
>>>> Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
>>>> 
>>>> 
> 

- -- 
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:      Rainer@krugs.de

Skype:      RMkrug
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Re: How to use ox-bibtex

[Christian Moe]

Rainer M Krug writes:

>
> Thanks for this thread - very interesting. Just one correction (or is
> it a bug?): Even the export to text - ASCII aborts the bibtex2htlm
> installation.
>
> But also: I don't get it to work. I evaluated (require 'ox-bibtex)
> which worked, but export to te4xt and html gives the following error:
>
> org-babel-exp process emacs-lisp at line 78...
> if: Executing bibtex2html failed
>
>
> but bibtex2html is installed (homebrew)

Check if b2h is  working from the command line at all.

  bibtex2html ox-bibtex-example.bib

In my case (homebrew install on OSX 10.6.8), it doesn't. It fails to
write to a temporary folder.

The documentation (https://www.lri.fr/~filliatr/bibtex2html/) suggests
it's due to interference from TexLive 2010 on the Mac (doesn't say if
later versions fix it, and I don't have time right now to check).

Yours,
Christian

Re: How to use ox-bibtex

[Rainer M Krug]

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On 01/28/14, 10:04 , Christian Moe wrote:
> 
> Rainer M Krug writes:
> 
>> 
>> Thanks for this thread - very interesting. Just one correction
>> (or is it a bug?): Even the export to text - ASCII aborts the
>> bibtex2htlm installation.
>> 
>> But also: I don't get it to work. I evaluated (require
>> 'ox-bibtex) which worked, but export to te4xt and html gives the
>> following error:
>> 
>> org-babel-exp process emacs-lisp at line 78... if: Executing
>> bibtex2html failed
>> 
>> 
>> but bibtex2html is installed (homebrew)
> 
> Check if b2h is  working from the command line at all.
> 
> bibtex2html ox-bibtex-example.bib

It doesn't - that seems to be the problem.

I am using TeXLive 2013

The workaround: I created a shell script changing the TMPDIR to .:

#!/bin/bash
export TMPDIR=.
/usr/local/bin/bibtex2html "$@"

and saved it in ~/bin/bibtex2html

As ~/bin is first in my path, this script is called and it is working
for html and ascii.

The .tex looks fine, but the bibliography is still not included.

I get the following warnings when compiling the .tex file:

LaTeX Warning: Citation `dominik2010org' on page 1 undefined on input
line 32.
LaTeX Warning: Citation `schulte2012multi' on page 1 undefined on
input line 34.


Is this a problem on my side here?

Cheers,

Rainer


> 
> In my case (homebrew install on OSX 10.6.8), it doesn't. It fails
> to write to a temporary folder.
> 
> The documentation (https://www.lri.fr/~filliatr/bibtex2html/)
> suggests it's due to interference from TexLive 2010 on the Mac
> (doesn't say if later versions fix it, and I don't have time right
> now to check).
> 
> Yours, Christian
> 

- -- 
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:      Rainer@krugs.de

Skype:      RMkrug
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Re: How to use ox-bibtex

[Rainer M Krug]

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On 01/28/14, 09:32 , Rainer M Krug wrote:
> 
> 
> On 01/27/14, 15:36 , Eric Schulte wrote:
>> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> 
>> writes:
> 
>>> Hello Eric. I finally try the examples you attached above, and 
>>> I'm getting a problem. The file is not imported, because of an 
>>> error "Wrong type argument arrayp, nil".
>>> 
>>> Does anyone know what I am missing?
>>> 
>>> Cheers
>>> 
> 
>> My guess is that something is messed up in either your version of
>>  Org-mode or your personal config.  Please try the following to 
>> reproduce.
> 
>> 1. launch a version of Emacs with Org-mode loaded but without
>> your personal config, this may be conveniently done by running
> 
>> make vanilla
> 
>> from the base of your Org-mode installation.
> 
>> 2. evaluate the following
> 
>> (add-to-list 'load-path "contrib/lisp/") (require 'ox-bibtex)
> 
>> 3. open the example .org file attached previously (with the
>> example .bib file in the same directory), and export to latex.
> 
>> You should now see appropriate \cite{ref} and \bibliography 
>> elements in the exported latex.  This all works for me, if you
>> get an error please send the whole debug trace along with version
>> info for your Org-mode and Emacs.
> 
> Thanks for this thread - very interesting. Just one correction (or
> is it a bug?): Even the export to text - ASCII aborts the
> bibtex2htlm installation.
> 
> But also: I don't get it to work. I evaluated (require 'ox-bibtex) 
> which worked, but export to te4xt and html gives the following
> error:
> 
> org-babel-exp process emacs-lisp at line 78... if: Executing
> bibtex2html failed
> 
> 
> but bibtex2html is installed (homebrew)
> 
> Export to LaTeX gives the attached .tex file, but the pdf contains 
> corrupt citations "[?]" and no bibliograhy.
> 
> Is this my setup? Bibliographies work in LaTex here.

OK - I have to run pdflatex - bibtex - pdflatex manually after .tex
file creation. Then I get the references in. But is this intended?

I thought that this would be done automatically?

Rainer

> 
> Cheers,
> 
> Rainer
> 
> 
>> Best,
> 
>>> 
>>> 
>>> On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com
>>> < o.castillo.felisola@gmail.com> wrote:
>>> 
>>>> Thank you Eric, I'll try it asap! Cheers! On Jan 26, 2014
>>>> 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
>>>> 
>>>>> "o.castillo.felisola@gmail.com" 
>>>>> <o.castillo.felisola@gmail.com> writes:
>>>>> 
>>>>>> Dear community,
>>>>>> 
>>>>>> I'm using org-mode to draft most of my activities, and
>>>>>> day after day I
>>>>> get
>>>>>> closer to managing my paper writing. Nonetheless, there
>>>>>> is a point still drives me crazy.
>>>>>> 
>>>>>> All over the web I find post about using such or what
>>>>>> tool to get emacs org-mode to work with Bibtex... all of
>>>>>> them seems complex to execute. I found the exported
>>>>>> ox-bibtex.el [1] (included in my installation from
>>>>> git),
>>>>>> which 'It also introduces "cite" syntax for Org links.', 
>>>>>> but no
>>>>> examples of
>>>>>> the usage are included in this document.
>>>>>> 
>>>>>> *Question*
>>>>>> 
>>>>>> Can anyone provide a minimal example of the use to this 
>>>>>> tool, including
>>>>> the
>>>>>> configuration (if needed), and the necessary external 
>>>>>> (non-org) files?
>>>>>> 
>>>>> 
>>>>> The attached two files (.org and .bib) provide an example
>>>>> of usage.
>>>>> 
>>>>> 
>>>>> 
>>>>> Best,
>>>>> 
>>>>> 
>>>>>> 
>>>>>> Thank you!
>>>>>> 
>>>>>> [1]
>>>>>> 
>>>>> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>>>>>
>>>>>
>>>>>
>
>>>>> 
- --
>>>>> Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
>>>>> 
>>>>> 
> 
> 
> 

- -- 
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:      Rainer@krugs.de

Skype:      RMkrug
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Re: How to use ox-bibtex

[o.castillo.felisola]

[-- Attachment #1: Type: text/plain, Size: 5696 bytes --]

My problem continues... however, It seems has to be with the exportation,
because if I open de file before evaluating =(requier 'ox-bibtex)= the
links are not recognised.

I tried using the latest git code

$ git fetch origin
$ make all
$ make install

Then I repeated the =vanilla= calling of emacs, and nothing.

If I try to export something (no ox-bibtex), obtain the same error. If I
uninstall the newest =org-mode=.... the 6.XX version does extort!

:-S


On Tue, Jan 28, 2014 at 9:38 AM, Rainer M Krug <Rainer@krugs.de> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> On 01/28/14, 09:32 , Rainer M Krug wrote:
> >
> >
> > On 01/27/14, 15:36 , Eric Schulte wrote:
> >> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com>
> >> writes:
> >
> >>> Hello Eric. I finally try the examples you attached above, and
> >>> I'm getting a problem. The file is not imported, because of an
> >>> error "Wrong type argument arrayp, nil".
> >>>
> >>> Does anyone know what I am missing?
> >>>
> >>> Cheers
> >>>
> >
> >> My guess is that something is messed up in either your version of
> >>  Org-mode or your personal config.  Please try the following to
> >> reproduce.
> >
> >> 1. launch a version of Emacs with Org-mode loaded but without
> >> your personal config, this may be conveniently done by running
> >
> >> make vanilla
> >
> >> from the base of your Org-mode installation.
> >
> >> 2. evaluate the following
> >
> >> (add-to-list 'load-path "contrib/lisp/") (require 'ox-bibtex)
> >
> >> 3. open the example .org file attached previously (with the
> >> example .bib file in the same directory), and export to latex.
> >
> >> You should now see appropriate \cite{ref} and \bibliography
> >> elements in the exported latex.  This all works for me, if you
> >> get an error please send the whole debug trace along with version
> >> info for your Org-mode and Emacs.
> >
> > Thanks for this thread - very interesting. Just one correction (or
> > is it a bug?): Even the export to text - ASCII aborts the
> > bibtex2htlm installation.
> >
> > But also: I don't get it to work. I evaluated (require 'ox-bibtex)
> > which worked, but export to te4xt and html gives the following
> > error:
> >
> > org-babel-exp process emacs-lisp at line 78... if: Executing
> > bibtex2html failed
> >
> >
> > but bibtex2html is installed (homebrew)
> >
> > Export to LaTeX gives the attached .tex file, but the pdf contains
> > corrupt citations "[?]" and no bibliograhy.
> >
> > Is this my setup? Bibliographies work in LaTex here.
>
> OK - I have to run pdflatex - bibtex - pdflatex manually after .tex
> file creation. Then I get the references in. But is this intended?
>
> I thought that this would be done automatically?
>
> Rainer
>
> >
> > Cheers,
> >
> > Rainer
> >
> >
> >> Best,
> >
> >>>
> >>>
> >>> On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com
> >>> < o.castillo.felisola@gmail.com> wrote:
> >>>
> >>>> Thank you Eric, I'll try it asap! Cheers! On Jan 26, 2014
> >>>> 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
> >>>>
> >>>>> "o.castillo.felisola@gmail.com"
> >>>>> <o.castillo.felisola@gmail.com> writes:
> >>>>>
> >>>>>> Dear community,
> >>>>>>
> >>>>>> I'm using org-mode to draft most of my activities, and
> >>>>>> day after day I
> >>>>> get
> >>>>>> closer to managing my paper writing. Nonetheless, there
> >>>>>> is a point still drives me crazy.
> >>>>>>
> >>>>>> All over the web I find post about using such or what
> >>>>>> tool to get emacs org-mode to work with Bibtex... all of
> >>>>>> them seems complex to execute. I found the exported
> >>>>>> ox-bibtex.el [1] (included in my installation from
> >>>>> git),
> >>>>>> which 'It also introduces "cite" syntax for Org links.',
> >>>>>> but no
> >>>>> examples of
> >>>>>> the usage are included in this document.
> >>>>>>
> >>>>>> *Question*
> >>>>>>
> >>>>>> Can anyone provide a minimal example of the use to this
> >>>>>> tool, including
> >>>>> the
> >>>>>> configuration (if needed), and the necessary external
> >>>>>> (non-org) files?
> >>>>>>
> >>>>>
> >>>>> The attached two files (.org and .bib) provide an example
> >>>>> of usage.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>>
> >>>>>>
> >>>>>> Thank you!
> >>>>>>
> >>>>>> [1]
> >>>>>>
> >>>>>
> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
> >>>>>
> >>>>>
> >>>>>
> >
> >>>>>
> - --
> >>>>> Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
> >>>>>
> >>>>>
> >
> >
> >
>
> - --
> 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:      Rainer@krugs.de
>
> Skype:      RMkrug
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
> Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
>
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> =wIOA
> -----END PGP SIGNATURE-----
>



-- 
_____________________________________
Oscar Castillo-Felisola.
Grupo de Fisica Teorica.
UTFSM -- CCTVal.
Av. Espana, 1680, Valparaiso-Chile.
______________________________________

[-- Attachment #2: Type: text/html, Size: 9145 bytes --]

Re: How to use ox-bibtex

[Eric Schulte]

There is not enough information to address your bug.  Please read [1]
and re-send.  It sounds to me like your installation may be bad, in
which case it may also be worthwhile to read [2].

Best,

Footnotes: 
[1]  http://orgmode.org/org.html#Feedback

[2]  http://orgmode.org/worg/org-faq.html#keeping-current-with-Org-mode-development

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: How to use ox-bibtex

[o.castillo.felisola]

[-- Attachment #1: Type: text/plain, Size: 1524 bytes --]

I finally did it!!!!!!! (with your help of course).

Thank you.

A single doubt is left... the bibtex compilation is not performed during
the exportation process, should be done manually, Am I write?

**** For completeness ****

$ cd ~/.emacs.d/

Either create the repository

$ git clone git://orgmode.org/org-mode.git
$ cd org-mode

or update it

$ cd org-mode
$make up1

Then compile the sources

$ make all
$ sudo make install

After this... I followed the advice of Eric,  open an emacs session without
personal configuration

$ make vanilla

in the emacs session evaluate one line at the time, for that use =M-:=

(add-to-list 'load-path "contrib/lisp/")
(require 'ox-bibtex)

Finally, open the =ox-bibtex-example.org= and export it!!!

I did the work for me, however, the bibtex compilation should be done by
hand.

Cheers.


On Tue, Jan 28, 2014 at 11:16 PM, Eric Schulte <schulte.eric@gmail.com>wrote:

> There is not enough information to address your bug.  Please read [1]
> and re-send.  It sounds to me like your installation may be bad, in
> which case it may also be worthwhile to read [2].
>
> Best,
>
> Footnotes:
> [1]  http://orgmode.org/org.html#Feedback
>
> [2]
> http://orgmode.org/worg/org-faq.html#keeping-current-with-Org-mode-development
>
> --
> Eric Schulte
> https://cs.unm.edu/~eschulte
> PGP: 0x614CA05D
>



-- 
_____________________________________
Oscar Castillo-Felisola.
Grupo de Fisica Teorica.
UTFSM -- CCTVal.
Av. Espana, 1680, Valparaiso-Chile.
______________________________________

[-- Attachment #2: Type: text/html, Size: 2759 bytes --]

Re: How to use ox-bibtex

[Nick Dokos]

"o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:


> A single doubt is left... the bibtex compilation is not performed
> during the exportation process, should be done manually, Am I write?
>

You can customize org-latex-pdf-process to do what you want.
By default, it does three pdflatex runs in a row. If texi2dvi
works for you, it might be preferable. But you can always add
a bibtex run after the first pdflatex run.

Nick

Re: How to use ox-bibtex

[Ahmadou Dicko]

[-- Attachment #1: Type: text/plain, Size: 1346 bytes --]

You  can also use
latexmk<http://users.phys.psu.edu/~collins/software/latexmk-jcc/>which
was designed to solve this kind of problem.
I have this in my init.el

(setq org-latex-pdf-process
      '("latexmk -pdflatex=xelatex -pdf -latexoption=-shell-escape %f"))



On Wed, Jan 29, 2014 at 2:46 PM, Nick Dokos <ndokos@gmail.com> wrote:

> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:
>
>
> > A single doubt is left... the bibtex compilation is not performed
> > during the exportation process, should be done manually, Am I write?
> >
>
> You can customize org-latex-pdf-process to do what you want.
> By default, it does three pdflatex runs in a row. If texi2dvi
> works for you, it might be preferable. But you can always add
> a bibtex run after the first pdflatex run.
>
> Nick
>
>
>


-- 
Ahmadou H. DICKO
statistician economist (Ingénieur Statisticien Économiste)
PhD candidate in Climate change economics
Faculty of economics and managment - Cheikh Anta Diop University
West African Science Service Center on Climate Change and Adaptated Land
Use (WASCAL)
Center for Development Research (ZEF) - University of Bonn
email : ahmadou.dicko@ucad.edu.sn
twitter : @dickoah
github : github/dickoa <https://github.com/dickoa>
tel : +221 33 827 55 16
portable: +221 77 123 81 69

[-- Attachment #2: Type: text/html, Size: 2080 bytes --]

Re: How to use ox-bibtex

[o.castillo.felisola]

[-- Attachment #1: Type: text/plain, Size: 3575 bytes --]

Hello again,

I'm still having the problem... please correct me if I'm wrong:

1) In a terminal:
$ cd path/to/org-mode
$ make vanilla

an emacs window (without the personal configuration but with the org-mode
conf. opens)

2) I run the command you suggest using =M-: (add-to-list 'load-path
"contrib/lisp/")= and again =M-: (require 'ox-bibtex)=

3) Open the =ox-bibtex-example.org= and export it with =C-c C-e l o=


After all that I get "Wrong type argument: arrayp, nil"

Am I doing something wrong?

Best wishes



On Mon, Jan 27, 2014 at 11:36 AM, Eric Schulte <schulte.eric@gmail.com>wrote:

> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com> writes:
>
> > Hello Eric. I finally try the examples you attached above, and I'm
> getting
> > a problem. The file is not imported, because of an error "Wrong type
> > argument arrayp, nil".
> >
> > Does anyone know what I am missing?
> >
> > Cheers
> >
>
> My guess is that something is messed up in either your version of
> Org-mode or your personal config.  Please try the following to
> reproduce.
>
> 1. launch a version of Emacs with Org-mode loaded but without your
>    personal config, this may be conveniently done by running
>
>      make vanilla
>
>    from the base of your Org-mode installation.
>
> 2. evaluate the following
>
>    (add-to-list 'load-path "contrib/lisp/")
>    (require 'ox-bibtex)
>
> 3. open the example .org file attached previously (with the example .bib
>    file in the same directory), and export to latex.
>
> You should now see appropriate \cite{ref} and \bibliography elements in
> the exported latex.  This all works for me, if you get an error please
> send the whole debug trace along with version info for your Org-mode and
> Emacs.
>
> Best,
>
> >
> >
> > On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com <
> > o.castillo.felisola@gmail.com> wrote:
> >
> >> Thank you Eric, I'll try it asap! Cheers!
> >> On Jan 26, 2014 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com> wrote:
> >>
> >>> "o.castillo.felisola@gmail.com" <o.castillo.felisola@gmail.com>
> writes:
> >>>
> >>> > Dear community,
> >>> >
> >>> > I'm using org-mode to draft most of my activities, and day after day
> I
> >>> get
> >>> > closer to managing my paper writing. Nonetheless, there is a point
> still
> >>> > drives me crazy.
> >>> >
> >>> > All over the web I find post about using such or what tool to get
> emacs
> >>> > org-mode to work with Bibtex... all of them seems complex to
> execute. I
> >>> > found the exported ox-bibtex.el [1] (included in my installation from
> >>> git),
> >>> > which 'It also introduces "cite" syntax for Org links.', but no
> >>> examples of
> >>> > the usage are included in this document.
> >>> >
> >>> > *Question*
> >>> >
> >>> > Can anyone provide a minimal example of the use to this tool,
> including
> >>> the
> >>> > configuration (if needed), and the necessary external (non-org)
> files?
> >>> >
> >>>
> >>> The attached two files (.org and .bib) provide an example of usage.
> >>>
> >>>
> >>>
> >>> Best,
> >>>
> >>>
> >>> >
> >>> > Thank you!
> >>> >
> >>> > [1]
> >>> >
> >>>
> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
> >>>
> >>> --
> >>> Eric Schulte
> >>> https://cs.unm.edu/~eschulte
> >>> PGP: 0x614CA05D
> >>>
> >>>
>
> --
> Eric Schulte
> https://cs.unm.edu/~eschulte
> PGP: 0x614CA05D
>



-- 
_____________________________________
Oscar Castillo-Felisola.
Grupo de Fisica Teorica.
UTFSM -- CCTVal.
Av. Espana, 1680, Valparaiso-Chile.
______________________________________

[-- Attachment #2: Type: text/html, Size: 5857 bytes --]

Re: How to use ox-bibtex

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



On 01/27/14, 14:52 , o.castillo.felisola@gmail.com wrote:
> Hello Eric. I finally try the examples you attached above, and I'm 
> getting a problem. The file is not imported, because of an error
> "Wrong type argument arrayp, nil".

I get this error message, when clicking on the link in org:

Debugger entered--Lisp error: (void-function nil)
  nil(#("schulte2012multi" 0 16 (org-attr nil)))
  org-open-at-point()
  org-open-at-mouse((mouse-2 (#<window 3 on ox-bibtex-example.org> 346
(277 . 92) 108393393 nil 346 (46 . 8) nil (1 . 8) (6 . 12))))
  call-interactively(org-open-at-mouse nil nil)

Strange.

Rainer

> 
> Does anyone know what I am missing?
> 
> Cheers
> 
> 
> On Sun, Jan 26, 2014 at 4:37 PM, o.castillo.felisola@gmail.com 
> <mailto:o.castillo.felisola@gmail.com>
> <o.castillo.felisola@gmail.com 
> <mailto:o.castillo.felisola@gmail.com>> wrote:
> 
> Thank you Eric, I'll try it asap! Cheers!
> 
> On Jan 26, 2014 4:20 PM, "Eric Schulte" <schulte.eric@gmail.com 
> <mailto:schulte.eric@gmail.com>> wrote:
> 
> "o.castillo.felisola@gmail.com 
> <mailto:o.castillo.felisola@gmail.com>" 
> <o.castillo.felisola@gmail.com 
> <mailto:o.castillo.felisola@gmail.com>> writes:
> 
>> Dear community,
>> 
>> I'm using org-mode to draft most of my activities, and day
> after day I get
>> closer to managing my paper writing. Nonetheless, there is a
> point still
>> drives me crazy.
>> 
>> All over the web I find post about using such or what tool to
> get emacs
>> org-mode to work with Bibtex... all of them seems complex to
> execute. I
>> found the exported ox-bibtex.el [1] (included in my
> installation from git),
>> which 'It also introduces "cite" syntax for Org links.', but
> no examples of
>> the usage are included in this document.
>> 
>> *Question*
>> 
>> Can anyone provide a minimal example of the use to this tool,
> including the
>> configuration (if needed), and the necessary external
> (non-org) files?
>> 
> 
> The attached two files (.org and .bib) provide an example of
> usage.
> 
> 
> 
> Best,
> 
> 
>> 
>> Thank you!
>> 
>> [1]
>> 
> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>
>  -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
> 
> 
> 
> 
> -- _____________________________________ Oscar Castillo-Felisola. 
> Grupo de Fisica Teorica. UTFSM -- CCTVal. Av. Espana, 1680,
> Valparaiso-Chile. ______________________________________

- -- 
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:      Rainer@krugs.de

Skype:      RMkrug
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Clojure Code Block Results not Tabularized

[Soapy Smith]

Hello to the list, my first message here.

This is in regards to code blocks in the Clojure language.

The problem is that the results inserted into the org document should be
tabularized.  This is not happening using the latest version of org.
Here is the simplest possible example:

#+begin_src clojure :results value raw
[1 2 3 4]
#+end_src

#+RESULTS:
[1 2 3 4]

The result block is not tabularized.
In an older system, the result block is properly changed to an org
table:

#+RESULTS:
| 1 | 2 | 3 | 4 |

Here is a comparison of the systems, old and new, which produced the
above results:


Platform	Old	New
emacs		24.3.1	24.3.1
Leiningen	2.3.4	2.3.4
Java		1.7._51	1.6.0_27   
(both are OpenJDK 64 bit server VM)
org		7.9	8.2.4


Old REPL: nrepl 0.1.8-preview	
New REPL: cider 0.6.0alpha

The only thing strange I discovered about my new system is that it is
using an older version of Java than the old system.

Regards,
Greg

Re: Clojure Code Block Results not Tabularized

[Christian Moe]

Soapy Smith writes:
> The problem is that the results inserted into the org document should be
> tabularized.  This is not happening using the latest version of org.
> Here is the simplest possible example:
>
> #+begin_src clojure :results value raw
> [1 2 3 4]
> #+end_src
>
> #+RESULTS:
> [1 2 3 4]

Hi,

I don't use Clojure so I may get this wrong, but: isn't this what you
would expect with `:results raw'?

Cf. these Python examples:

#+begin_src python :results raw
  a = (1, 2, 3)
  return a
#+end_src

#+RESULTS:
(1, 2, 3)

#+begin_src python
  a = (1, 2, 3)
  return a
#+end_src

#+RESULTS:
| 1 | 2 | 3 |

Yours,
Christian

Re: Clojure Code Block Results not Tabularized

[Soapy Smith]

Hi Christian, I think that is a very good point!

From the manual, the explanation of what is returned as a result
using :results raw

"raw The results are interpreted as raw Org mode code and are inserted
directly into
the buffer. If the results look like a table they will be aligned as
such by Org mode.
E.g., :results value raw."

So, it doesn't say it will result in a table, but it will be aligned
like a table!

Whatever the case, the behavior of Clojure should be consistent with the
other languages.

Looking into the "old" set further, I find the :results header argument
makes no difference:
:results value
:results value raw
:results table
(no header argument)

All result in the same org table.  So it looks like the old version was
not behaving properly either.  However, it was able to coerce the
Clojure vector into an org table successfully.

With the new system (version 8 org and CIDER),
there are in fact 3 different results blocks:

(no header argument)
#+RESULTS:
: [1 2 3 4]

:results value raw
#+RESULTS:
[1 2 3 4]

:results value
#+RESULTS:
: [1 2 3 4]

:results table
#+RESULTS:
| [1 2 3 4] |

Christian, could you try :results table with Python and reply back with
the #+RESULTS:?

Regards,
Greg


On Wed, 2014-01-29 at 08:57 +0100, Christian Moe wrote:
> Hi,
> 
> I don't use Clojure so I may get this wrong, but: isn't this what you
> would expect with `:results raw'?
> 
> Cf. these Python examples:
> 
> #+begin_src python :results raw
>   a = (1, 2, 3)
>   return a
> #+end_src
> 
> #+RESULTS:
> (1, 2, 3)
> 
> #+begin_src python
>   a = (1, 2, 3)
>   return a
> #+end_src
> 
> #+RESULTS:
> | 1 | 2 | 3 |
> 
> Yours,
> Christian

Re: Clojure Code Block Results not Tabularized

[Christian Moe]

Soapy Smith writes:

> Christian, could you try :results table with Python and reply back with
> the #+RESULTS:?

Same as the default, i.e. a table, as expected.
#+RESULTS:
| 1 | 2 | 3 |

The Babel/Clojure behavior you report does seem buggy. 

I'm afraid I can't be of further help, but hopefully others will pick up
on this.

Yours,
Christian

Re: Clojure Code Block Results not Tabularized

[Soapy Smith]

Yes, I agree the Clojure behavior is not quite correct.  But all the
functionality is there if both the old and new are combined.  I think
only a rearrangement of existing code is required.

I like the idea of comparing to the behavior of Python code blocks.
I've got a Coursera class coming up which will use Python, so I need to
get it set it up here.

Thank you for the assistance!
Greg

On Wed, 2014-01-29 at 13:58 +0100, Christian Moe wrote:
> Soapy Smith writes:
> 
> > Christian, could you try :results table with Python and reply back with
> > the #+RESULTS:?
> 
> Same as the default, i.e. a table, as expected.
> #+RESULTS:
> | 1 | 2 | 3 |
> 
> The Babel/Clojure behavior you report does seem buggy. 
> 
> I'm afraid I can't be of further help, but hopefully others will pick up
> on this.
> 
> Yours,
> Christian

Re: Clojure Code Block Results not Tabularized

[Eric Schulte]

Soapy Smith <soapy-smith@comcast.net> writes:

> Yes, I agree the Clojure behavior is not quite correct.  But all the
> functionality is there if both the old and new are combined.  I think
> only a rearrangement of existing code is required.
>

Try evaluating the following and see how it works.  This simply copies
the results handling from the slime backend to the cider backend (which
currently does not appear to have any results handling).  While you're
at it the nrepl results handling looks broken to me as well.  Maybe
Bastien (who I believe wrote or committed this code) can help.

(defun org-babel-execute:clojure (body params)
  "Execute a block of Clojure code with Babel."
  (let ((expanded (org-babel-expand-body:clojure body params)))
    (case org-babel-clojure-backend
      (cider
       (require 'cider)
       (let ((result
	      (or (nth 1 (nrepl-send-string-sync
			  expanded
			  (cider-current-ns)
			  (nrepl-current-tooling-session)))
		  (error "nREPL not connected!  Use M-x cider-jack-in RET"))))
	 (org-babel-result-cond (cdr (assoc :result-params params))
	   result
	   (condition-case nil (org-babel-script-escape result)
	     (error result)))))
      (nrepl
       (require 'nrepl)
       (if (nrepl-current-connection-buffer)
    	   (let* ((result (nrepl-eval expanded))
    		  (s (plist-get result :stdout))
    		  (r (plist-get result :value)))
    	     (if s (concat s "\n" r) r))
    	 (error "nREPL not connected!  Use M-x nrepl-jack-in RET")))
      (slime
       (require 'slime)
       (with-temp-buffer
    	 (insert expanded)
    	 ((lambda (result)
    	    (let ((result-params (cdr (assoc :result-params params))))
    	      (org-babel-result-cond result-params
    		result
    		(condition-case nil (org-babel-script-escape result)
    		  (error result)))))
	  (slime-eval
	   `(swank:eval-and-grab-output
	     ,(buffer-substring-no-properties (point-min) (point-max)))
	   (cdr (assoc :package params)))))))))

I don't have clojure installed locally and can't test.

Best,

>
> I like the idea of comparing to the behavior of Python code blocks.
> I've got a Coursera class coming up which will use Python, so I need to
> get it set it up here.
>
> Thank you for the assistance!
> Greg
>
> On Wed, 2014-01-29 at 13:58 +0100, Christian Moe wrote:
>> Soapy Smith writes:
>> 
>> > Christian, could you try :results table with Python and reply back with
>> > the #+RESULTS:?
>> 
>> Same as the default, i.e. a table, as expected.
>> #+RESULTS:
>> | 1 | 2 | 3 |
>> 
>> The Babel/Clojure behavior you report does seem buggy. 
>> 
>> I'm afraid I can't be of further help, but hopefully others will pick up
>> on this.
>> 
>> Yours,
>> Christian
>
>
>

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: Clojure Code Block Results not Tabularized

[Bastien]

Eric Schulte <schulte.eric@gmail.com> writes:

> Try evaluating the following and see how it works.

It works fine for me:

,----
| #+BEGIN_SRC clojure :results table
| (map #(* %1 3) '(1 2 3))
| #+END_SRC
| 
| #+RESULTS:
| | 3 | 6 | 9 |
`----

> This simply copies
> the results handling from the slime backend to the cider backend (which
> currently does not appear to have any results handling).  While you're
> at it the nrepl results handling looks broken to me as well.

Yep.

Greg, please test Eric's function above for all your use cases and let
us know if it covers them all -- then I'll fix this and the nrepl case
too.

Thanks Eric!

-- 
 Bastien

Re: Clojure Code Block Results not Tabularized

[Phill Wolf]

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It is better.  To really stress it, I tried a two-row table:

#+begin_src clojure :results table
  [[:ny :nj :ct]
   [  7   9   4]]
#+end_src

#+RESULTS:
| :ny | :nj | :ct |
|   7 |   9 |   4 |


On Wed, Jan 29, 2014 at 10:28 AM, Bastien <bzg@gnu.org> wrote:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
> > Try evaluating the following and see how it works.
>
> It works fine for me:
>
> ,----
> | #+BEGIN_SRC clojure :results table
> | (map #(* %1 3) '(1 2 3))
> | #+END_SRC
> |
> | #+RESULTS:
> | | 3 | 6 | 9 |
> `----
>
> > This simply copies
> > the results handling from the slime backend to the cider backend (which
> > currently does not appear to have any results handling).  While you're
> > at it the nrepl results handling looks broken to me as well.
>
> Yep.
>
> Greg, please test Eric's function above for all your use cases and let
> us know if it covers them all -- then I'll fix this and the nrepl case
> too.
>
> Thanks Eric!
>
> --
>  Bastien
>
>

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Re: Clojure Code Block Results not Tabularized

[Bastien]

Hi Greg,

Soapy Smith <soapy-smith@comcast.net> writes:

> The problem is that the results inserted into the org document should be
> tabularized.

This should now be fixed in master -- thanks for further testing,
and thanks to Eric for giving the solution.

-- 
 Bastien

Re: Clojure Code Block Results not Tabularized

[Soapy Smith]

Great news!
I will update my system to the master.

I will create an org file with permutations of the :results option and
export to LaTeX and HTML.  Perhaps even compare to Python behavior.

I will attempt to push the test files to github later today.  I need the
git practice!

Regards,
Greg


On Thu, 2014-01-30 at 12:11 +0100, Bastien wrote:
> Hi Greg,
> 
> Soapy Smith <soapy-smith@comcast.net> writes:
> 
> > The problem is that the results inserted into the org document should be
> > tabularized.
> 
> This should now be fixed in master -- thanks for further testing,
> and thanks to Eric for giving the solution.
> 

Re: Clojure Code Block Results not Tabularized

[Soapy Smith]

Here are the files from testing of Clojure code blocks with the latest
master:

https://github.com/Greg-R/org-babel-clojure-tests?source=cc

The PDF file is the result of a LaTeX export.
The code blocks were forced to appear as they do in the org file by
wrapping them in begin_example/end_example.  Is there a way to get the
complete code blocks exported in an entire org file using a global
option?

Python code blocks are used for comparison.  There were some
differences.

The coercion to tables (where appropriate) is working well.

Regards,
Greg


On Thu, 2014-01-30 at 12:11 +0100, Bastien wrote:
> Hi Greg,
> 
> Soapy Smith <soapy-smith@comcast.net> writes:
> 
> > The problem is that the results inserted into the org document should be
> > tabularized.
> 
> This should now be fixed in master -- thanks for further testing,
> and thanks to Eric for giving the solution.
> 

Re: Clojure Code Block Results not Tabularized

[Bastien]

Hi Greg,

Soapy Smith <soapy-smith@comcast.net> writes:

> Is there a way to get the
> complete code blocks exported in an entire org file using a global
> option?

I think you want :export both -- see tangle export options in the
manual. 

> Python code blocks are used for comparison.  There were some
> differences.

Please report further bugs -- thanks!

-- 
 Bastien