* How to use ox-bibtex @ 2014-01-24 13:41 o.castillo.felisola 2014-01-26 18:02 ` Eric Schulte 2014-01-28 13:23 ` Clojure Code Block Results not Tabularized Soapy Smith 0 siblings, 2 replies; 28+ messages in thread From: o.castillo.felisola @ 2014-01-24 13:41 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 968 bytes --] 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. ______________________________________ [-- Attachment #2: Type: text/html, Size: 1393 bytes --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-24 13:41 How to use ox-bibtex o.castillo.felisola @ 2014-01-26 18:02 ` Eric Schulte 2014-01-26 19:37 ` o.castillo.felisola 2014-01-28 13:23 ` Clojure Code Block Results not Tabularized Soapy Smith 1 sibling, 1 reply; 28+ messages in thread From: Eric Schulte @ 2014-01-26 18:02 UTC (permalink / raw) To: o.castillo.felisola@gmail.com; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 853 bytes --] "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. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: ox-bibtex-example.org --] [-- Type: text/x-org, Size: 2403 bytes --] #+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 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #3: ox-bibtex-example.bib --] [-- Type: text/x-bibtex, Size: 543 bytes --] @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} } [-- Attachment #4: Type: text/plain, Size: 182 bytes --] 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-26 18:02 ` Eric Schulte @ 2014-01-26 19:37 ` o.castillo.felisola 2014-01-27 13:52 ` o.castillo.felisola 0 siblings, 1 reply; 28+ messages in thread From: o.castillo.felisola @ 2014-01-26 19:37 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1229 bytes --] 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 > > [-- Attachment #2: Type: text/html, Size: 1957 bytes --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-26 19:37 ` o.castillo.felisola @ 2014-01-27 13:52 ` o.castillo.felisola 2014-01-27 14:36 ` Eric Schulte 2014-01-28 12:01 ` Rainer M Krug 0 siblings, 2 replies; 28+ messages in thread From: o.castillo.felisola @ 2014-01-27 13:52 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1784 bytes --] 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. ______________________________________ [-- Attachment #2: Type: text/html, Size: 3129 bytes --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-27 13:52 ` o.castillo.felisola @ 2014-01-27 14:36 ` Eric Schulte 2014-01-28 8:32 ` Rainer M Krug 2014-01-28 12:33 ` o.castillo.felisola 2014-01-28 12:01 ` Rainer M Krug 1 sibling, 2 replies; 28+ messages in thread From: Eric Schulte @ 2014-01-27 14:36 UTC (permalink / raw) To: o.castillo.felisola@gmail.com; +Cc: emacs-orgmode "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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-27 14:36 ` Eric Schulte @ 2014-01-28 8:32 ` Rainer M Krug 2014-01-28 9:04 ` Christian Moe 2014-01-28 12:38 ` Rainer M Krug 2014-01-28 12:33 ` o.castillo.felisola 1 sibling, 2 replies; 28+ messages in thread From: Rainer M Krug @ 2014-01-28 8:32 UTC (permalink / raw) To: Eric Schulte, o.castillo.felisola@gmail.com; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 4309 bytes --] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJS52svAAoJENvXNx4PUvmCQeIH/2H0k9onPCLugYkcY5v2kF7b lD1KEDPK6oMwvvjbP7BpX/nf5SjnNi8F5vV/VMTfcxgTrq8Nzn+Vacyh7JmkGQVO bKBl6LyyZjHVobUzLxWzGeaIKX8WHmsssMnIu3GAvyuQw9sniYdwz2T45SpEXNjn t6+2mf/3tczO3OiBG0DR32lUnCFdkxDR6y24MQ4eVxaPpn3j4wSev/B+n+td6Hij EafRF9ElP4wt5xOkeCFfliqG6sxNkZ7m4q7lwsoMn3sEXiGbZ55KZDtbvuAtzngt SKvqXHly2OMEcexzlsIzpzHXx9Ah90tq2Ydxipo6Fi39h4OOVFhcUOonRc6mahs= =TE2t -----END PGP SIGNATURE----- [-- Attachment #2: ox-bibtex-example.tex --] [-- Type: application/x-tex, Size: 3650 bytes --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-28 8:32 ` Rainer M Krug @ 2014-01-28 9:04 ` Christian Moe 2014-01-28 10:08 ` Rainer M Krug 2014-01-28 12:38 ` Rainer M Krug 1 sibling, 1 reply; 28+ messages in thread From: Christian Moe @ 2014-01-28 9:04 UTC (permalink / raw) To: Rainer; +Cc: emacs-orgmode, Eric Schulte, o.castillo.felisola@gmail.com 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-28 9:04 ` Christian Moe @ 2014-01-28 10:08 ` Rainer M Krug 0 siblings, 0 replies; 28+ messages in thread From: Rainer M Krug @ 2014-01-28 10:08 UTC (permalink / raw) To: Christian Moe; +Cc: emacs-orgmode, Eric Schulte, o.castillo.felisola@gmail.com -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJS54G3AAoJENvXNx4PUvmCQSAH/2khaNs7GnzF1nsSg08tM2Fy 3tu+hk78lsY47+Uo5JkwS4cFI99jJZb5pzIP6qNY23LXNkVX3oCO9FL5UG2V9BuR 2RkDt5Hl/xO8INvSAbUs7SBjhXJMBpxo0hLDo/piMqIr9VuXyGHV7Ztxwi4T/+2L aO9FNodMXmHIzOgdjs7hqtt3CZSf7P2/FF4FG4f2ccDVK2lC1W94Wy3YXRn3Oiro aroBWcpnacrwwlhKCy3XWTYxgQml795xf4aLqEDMVIrL9STp+mwgitO1BvvVuUEc Dq5b9uLkMoOTxInTsAL+XCms4FwGGTMRf06FXduWFcX6TyQ5Kc/jFQlFeeW+ezU= =sS0z -----END PGP SIGNATURE----- ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-28 8:32 ` Rainer M Krug 2014-01-28 9:04 ` Christian Moe @ 2014-01-28 12:38 ` Rainer M Krug 2014-01-28 15:19 ` o.castillo.felisola 1 sibling, 1 reply; 28+ messages in thread From: Rainer M Krug @ 2014-01-28 12:38 UTC (permalink / raw) To: Eric Schulte, o.castillo.felisola@gmail.com; +Cc: emacs-orgmode -----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/ iQEcBAEBAgAGBQJS56S+AAoJENvXNx4PUvmC6S4H/37H8xH4kFFaEF3etvlUyLSc nLQTJVuD1T9lCCPBDlurtzC6uubeamd8XvNY6lfgNhwJe8Oe24lw8xIOzD8yeITy apryBkCnPmQHzqIrsDXmN3i/+LaNurkhjBqEaD4tUggJ2xOz4LGnCjmNZcNPpc1g BrR+H6WLMTir23GIk035Y5/NVmnfjlU6dVBV8of6q8anmM7xboyqM44TXqzd4xSn ++zXuRFA9SrMjy6Pbxslonk6wdPfK2pf3b6BsudkqnLhqDfdvDJTcxr1LoL+X0MO VBNjp20Oy5Qxkywcw/6zOKfsxvoiYow4Ja1LsOGEFDxUj1kjISe7e1/Rv797zBU= =wIOA -----END PGP SIGNATURE----- ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-28 12:38 ` Rainer M Krug @ 2014-01-28 15:19 ` o.castillo.felisola 2014-01-29 2:16 ` Eric Schulte 0 siblings, 1 reply; 28+ messages in thread From: o.castillo.felisola @ 2014-01-28 15:19 UTC (permalink / raw) To: Rainer; +Cc: emacs-orgmode, Eric Schulte [-- 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/ > > iQEcBAEBAgAGBQJS56S+AAoJENvXNx4PUvmC6S4H/37H8xH4kFFaEF3etvlUyLSc > nLQTJVuD1T9lCCPBDlurtzC6uubeamd8XvNY6lfgNhwJe8Oe24lw8xIOzD8yeITy > apryBkCnPmQHzqIrsDXmN3i/+LaNurkhjBqEaD4tUggJ2xOz4LGnCjmNZcNPpc1g > BrR+H6WLMTir23GIk035Y5/NVmnfjlU6dVBV8of6q8anmM7xboyqM44TXqzd4xSn > ++zXuRFA9SrMjy6Pbxslonk6wdPfK2pf3b6BsudkqnLhqDfdvDJTcxr1LoL+X0MO > VBNjp20Oy5Qxkywcw/6zOKfsxvoiYow4Ja1LsOGEFDxUj1kjISe7e1/Rv797zBU= > =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 --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-28 15:19 ` o.castillo.felisola @ 2014-01-29 2:16 ` Eric Schulte 2014-01-29 14:16 ` o.castillo.felisola 0 siblings, 1 reply; 28+ messages in thread From: Eric Schulte @ 2014-01-29 2:16 UTC (permalink / raw) To: o.castillo.felisola@gmail.com; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-29 2:16 ` Eric Schulte @ 2014-01-29 14:16 ` o.castillo.felisola 2014-01-29 14:46 ` Nick Dokos 0 siblings, 1 reply; 28+ messages in thread From: o.castillo.felisola @ 2014-01-29 14:16 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode [-- 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 --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-29 14:16 ` o.castillo.felisola @ 2014-01-29 14:46 ` Nick Dokos 2014-01-30 10:02 ` Ahmadou Dicko 0 siblings, 1 reply; 28+ messages in thread From: Nick Dokos @ 2014-01-29 14:46 UTC (permalink / raw) To: emacs-orgmode "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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-29 14:46 ` Nick Dokos @ 2014-01-30 10:02 ` Ahmadou Dicko 0 siblings, 0 replies; 28+ messages in thread From: Ahmadou Dicko @ 2014-01-30 10:02 UTC (permalink / raw) To: Nick Dokos; +Cc: emacs-orgmode [-- 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 --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-27 14:36 ` Eric Schulte 2014-01-28 8:32 ` Rainer M Krug @ 2014-01-28 12:33 ` o.castillo.felisola 1 sibling, 0 replies; 28+ messages in thread From: o.castillo.felisola @ 2014-01-28 12:33 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode [-- 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 --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: How to use ox-bibtex 2014-01-27 13:52 ` o.castillo.felisola 2014-01-27 14:36 ` Eric Schulte @ 2014-01-28 12:01 ` Rainer M Krug 1 sibling, 0 replies; 28+ messages in thread From: Rainer M Krug @ 2014-01-28 12:01 UTC (permalink / raw) To: o.castillo.felisola@gmail.com, Eric Schulte; +Cc: emacs-orgmode -----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 -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJS55wXAAoJENvXNx4PUvmCu84IALzV8aEfGMltp5tz8pszekIj KEs2oDXMglCEAuIX0VZ1p2G3YMxRhwJD0BBKxkY94xc5OK+N5Vl+NpAcd8R8sLcm f80nE5od81OoGW5L4PoOPsyUDL32q2GFnm7iaWG17Am5KCQ6kcF9E6T1iBNuJrfn YGIyWzGbkgtXwiDYZP2YA39GsZFaDMeaifGDgo2D7Axe+yVH9HAk5FSfPu5cFjDP TImwMIIctyyPSUVTxLEAQtbJDOlMOhfcqrJDNswXLATQvNgrlFZzgLcTExo4p6OD Q6fp8Vtd/UiLjr/Thde5kx17ri8lis3lgGulrl+jFDxuMAKIsZuWUKqKWh0APOs= =uknP -----END PGP SIGNATURE----- ^ permalink raw reply [flat|nested] 28+ messages in thread
* Clojure Code Block Results not Tabularized 2014-01-24 13:41 How to use ox-bibtex o.castillo.felisola 2014-01-26 18:02 ` Eric Schulte @ 2014-01-28 13:23 ` Soapy Smith 2014-01-29 7:57 ` Christian Moe 2014-01-30 11:11 ` Bastien 1 sibling, 2 replies; 28+ messages in thread From: Soapy Smith @ 2014-01-28 13:23 UTC (permalink / raw) To: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-28 13:23 ` Clojure Code Block Results not Tabularized Soapy Smith @ 2014-01-29 7:57 ` Christian Moe 2014-01-29 12:36 ` Soapy Smith 2014-01-30 11:11 ` Bastien 1 sibling, 1 reply; 28+ messages in thread From: Christian Moe @ 2014-01-29 7:57 UTC (permalink / raw) To: Soapy Smith; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 7:57 ` Christian Moe @ 2014-01-29 12:36 ` Soapy Smith 2014-01-29 12:58 ` Christian Moe 0 siblings, 1 reply; 28+ messages in thread From: Soapy Smith @ 2014-01-29 12:36 UTC (permalink / raw) To: Christian Moe; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 12:36 ` Soapy Smith @ 2014-01-29 12:58 ` Christian Moe 2014-01-29 13:06 ` Soapy Smith 0 siblings, 1 reply; 28+ messages in thread From: Christian Moe @ 2014-01-29 12:58 UTC (permalink / raw) To: Soapy Smith; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 12:58 ` Christian Moe @ 2014-01-29 13:06 ` Soapy Smith 2014-01-29 15:02 ` Eric Schulte 0 siblings, 1 reply; 28+ messages in thread From: Soapy Smith @ 2014-01-29 13:06 UTC (permalink / raw) To: Christian Moe; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 13:06 ` Soapy Smith @ 2014-01-29 15:02 ` Eric Schulte 2014-01-29 15:28 ` Bastien 0 siblings, 1 reply; 28+ messages in thread From: Eric Schulte @ 2014-01-29 15:02 UTC (permalink / raw) To: Soapy Smith; +Cc: emacs-orgmode, Christian Moe 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 15:02 ` Eric Schulte @ 2014-01-29 15:28 ` Bastien 2014-01-29 23:40 ` Phill Wolf 0 siblings, 1 reply; 28+ messages in thread From: Bastien @ 2014-01-29 15:28 UTC (permalink / raw) To: Eric Schulte; +Cc: Soapy Smith, emacs-orgmode, Christian Moe 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-29 15:28 ` Bastien @ 2014-01-29 23:40 ` Phill Wolf 0 siblings, 0 replies; 28+ messages in thread From: Phill Wolf @ 2014-01-29 23:40 UTC (permalink / raw) To: Bastien; +Cc: Soapy Smith, emacs-orgmode, Christian Moe, Eric Schulte [-- Attachment #1: Type: text/plain, Size: 972 bytes --] 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 > > [-- Attachment #2: Type: text/html, Size: 1591 bytes --] ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-28 13:23 ` Clojure Code Block Results not Tabularized Soapy Smith 2014-01-29 7:57 ` Christian Moe @ 2014-01-30 11:11 ` Bastien 2014-01-30 13:46 ` Soapy Smith 2014-01-31 1:58 ` Soapy Smith 1 sibling, 2 replies; 28+ messages in thread From: Bastien @ 2014-01-30 11:11 UTC (permalink / raw) To: Soapy Smith; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-30 11:11 ` Bastien @ 2014-01-30 13:46 ` Soapy Smith 2014-01-31 1:58 ` Soapy Smith 1 sibling, 0 replies; 28+ messages in thread From: Soapy Smith @ 2014-01-30 13:46 UTC (permalink / raw) To: Bastien; +Cc: emacs-orgmode 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. > ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-30 11:11 ` Bastien 2014-01-30 13:46 ` Soapy Smith @ 2014-01-31 1:58 ` Soapy Smith 2014-01-31 9:11 ` Bastien 1 sibling, 1 reply; 28+ messages in thread From: Soapy Smith @ 2014-01-31 1:58 UTC (permalink / raw) To: Bastien; +Cc: emacs-orgmode 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. > ^ permalink raw reply [flat|nested] 28+ messages in thread
* Re: Clojure Code Block Results not Tabularized 2014-01-31 1:58 ` Soapy Smith @ 2014-01-31 9:11 ` Bastien 0 siblings, 0 replies; 28+ messages in thread From: Bastien @ 2014-01-31 9:11 UTC (permalink / raw) To: Soapy Smith; +Cc: emacs-orgmode 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 ^ permalink raw reply [flat|nested] 28+ messages in thread
end of thread, other threads:[~2014-01-31 9:12 UTC | newest] Thread overview: 28+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2014-01-24 13:41 How to use ox-bibtex o.castillo.felisola 2014-01-26 18:02 ` Eric Schulte 2014-01-26 19:37 ` o.castillo.felisola 2014-01-27 13:52 ` o.castillo.felisola 2014-01-27 14:36 ` Eric Schulte 2014-01-28 8:32 ` Rainer M Krug 2014-01-28 9:04 ` Christian Moe 2014-01-28 10:08 ` Rainer M Krug 2014-01-28 12:38 ` Rainer M Krug 2014-01-28 15:19 ` o.castillo.felisola 2014-01-29 2:16 ` Eric Schulte 2014-01-29 14:16 ` o.castillo.felisola 2014-01-29 14:46 ` Nick Dokos 2014-01-30 10:02 ` Ahmadou Dicko 2014-01-28 12:33 ` o.castillo.felisola 2014-01-28 12:01 ` Rainer M Krug 2014-01-28 13:23 ` Clojure Code Block Results not Tabularized Soapy Smith 2014-01-29 7:57 ` Christian Moe 2014-01-29 12:36 ` Soapy Smith 2014-01-29 12:58 ` Christian Moe 2014-01-29 13:06 ` Soapy Smith 2014-01-29 15:02 ` Eric Schulte 2014-01-29 15:28 ` Bastien 2014-01-29 23:40 ` Phill Wolf 2014-01-30 11:11 ` Bastien 2014-01-30 13:46 ` Soapy Smith 2014-01-31 1:58 ` Soapy Smith 2014-01-31 9:11 ` Bastien
Code repositories for project(s) associated with this public inbox https://git.savannah.gnu.org/cgit/emacs/org-mode.git This is a public inbox, see mirroring instructions for how to clone and mirror all data and code used for this inbox; as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).