Re: [O] Code vanishes on export

2011-08-24 Thread cberry
suvayu ali fatkasuvayu+li...@gmail.com writes: Hi Eric, On Wed, Aug 24, 2011 at 3:58 PM, Eric Schulte schulte.e...@gmail.com wrote: Vikas Rawal vikasli...@agrarianresearch.org writes: I obviously do not want the code to be removed from my org file. There are ways of controlling whether

Re: [O] Not overwriting unchanged source code files when tangling

2011-11-19 Thread cberry
  emacs -batch --eval #39;(org-babel-tangle-file http://somefile.org;)#39;   cc file.o - Carsten -- Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La

[O] [babel] PROPERTY doesn't do what BABEL did

2011-12-14 Thread cberry
I would like to get the same behavior as when I export a file with (say) these three lines: #+begin_src emacs-lisp :var foo=1 :var bar=2 :results value :exports both (+ foo bar) #+end_src But I'd like to set a buffer wide PROPERTY to achieve that as with a file with these lines: #+property:

Re: [O] [babel] PROPERTY doesn't do what BABEL did

2011-12-14 Thread cberry
Eric Schulte eric.schu...@gmx.com writes: cbe...@tajo.ucsd.edu writes: I would like to get the same behavior as when I export a file with (say) these three lines: #+begin_src emacs-lisp :var foo=1 :var bar=2 :results value :exports both (+ foo bar) #+end_src But I'd like to set a

Re: [O] About the use of PROPERTY meta lines...

2012-01-06 Thread cberry
Torsten Wagner torsten.wag...@gmail.com writes: Hmm... but this point is really interesting at least worse to write down in the manual. From my understanding a #+PROPERTY: var bar=2 sets bar globally to 2 somewhere and many lines and headers later #+PROPERTY: var bar=5 would change this

Re: [O] how do scientists use org mode?

2012-01-30 Thread cberry
: mini.tex | :EXPORT_TITLE: Minimal Report | :EXPORT_AUTHOR: Mister CCB | :END: | | #+begin_src latex :noweb yes | chunk1 | chunk2 | #+end_src ` HTH, Chuck Thanks very much. --Chris [snip] -- Charles C. BerryDept of Family/Preventive Medicine cberry

Re: [O] New Exporter html - latex - beamer

2013-03-19 Thread cberry
Robert Eckl eck...@gmx.de writes: Eric S Fraga e.fr...@ucl.ac.uk writes: Robert Eckl eck...@gmx.de writes: I have to provide weekly newsletters in the format pdf and html. Up to now i did this with exporting to scrartcl, known as koma-script. Including images is a bit booring because i

Re: [O] conditional export based on babel result

2012-09-06 Thread cberry
for the pointers to possible entry-points for an implementation. I hope, I'll find time to to go for it. Would be good for my elisp, anyway... Regards, Andreas -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC

[O] new exporter now drops labels

2012-09-12 Thread cberry
-label} | \begin{verbatim} | (org-version) | \end{verbatim} | | Org-mode version 7.8.11 ` Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla

Re: [O] new exporter now drops labels

2012-09-13 Thread cberry
block. Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] new exporter now drops labels

2012-09-13 Thread cberry
Nicolas Goaziou n.goaz...@gmail.com writes: cbe...@tajo.ucsd.edu writes: Pulled 343b648..0b13ec8 a few minutes ago. Still no version-label label for the src block. Indeed, it was a completely different problem. It should be fixed, this time. Thanks. Looks good, now. Thank you! Chuck

[O] [BABEL][BUG] lists and inline src

2012-09-18 Thread cberry
My apologies if this is already reported (I recall seeing something like this, but cannot find it in the archives). A list element starting with an inline src block is improperly parsed. for example - src_emacs-lisp{(org-version)} is not executed by babel. An ECM: , | * virgin version |

Re: [O] [BABEL][BUG] lists and inline src

2012-09-19 Thread cberry
Bastien b...@altern.org writes: Hi Chuck, cbe...@tajo.ucsd.edu writes: My apologies if this is already reported (I recall seeing something like this, but cannot find it in the archives). A list element starting with an inline src block is improperly parsed. I cannot reproduce this

Re: [O] org-e-groff-export-to-groff produces empty output file

2012-09-21 Thread cberry
Eric Schulte eric.schu...@gmx.com writes: Hi, Maybe I'm missing something obvious here, but I can't get org-e-groff to generate anything but an empty output file. I've boiled this down to the following minimal example. First save the attached example.org file to /tmp/example.org. Then

Re: [O] [wish] also provide documentation for contrib

2012-10-07 Thread cberry
Thomas Koch tho...@koch.ro writes: Hi, I was about to fill a bug about debians org-mode package because it does not come with documentation for the org-mode contrib org-drill. However I believe that this issue should rather be raised to you as the upstream. ,[from contrib/README] |

Re: [O] Problem orgmode, beamer and macport

2012-10-08 Thread cberry
Nick Dokos nicholas.do...@hp.com writes: Nick Dokos nicholas.do...@hp.com wrote: Steve Prud'Homme sprud...@gmail.com wrote: ! LaTeX Error: File `wrapfig.sty' not found. Type X to quit or RETURN to proceed, or enter new name. (Default extension: sty) Enter file name: !

Re: [O] [new exporter] latex: why does {{}} become \{\{\}\} ?

2012-10-21 Thread cberry
Charles Berry ccbe...@ucsd.edu writes: NEVER MIND. I just restarted my emacs and the export went as it should without the offending \begin{latex} \end{latex} lines. Likely someting weird in my setup caused this. Sorry for the noise. Chuck Sebastien Vauban wxhgmqzgwmuf@... writes: Hi

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread cberry
John Hendy jw.he...@gmail.com writes: I edited the subject to be more concise/clear.I let orgmode chug away on reading in some ~10-30mb csv files for nearly 30min. [rest deleted] You need an ECM. I cannot reproduce your issue. This runs in the same amount of time, whether I execute the

Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly

2012-10-31 Thread cberry
| : /Users/cberry/Downloads/test-file.csv | | #+name: readbig | #+begin_src R :results output | system.time( | tmp - read.csv(bigcsv) | ) | | #+end_src | | #+RESULTS: readbig | :user system elapsed | : 5.679 0.306 6.002 | ` About the same as running from ESS. FYI, dim

Re: [O] Generating captions--is there a better way?

2012-11-01 Thread cberry
Michael Gauland mikely...@no8wireless.co.nz writes: I use R to plot data, and like to include information about the plot in the caption. I do this by combining two named SRC blocks--one for the image, and one for the caption--and then put their #+RESULTS: together. The caption is the tricky

[O] new exporter - noweb substitution issues

2012-11-20 Thread cberry
When I tried to export a large subtree, it took over *5 minutes* to export with release_7.9.2-597-gd4b739. Using the contrib/lisp/*.el files from org-mode-7.8.11 it took *5 seconds*. The subtree has a couple dozen '...'s in src blocks with ':noweb yes' and the file itself is 9600 lines long. If

Re: [O] new exporter - noweb substitution issues

2012-11-20 Thread cberry
| 0.0063721821 | | 7.9.2-nil | org-babel-params-from-properties | 280 | 1.750548 | 0.0062519571 | The last line used (setq *org-babel-use-quick-and-dirty-noweb-expansion* nil). The only difference between '7.9.2' and '7.8.11' is I do this: #+BEGIN_SRC emacs-lisp (load /Users/cberry/elisp

[O] [BUG] org-export-with-current-buffer-copy drops local variable WAS:Re: new exporter - noweb substitution issues

2012-11-21 Thread cberry
cbe...@tajo.ucsd.edu writes: cbe...@tajo.ucsd.edu writes: When I tried to export a large subtree, it took over *5 minutes* to export with release_7.9.2-597-gd4b739. Using the contrib/lisp/*.el files from org-mode-7.8.11 it took *5 seconds*. [...] Both cases use: # Local variables:

Re: [O] [BUG] org-export-with-current-buffer-copy drops local variable WAS:Re: new exporter - noweb substitution issues

2012-11-28 Thread cberry
Nicolas Goaziou n.goaz...@gmail.com writes: Hello, cbe...@tajo.ucsd.edu writes: Thank you for all the debugging. org-export-with-current-buffer-copy calls org-clone-local-variables which uses a regexp to detect buffer-local variables, but *org-babel-use-quick-and-dirty-noweb-expansion*

Re: [O] new exporter, conditional options according to backend

2013-01-25 Thread cberry
Nicolas Goaziou n.goaz...@gmail.com writes: Hello, Ezequiel Birman stormwa...@espiga4.com.ar writes: Is it possible to write something like this with the new exporter? #+OPTIONS: (if (and (boundp 'org-export-current-backend) (eq org-export-current-backend 'e-beamer)) H:1 H:3) There is

[O] org-md fixed-width filter problems

2013-01-28 Thread cberry
The :translate-alist for the md backend has no entry for fixed-width, so it defaults to the parent org-e-html-fixed-width which uses (format pre class=\example\\n%s/pre ... So elements , | : like | : this ` get the html style markup. Some of the markdown processors I use don't

Re: [O] org-md fixed-width filter problems

2013-01-28 Thread cberry
cbe...@tajo.ucsd.edu writes: The :translate-alist for the md backend has no entry for fixed-width, so it defaults to the parent org-e-html-fixed-width which uses (format pre class=\example\\n%s/pre ... So elements , | : like | : this ` get the html style markup. Some of

[O] org-html-link problem

2013-02-06 Thread cberry
M-x org-export-dispatch RET h H terminates with an error , | | * https link | | | Here is the | [[https://github.com/downloads/yihui/knitr/knitr-minimal.html][link]] | ` The problem seems to be here: lisp/ox-html.el around line 2172: (unless (and desc (string-match (regexp-quote

[O] Selectively export RESULTS

2012-02-28 Thread cberry
Dept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
on when cache yes is set and see if I can do so more directly. Chuck Best, Footnotes: [1] http://orgmode.org/manual/cache.html -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http

Re: [O] Selectively export RESULTS

2012-03-02 Thread cberry
Eric Schulte eric.schu...@gmx.com writes: Matthew Landis lan...@isciences.com writes: cberry at tajo.ucsd.edu writes: Eric Schulte eric.schulte at gmx.com writes: Does this do what you want? Have you looked at the :cache header argument [1], from my understanding of your use

Re: [O] Selectively export RESULTS

2012-03-02 Thread cberry
cbe...@tajo.ucsd.edu writes: inline correction below. Eric Schulte eric.schu...@gmx.com writes: Matthew Landis lan...@isciences.com writes: cberry at tajo.ucsd.edu writes: Eric Schulte eric.schulte at gmx.com writes: Does this do what you want? Have you looked at the :cache

Re: [O] Selectively export RESULTS

2012-03-02 Thread cberry
Nick Dokos nicholas.do...@hp.com writes: cbe...@tajo.ucsd.edu wrote: cbe...@tajo.ucsd.edu writes: inline correction below. Eric Schulte eric.schu...@gmx.com writes: Matthew Landis lan...@isciences.com writes: cberry at tajo.ucsd.edu writes: Eric Schulte eric.schulte

Re: [O] Archiving only with confirmation

2012-03-03 Thread cberry
have an idea how to achieve what I want? Thanks in advance, Markus -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] R sessionInfo() and orgmode footnotes

2012-03-23 Thread cberry
-- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Auto-fill-mode with code sections

2012-05-04 Thread cberry
via reply e-mail and destroy all copies of the original message. Thank you. -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] new exporter drops :parameters ?

2012-07-04 Thread cberry
---cut here---end---8--- and see what is really parsed: the removal happens on the Babel side. [snip] -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu

Re: [O] new exporter drops :parameters ?

2012-07-06 Thread cberry
, -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Output of R babel blocks with quotes is mangled/truncated

2012-07-08 Thread cberry
The expected result would be entire string, i.e. 'cat=S' (without single quotes). Is there a workaround? I've tried escaping with backslashes to no avail. Cheers, Viktor -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu

Re: [O] Converting Org to Sweave (*.Rnw)

2012-07-17 Thread cberry
colleagues and I would be very interested in contributing in projects in this direction. Best Julian [1] http://en.wikipedia.org/wiki/Sweave -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http

[O] [BUG] new exporter and #+BEGIN_CENTER

2012-07-17 Thread cberry
in running the src block and producing the expected result. My last pull was yesterday: b7be665..69af091 HTH, Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry

Re: [O] Converting Org to Sweave (*.Rnw)

2012-07-17 Thread cberry
Julian Gehring julian.gehr...@gmail.com writes: Hi Chuck, thanks, what you describe seems to me like a already quite elaborated solution. I would be very interested in your existing implementation for this. As you mentioned, there will probably have to be a trade-off between the

Re: [O] [BUG] new exporter and #+BEGIN_CENTER

2012-07-17 Thread cberry
the expected result. My last pull was yesterday: b7be665..69af091 HTH, Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901