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

2013-03-19 Thread cberry
Robert Eckl writes: > Eric S Fraga writes: > >> Robert Eckl 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 handle two formats, for example

[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 (

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 "\n%s" ... > > So elements > > , > | : like > | : this > ` > > get the html style markup. > > Some of the mar

[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 "\n%s" ... So elements , | : like | : this ` get the html style markup. Some of the markdown processors I use don't like this. pandoc ignores

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

2013-01-25 Thread cberry
Nicolas Goaziou writes: > Hello, > > Ezequiel Birman 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 no `org-export-current-back

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 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* is not de

[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: >> >>

Re: [O] new exporter - noweb substitution issues

2012-11-20 Thread cberry
fference between '7.9.2' and '7.8.11' is I do this: #+BEGIN_SRC emacs-lisp (load "/Users/cberry/elisp/org-mode-7.8.11/contrib/lisp/org-element.el") (load "/Users/cberry/elisp/org-mode-7.8.11/contrib/lisp/org-export.el") (load "/Users/cberry/elisp/org

[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.

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

2012-11-01 Thread cberry
Michael Gauland 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 bit; I use R to print

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

2012-10-31 Thread cberry
<- Sys.glob("~/Downloads/*.csv") | #+end_src | | #+RESULTS: bigcsv | : /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 elaps

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

2012-10-31 Thread cberry
John Hendy 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 src block or run th

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

2012-10-21 Thread cberry
Charles Berry 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 writes: > >> >> Hi Nicolas, >> >> Nicolas Goa

Re: [O] Problem orgmode, beamer and macport

2012-10-08 Thread cberry
Nick Dokos writes: > Nick Dokos wrote: > >> Steve Prud'Homme wrote: >> >> > >> > ! LaTeX Error: File `wrapfig.sty' not found. >> > >> > Type X to quit or to proceed, >> > or enter new name. (Default extension: sty) >> > >> > Enter file name: >> > ! Emergency stop. >> > >> > >> >

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

2012-10-07 Thread cberry
Thomas Koch 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] | These cont

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

2012-09-21 Thread cberry
Eric Schulte 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 run the following

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

2012-09-19 Thread cberry
Bastien 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 wit

[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] new exporter now drops labels

2012-09-13 Thread cberry
Nicolas Goaziou 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

Re: [O] new exporter now drops labels

2012-09-13 Thread cberry
s lost: > > It should be fixed. Thanks for reporting this. > Pulled 343b648..0b13ec8 a few minutes ago. Still no "version-label" label for the src block. Chuck -- Charles C. Berry Dept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

[O] new exporter now drops labels

2012-09-12 Thread cberry
sec-1} | \label{version-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/cb

Re: [O] conditional export based on babel result

2012-09-06 Thread cberry
t; > Hi Eric, > > in my opinion, there are more complex things in org-mode already ;-) > > I agree, that such functionality doesn't need to be provided in org > itself. > Thanks a lot 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 San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

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

2012-07-17 Thread cberry
lement-export-snippet-successor(31) >> [rest deleted] >> >> Removing the whitespace between the BEGIN_CENTER and BEGIN_SRC lines >> runs, but wrongly fails to execute the src block. >> >> Removing the CENTER results in running the src block and producing

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

2012-07-17 Thread cberry
Julian Gehring 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 syntax/functionality of O

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

2012-07-17 Thread cberry
block. Removing the CENTER results 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

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

2012-07-17 Thread cberry
ave to integrate it in the > R package. > > If anyone has some comments regarding this or is interested in working > on this, please let me know. My colleagues and I would be very > interested in contributing in projects in this direction. > > > Best > Julian > &

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

2012-07-08 Thread cberry
'cat="S"' > q > #+END_SRC > > #+RESULTS: > : S > > 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. > >

Re: [O] new exporter drops :parameters ?

2012-07-06 Thread cberry
thing I can reliably reproduce. If I come up with anything, I'll get back to you. Chuck > > > Regards, -- 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
---start->8--- > #+name: bblock > #+BEGIN_SRC R :exports code :et-cetera > rnorm(2)+1 > #+END_SRC > --8<---cut here---end--->8--- > > and see what is really parsed: the removal happens on the Babel sid

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

2012-05-04 Thread cberry
>> >> CONFIDENTIALITY NOTICE: This e-mail message is for the sole use of the >> intended recipient(s) and may contain confidential and privileged >> information. Any unauthorized review, use, disclosure or distribution >> of any kind is strictly prohibited. If you are

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

2012-03-23 Thread cberry
atest version of org-mode and emacs. > Cheers, > > Alejandro > > -- 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] Archiving only with confirmation

2012-03-03 Thread cberry
want to archive and as far as I see it does not change the default > behavior. > > Does anybody 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] Selectively export RESULTS

2012-03-02 Thread cberry
t; > | * headline 1 >> > | :PROPERTIES: >> > | :cache: no >> > | :END: >> > | >> > | #+CALL: Ablock() :exports results >> > | >> > ` >> > >> > When I place point under the headline and issue

Re: [O] Selectively export RESULTS

2012-03-02 Thread cberry
Date: 2012-03-02 11:28:54 PST > | > | > | > | > | Fri Mar 2 11:28:52 2012 > | > ` > > showing that Ablock() actually was executed. > > If the :cache setting under 'headline 1' is omitted then no update of > the time string is performed. > > I understand that this behavior might be considered a *feature*, not a > *bug*. > > Either way, having an easy way to copy results into other parts of a > document would help me out. > > Best, > > Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

2012-03-02 Thread cberry
x27; is omitted then no update of the time string is performed. I understand that this behavior might be considered a *feature*, not a *bug*. Either way, having an easy way to copy results into other parts of a document would help me out. Best, Chuck -- Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
and needed for a quick report worries me. Its pretty clear that the machinery needed to capture results is all there. If I can find time, I'll trace thru what is going on when cache yes is set and see if I can do so more directly. Chuck > Best, > > Footnotes: > [1] http://org

Re: [O] Selectively export RESULTS

2012-02-29 Thread cberry
; > * Selectively Export Some Results >:PROPERTIES: >:EXPORT_FILE_NAME: Selected_Results.pdf > :EXPORT_TITLE: Selected Results >:END: > > Here are the results from block named "Ablock": > > #+CALL: Ablock() :exports results > > and here they are for a block named "Bblock": > > #+CALL: Bblock() :exports results > > All the best, > Tom -- 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

[O] Selectively export RESULTS

2012-02-28 Thread cberry
-results() function. TIA, Chuck -- Charles C. Berry 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] how do scientists use org mode?

2012-01-30 Thread cberry
\cos\theta | \end{displaymath} | #+end_src | | | * mini report | :PROPERTIES: | :EXPORT_FILE_NAME: mini.tex | :EXPORT_TITLE: Minimal Report | :EXPORT_AUTHOR: Mister CCB | :END: | | #+begin_src latex :noweb yes | <> | <> | #+end_src ` HTH, Chuck > > Thanks very m

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

2012-01-06 Thread cberry
Torsten Wagner 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 value to 5 for e

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

2011-12-14 Thread cberry
Eric Schulte 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 buffer

[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: v

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

2011-11-19 Thread cberry
#x27;(org-babel-tangle-file "http://somefile.org";)' >   cc file.o > > - Carsten -- Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

Re: [O] Code vanishes on export

2011-08-24 Thread cberry
suvayu ali writes: > Hi Eric, > > On Wed, Aug 24, 2011 at 3:58 PM, Eric Schulte wrote: >> Vikas Rawal writes: >> >>> I obviously do not want the code to be removed from my org file. >>> >> >> There are ways of controlling whether code or results or both or neither >> are included in code export