Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-07 Thread Thomas S. Dye
t, 4 Dec 2010, Thomas S. Dye wrote: Aloha Detlef On Dec 2, 2010, at 9:58 PM, Detlef Steuer wrote: Hi! [rest deleted] Charles C. BerryDept of Family/ Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty/cbe

Re: [Orgmode] source code block export no expansion

2010-12-07 Thread Thomas S. Dye
Aloha Andreas, Perhaps :noweb tangle will do what you want. hth, Tom On Dec 7, 2010, at 7:38 AM, Andreas Leha wrote: Hi all, I have a question about exporting source code blocks. Say, I have several modules (mod1, mod2), that build a bigger part (part1) of my program, e.g.: #+srcname: mo

Re: [Orgmode] source code block export no expansion

2010-12-07 Thread Thomas S. Dye
n't how it works for me. :noweb tangle inhibits noweb expansion during export only. So, is this not possible right now? It is possible now. If the :exports header argument doesn't fix your problem, come back to the list. All the best, Tom Cheers, Andreas Am 07.12.2010 19

Re: [Orgmode] source code block export no expansion

2010-12-07 Thread Thomas S. Dye
tlisting} print("mod1") print("mod2") \end{lstlisting} ... Am 07.12.2010 20:33, schrieb Thomas S. Dye: Aloha Andreas, On Dec 7, 2010, at 8:49 AM, Andreas Leha wrote: Hi Tom, thanks for this answer. This indeed comes closer to what I want. But, some comments: (1) Ther

Re: [Orgmode] Elsevier's "Executable Paper Grand Challenge"

2010-12-07 Thread Thomas S. Dye
Aloha Bill, On Dec 7, 2010, at 9:26 AM, Bill White wrote: In light of recent paper by Davison, Dominik, Dye and Schulte, this sounds like something org-mode could address: http://www.executablepapers.com There is a USD 1 first-place award. Executable Paper Grand Challenge is a contest cr

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-09 Thread Thomas S. Dye
Aloha Seb, Thanks for your detailed and thorough review. Your comments will help us revise the paper. Much appreciated. All the best, Tom On Dec 7, 2010, at 12:55 PM, Sébastien Vauban wrote: Hi Eric, Let's see if I'm a good proof-reader. Here are my comments, looking at things not al

Re: [Orgmode] source code block export no expansion

2010-12-09 Thread Thomas S. Dye
ssion is a valid work-around for me, since I do not need several sessions right now. Thanks for this hint. Cheers, Andreas Am 07.12.2010 21:14, schrieb Thomas S. Dye: Aloha Andreas, Thanks for your patience and persistence. I think this might qualify as a bug. Using your code, if I d

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-09 Thread Thomas S. Dye
Hi Chuck, I put Rpackage.org up on Worg. When you have the Worg setup worked out you might want to change uses.org, where your contribution is described. Thanks for the contribution. All the best, Tom On Dec 8, 2010, at 9:20 PM, Charles C. Berry wrote: On Tue, 7 Dec 2010, Thomas S

Re: [Orgmode] Are there better ways to export wide LaTeX tables/figures?

2010-12-09 Thread Thomas S. Dye
Aloha Kai, I've just pushed one solution to the problem of wide tables up to http://orgmode.org/worg/org-tutorials/org-latex-export.php . Here it is for your convenience: The LaTeX exporter is currently able to export tabular and longtable environments. In situations where the width of the ta

Re: [Orgmode] Captionshttp://adzes.tsdye2.com Source Code

2010-12-09 Thread Thomas S. Dye
Aloha Andreas, Here's one way to get captions with source code listings and a list of listings. Use org-special-blocks to export a listing environment, e.g. #+BEGIN_listing #+source: identification-part #+begin_src latex :exports code \NeedsTeXFormat{LaTeX2e} \ProvidesClass{org-article}[

Re: [Orgmode] latex export of source code in lists

2010-12-09 Thread Thomas S. Dye
Hi Andreas, In my experience, lists are a bit fragile this way (probably necessarily). One workaround might be to float the source code block (in the way I mentioned in a previous message) and then cross reference it from the list. * Test 1) this is the first item (Listing \ref{fig:fir

Re: [Orgmode] latex export of source code in lists

2010-12-09 Thread Thomas S. Dye
d yet, as I have a lot of code snippets in the one file, which would result in several pages of floating listings. But I'll use that option anyway or do completely without lists then. Thanks again, Andreas Am 09.12.2010 18:25, schrieb Thomas S. Dye: Hi Andreas, In my experience, lists

Re: [Orgmode] Captionshttp://adzes.tsdye2.com Source Code

2010-12-09 Thread Thomas S. Dye
ument) would also produce a caption in the latex output. But I could not find an option or header switch. So I guess it's just not there... Cheers, Andreas Am 09.12.2010 16:44, schrieb Thomas S. Dye: Aloha Andreas, Here's one way to get captions with source code listings and a list

Re: [Orgmode] Here is my article on date-trees and capture mode

2010-12-09 Thread Thomas S. Dye
Aloha Charles, The idea to have Org-mode add meaningful structure to notes files solves a big problem for people like me who lose track of the organization schemes they design. It was a revelation (and a huge relief) to see your date trees. Many thanks, Tom P.S. I found the article cle

[Orgmode] [RFC] Self-configuring Org-mode files

2010-12-09 Thread Thomas S. Dye
Aloha all, I'm eager to learn how to build a self-configuring Org-mode file. I think Org-mode is uniquely positioned to produce reproducible research documents, but frankly speaking, the author of a reproducible Org-mode research document would be foolish to release it. The probability t

[Orgmode] eval: Invalid read syntax: "#"Error during redisplay: (void-function -mode)

2010-12-10 Thread Thomas S. Dye
Aloha all, I get subject error when exporting this subtree to LaTeX: * Export problem #+begin_src emacs-lisp :results wrap :exports both "code block results" #+end_src #+begin_src emacs-lisp :var lst=a-list :results list (reverse lst) #+end_src The error goes away and LaTeX export succe

Re: [Orgmode] eval: Invalid read syntax: "#"Error during redisplay: (void-function -mode)

2010-12-10 Thread Thomas S. Dye
So, Seb and I have two things that others can't reproduce: the error in the OP, and the version string for the latest Org-mode. Tom On Dec 10, 2010, at 8:15 AM, Nick Dokos wrote: Thomas S. Dye wrote: Aloha all, I get subject error when exporting this subtree to LaTeX: * Export pr

Re: [Orgmode] eval: Invalid read syntax: "#"Error during redisplay: (void-function -mode)

2010-12-10 Thread Thomas S. Dye
Aloha Nick, On Dec 10, 2010, at 8:34 AM, Nick Dokos wrote: Thomas S. Dye wrote: So, Seb and I have two things that others can't reproduce: the error in the OP, and the version string for the latest Org-mode. Looks that way :-) BTW, can you get a backtrace for the OP? Nick Her

Re: [Orgmode] Turning off hyperref in latex export?

2010-12-10 Thread Thomas S. Dye
Aloha Jeff, You might customize org-export-latex-default-packages-alist to suit your needs. All the best, Tom On Dec 10, 2010, at 7:35 PM, Jeff Horn wrote: Hey orgsters, Is there a way to turn off using the hyperref package for latex export? Ideally, I'm looking for a local variable or so

Re: [Orgmode] Re: eval: Invalid read syntax: "#"Error during redisplay: (void-function -mode)

2010-12-11 Thread Thomas S. Dye
d and switched off org-src-fontify-natively and org-src-tabify-natively, but neither of these made the error go away. All the best, Tom On Dec 11, 2010, at 10:26 AM, Sébastien Vauban wrote: Hi Thomas, Nick and others, "Thomas S. Dye" wrote: On Dec 10, 2010, at 8:15 AM, Nick Dokos

Re: [Orgmode] Re: eval: Invalid read syntax: "#"Error during redisplay: (void-function -mode)

2010-12-11 Thread Thomas S. Dye
Sorry Seb, I typed carelessly. The variable is org-src-tab-acts- natively. Tom On Dec 11, 2010, at 2:03 PM, Sébastien Vauban wrote: Footnotes: [1] Did not know about `org-src-tabify-natively'... Though, it does not exist (as variable) on my current git system!? _

Re: [Orgmode] org-mode and ebib

2010-12-11 Thread Thomas S. Dye
On Dec 10, 2010, at 7:19 AM, Ali Tofigh wrote: Hi everyone, A while ago I asked on this list about connecting org-mode with ebib, which is a bibtex database manager for emacs. Thanks to Joost Kremers, there is now a solution. I asked the developer of ebib, Joost Kremers, if he could write a fu

[Orgmode] Fwd: [RFC] Self-configuring Org-mode files

2010-12-11 Thread Thomas S. Dye
From: Stephen Eglen Date: December 11, 2010 7:18:26 AM HST To: "Thomas S. Dye" Cc: s.j.eg...@damtp.cam.ac.uk Subject: Re: [RFC] Self-configuring Org-mode files Hi Tom, I think you have hit the nail on the head -- it took me ages to get org up and running with all the extra confi

[Orgmode] Link descriptions

2010-12-14 Thread Thomas S. Dye
Aloha all, After reading through the documentation fairly carefully, link descriptions are yielding unexpected results. Perhaps I missed something? I have a link defined for citep: #+source: define-citep-link #+begin_src emacs-lisp (org-add-link-type "citep" 'ebib (lambda (path de

Re: [Orgmode] Link descriptions

2010-12-15 Thread Thomas S . Dye
On Dec 15, 2010, at 9:34 AM, David Maus wrote: At Tue, 14 Dec 2010 08:09:21 -1000, Thomas S. Dye wrote: Aloha all, After reading through the documentation fairly carefully, link descriptions are yielding unexpected results. Perhaps I missed something? I have a link defined for citep

Re: [Orgmode] allow table* specification with #+ATTR_LaTeX:

2010-12-15 Thread Thomas S . Dye
Hi Eric, It would be great to have a more general solution. Tables are hard to typeset, so it might take a while to come up with a good specification. Here is what I know about the LaTeX side of things. ** LaTeX destinations for an Org-mode table *** Environments for typesetting a table

Re: [Orgmode] allow table* specification with #+ATTR_LaTeX:

2010-12-16 Thread Thomas S. Dye
so for example, the following #+begin_src org #+CAPTION: A wide table #+LABEL: tbl:wide #+ATTR_LaTeX: table* tabulary align=l|lp{3cm}r|l | ... | ... | | ... | ... | #+end_src results in the following #+begin_src latex \begin{table*}[htb] \caption{A wide table} \label{tbl:wide} \begin{cent

Re: [Orgmode] Re: [Bug] Using org-article produces nil.sty error

2010-12-17 Thread Thomas S. Dye
Thanks Jeff, I've removed the parentheses per your recommendation. All the best, Tom On Dec 16, 2010, at 8:15 PM, Jeff Horn wrote: Aloha Thomas, I think I found the bug. I ran =C-c C-c= on the following lines of code from your 'article-class.org' file: #+begin_src emacs-lisp :exports code (

Re: [Orgmode] allow table* specification with #+ATTR_LaTeX:

2010-12-17 Thread Thomas S. Dye
atex- tables-centered "\n\\end{center}\n" "\n")) (if longtblp "\\end{longtable}" - (if floatp "\\end{table}" +

Re: [Orgmode] allow table* specification with #+ATTR_LaTeX:

2010-12-18 Thread Thomas S. Dye
end{tabular} \end{center} #+end_src Thanks -- Eric "Thomas S. Dye" writes: Hi Eric, A syntax like this, with a width attribute, seems most like Org-mode to me: #+ATTR_LaTeX table* tabularx width=\textwidth align=llXrl If that isn't a reasonable possibility, then, yes, the square

Re: [Orgmode] Link descriptions

2010-12-19 Thread Thomas S. Dye
Aloha David, Very nice. Thanks. All the best, Tom On Dec 19, 2010, at 4:00 AM, David Maus wrote: At Wed, 15 Dec 2010 17:33:38 -1000, Thomas S. Dye wrote: Perhaps it has to do with footnotes? That's an org-mode environment with square brackets and, in some instances, a superscript n

[Orgmode] Worg

2010-12-23 Thread Thomas S. Dye
Aloha all, I think Worg hasn't been updating for the last few days. Happy holidays, Tom ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode

[Orgmode] org-add-link-type

2010-12-26 Thread Thomas S. Dye
Aloha all, Sorry in advance for coming to the list with a beginner type question, but I'm stumped. I'm trying to use the extended link syntax to export citations to LaTeX. If the link lacks a description, then I don't want the \citep command to have an optional argument. As I understand

Re: [Orgmode] org-add-link-type

2010-12-26 Thread Thomas S. Dye
, Thomas, Try it with "if" rather than "when". Yours, Christian On 12/27/10 1:29 AM, Thomas S. Dye wrote: Aloha all, Sorry in advance for coming to the list with a beginner type question, but I'm stumped. I'm trying to use the extended link syntax to export citati

[Orgmode] Re: Unintended behavior? Links without description

2010-12-31 Thread Thomas S. Dye
Aloha Christian, I explored the possibility of bisecting but found two things: 1) with my setup I can't run versions of Org-mode earlier than approximately 7.01h because of requirements for ob.el, and 2) the current behavior has been around at least since last summer--Org-mode version 7.01t

[Orgmode] Documentation patch

2011-01-01 Thread Thomas S. Dye
Aloha all,The attached patch documents multi-line headers for source code blocks: babel-multi-line-header.patch Description: Binary data Thomas S. Dye, Ph.D.T. S. Dye & Colleagues, Archaeologists, Inc.Phone: (808) 529-0866 Fax: (808) 529-0884http://www.tsdye

Re: [Orgmode] [Babel] [Ann] varied updates and improvements

2011-01-01 Thread Thomas S. Dye
#+end_src #+results[bec9c8724e397d5df3b696502df3ed7892fc4f5f]: caller 0.254227238707244 Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com ___ Emacs-orgmode mailing l

Re: [Orgmode] [Babel] [Ann] varied updates and improvements

2011-01-01 Thread Thomas S. Dye
Aloha all, I'm seeing some unexpected behavior with source blocks as I'm adding :cache yes as a multi-line header argument. The top #+results: is with the addition of the #+header: :cache yes line. Note the lack of a :results name and also the lack of the SHA1 hash. The bottom # +result

Re: [Orgmode] [Babel] [Ann] varied updates and improvements

2011-01-01 Thread Thomas S. Dye
Aloha all, Sorry for the noise. I'm not sure how I was using version 7.01trans with release_7.4.93, but now that I'm using version 7.4 with that release, the code below works as expected. Tom On Jan 1, 2011, at 10:41 AM, Thomas S. Dye wrote: Aloha all, Code block caching do

[Orgmode] :cache documentation patch

2011-01-01 Thread Thomas S. Dye
Aloha all, The attached patch documents the behavior of the :cache header argument. All the best, Tom babel-cache-doc.patch Description: Binary data ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@g

Re: [Orgmode] Re: [babel] R: New handling of file output

2011-01-01 Thread Thomas S. Dye
Aloha all, Should :results graphic be documented in the :results header argument section of the Org-mode manual, or in the R-specific documentation? All the best, Tom On Dec 21, 2010, at 6:57 AM, Dan Davison wrote: Dan Davison writes: Please note the following changes to the way that or

Re: [Orgmode] Re: [babel] R: New handling of file output

2011-01-01 Thread Thomas S. Dye
Aloha all, Here is an example of the new handling of file output with an R source code block that doesn't use "base" graphics: #+srcname: r-edge-angle-histogram #+begin_src R :results output graphics :var x=whole-adzes :file r/ adze_edge_angle.png :width 400 :height 300 library(ggplot2)

[Orgmode] unnamed :results

2011-01-01 Thread Thomas S. Dye
Aloha all, In the course of updating an Org-mode file to take account of the new file output handling for R, I noticed a change in the naming of results blocks. In the example below, the top #+results: line was produced with the most recent Org-mode from git. The previous behavior is on

[Orgmode] org.texi vs. orgmode.org/manual

2011-01-01 Thread Thomas S. Dye
Aloha all, I'm not sure how the Org-mode manual online is updated, but I noticed today that org.texi has an entry for a :sep header argument that doesn't show up in the online manual. All the best, Tom ___ Emacs-orgmode mailing list Please use `R

Re: [Orgmode] org.texi vs. orgmode.org/manual

2011-01-02 Thread Thomas S. Dye
Aloha Bastien, This is a nice improvement to the Org-mode environment. Thanks for implementing it. All the best, Tom On Jan 2, 2011, at 9:00 AM, Bastien wrote: Carsten Dominik writes: up to now, the online manual was only updated at release time. But Bastien is changing this right no

Re: [Orgmode] org.texi vs. orgmode.org/manual

2011-01-02 Thread Thomas S. Dye
, at 10:12 AM, Carsten Dominik wrote: Hi Tom, Bastien, On Jan 2, 2011, at 8:52 PM, Thomas S. Dye wrote: Aloha Bastien, This is a nice improvement to the Org-mode environment. Thanks for implementing it. there was once a good reason for only updating the manual at release time. Because

Re: [Orgmode] [Babel] Finished my presentation on R using org-mode and Babel

2011-01-04 Thread Thomas S. Dye
Aloha Bernd, Thanks for sharing this. It strikes me as a clean and effective use of export to Beamer. I think Org-mode is a good choice for reproducible research and hope that it has sufficient following in the future to rate mention if you decide to revise your introduction someday. A

Re: [Orgmode] Reproducible Research Template

2011-01-05 Thread Thomas S. Dye
On Jan 4, 2011, at 9:55 AM, Andy Choens wrote: I am developing a reproducible research template for R. I am trying to implement most of a research "compendium" in org. I say "most" because I am going to allow the actual data to exist outside of org, simply because most of the data I work w

Re: [Orgmode] unnamed :results

2011-01-05 Thread Thomas S. Dye
results blocks after the code block when the code block has a name. I would expect your "new" behavior below to have been the standard behavior since the early days of babel. Best -- Eric "Thomas S. Dye" writes: Aloha all, In the course of updating an Org-mode file to

Re: [Orgmode] :cache documentation patch

2011-01-05 Thread Thomas S. Dye
your Desktop with a name like 0001-commit-message-stuff.patch Thanks Again -- Eric "Thomas S. Dye" writes: Aloha all, The attached patch documents the behavior of the :cache header argument. All the best, Tom ___ Emacs-orgmode mailing

Re: [Orgmode] :cache documentation patch

2011-01-05 Thread Thomas S. Dye
t file as does git format-patch. Thanks -- Eric "Thomas S. Dye" writes: Hi Eric, Will do. The earlier patch was made with magit. I used the d command, Diff working tree, then saved the output to the file I sent. If I understand correctly, the missing step was the commit. I sho

Re: [Orgmode] Images from R in LaTeX and PDF

2011-01-07 Thread Thomas S. Dye
Aloha Ben, Can you share an example that doesn't work for you? All the best, Tom On Jan 7, 2011, at 7:23 AM, Ben Ward wrote: Hi All, I've been doing some work with babel and R to generate graphs that I've then been including useing attr latex. But when I include images the always appear

Re: [Orgmode] org fontifies outside of src blocks

2011-01-09 Thread Thomas S. Dye
Aloha Jeff, I think I had this issue. IIRC, this is a Mac issue. I think you can fix it with this: (setq font-lock-verbose nil) If not, let me know and I'll look harder. Tom On Jan 9, 2011, at 4:54 PM, Jeff Horn wrote: Hey list, I have an annoying issue. When in *either* Aquamacs or

Re: [Orgmode] Re: org fontifies outside of src blocks

2011-01-10 Thread Thomas S. Dye
rd that the same fix should fix (1)? Dan On Sun, Jan 9, 2011 at 10:16 PM, Thomas S. Dye wrote: Aloha Jeff, I think I had this issue. IIRC, this is a Mac issue. I think you can fix it with this: (setq font-lock-verbose nil) If not, let me know and I'll look harder. Tom On Jan 9, 20

Re: [Orgmode] Basic organization question

2011-01-14 Thread Thomas S. Dye
On Jan 14, 2011, at 5:35 PM, Tommy Kelly wrote: I can see that TODOs can be organized using tags, or categories, or files, or simply subtrees (or several of those). Is there an obvious choice? All I'm really looking for is a basic organization, to let me "group" tasks of different broad functi

Re: [Orgmode] org-add-link-type

2011-01-18 Thread Thomas S. Dye
"\\citet{%s}" path) (format "\\citet[%s]{%s}" desc path) ) #+end_src All the best, Tom On Jan 17, 2011, at 8:35 AM, Bastien wrote: Hi Thomas, "Thomas S. Dye" writes: (org-add-link-type "citet" 'ebib (lambda (path desc format)

[Orgmode] Multiple publishing projects

2009-10-05 Thread Thomas S. Dye
to add a second one. If someone can offer an example, or a pointer to an example I've overlooked, I'll be appreciative. All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 F

Re: [Orgmode] Multiple publishing projects

2009-10-06 Thread Thomas S. Dye
Thanks Ian. Your example helped me make sense of the Org manual, which was a bit terse for my comprehension in this instance. My second publishing project is up and running now and I'm looking forward to the third. All the best, Tom On Oct 6, 2009, at 12:05 AM, Ian Barton wrote: Apologi

[Orgmode] [babel] language support

2009-10-17 Thread Thomas S. Dye
r the second concept \citep{author2}. ... #+end_src #+srcname: beamer-presentation #+begin_src latex :tangle beamer-thesis :exports none # <> # <> ... #+end_src #+srcname: latex-presentation #+begin_src latex :tangle latex-thesis :exports none # <> # <> ... #+end_src Tom

Re: [Orgmode] [babel] language support

2009-10-17 Thread Thomas S. Dye
prehend the possible paths to this end, especially in comparison to the capabilities of others on this list, and comments or suggestions are most welcome. All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http:/

[Orgmode] [babel] :session

2009-10-18 Thread Thomas S. Dye
-many, many possibilities ... Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com ___ Emacs-orgmode mailing list Remember: use `Reply All' to send replies to t

[Orgmode] [babel] noweb for :sessions?

2009-10-19 Thread Thomas S. Dye
ser_name", password="password", dbname="db_name", host="host_name") #+end_src #+srcname: r-query #+begin_src R :session session-1 # <> res <- dbGetQuery(con, "select * from table_name where 1") #+end_src Tom Thomas S. Dye,

Re: [Orgmode] [babel] noweb for :sessions?

2009-10-19 Thread Thomas S. Dye
Hi Eric, Yes, I think that's it. I appreciate your help. org-babel has me feeling like a kid at Christmas. Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com On Oct 19, 2009, at 8:15 AM, Eric Schu

[Orgmode] [babel] :noweb and R

2009-10-19 Thread Thomas S. Dye
block "funcall: Symbol's function definition is void: R-mode": #+srcname: noweb-example #+begin_src R a <- 28 a #+end_src #+resname: noweb-example : 28 #+begin_src R :noweb # <> b <- a + 4 b #+end_src The first block works fine for R. Tom Thomas S.

Re: [babel][Orgmode] Subtree exporting to different LaTeX_CLASS

2009-10-22 Thread Thomas S. Dye
hieve, decisions I've made, etc. and uses the export facilities of org-mode to create a user manual for my employees. Right now I'm targeting html for the user manual, but LaTeX export would also work. HTH, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, I

Re: [babel][Orgmode] Subtree exporting to different LaTeX_CLASS

2009-10-23 Thread Thomas S. Dye
workflow you devise. HTH, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com On Oct 23, 2009, at 2:48 AM, JBash wrote: Tom, Thanks very much for pointing this out. I had not taken the time to investigate

Re: [babel][Orgmode] Subtree exporting to different LaTeX_CLASS

2009-10-23 Thread Thomas S. Dye
Jerry, I forgot to mention a setup step. You'll need this in .emacs to register LaTeX as a source language in org-babel. (org-babel-add-interpreter "latex") (add-to-list 'org-babel-tangle-langs '("latex" "tex")) HTH, Tom Thomas S. Dye, Ph.D

Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-27 Thread Thomas S. Dye
On Oct 26, 2009, at 2:24 PM, Dan Davison wrote: Torsten Wagner writes: <...> < ... > The inline code blocks will not be processed inside source blocks. I'm not sure how to achieve what you want with the current machinery, but have you read the recent posts by Thomas Dye describing how he

Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-27 Thread Thomas S. Dye
On Oct 27, 2009, at 12:55 PM, Eric Schulte wrote: Torsten Wagner writes: Perhaps this will do what you want? When I run org-babel-tangle on the following org file, and then LaTeX the output, the resulting pdf file says: A bit of LATEX code, with the result: 6 I just wonder if th

Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-28 Thread Thomas S. Dye
On Oct 28, 2009, at 5:19 AM, Eric Schulte wrote: I see, you are using the org-mode file "a level above" the direct export. Maybe another option here would be to tag headlines based on which export target they are included within, and then base your exports on the headline tags (using #+EXPO

[babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-28 Thread Thomas S. Dye
On Oct 28, 2009, at 6:10 AM, Dan Davison wrote: Dear thread participants, please note that we were breaking the rule of prepending the subject line with the string [babel]! One question inline below. "Eric Schulte" writes: "Thomas S. Dye" writes: On Oct 27, 200

Re: [Orgmode] Differences html/pdf

2009-10-28 Thread Thomas S. Dye
On Oct 28, 2009, at 6:26 AM, Bastien wrote: Carsten Dominik writes: In the latex version they're not exported for some reasons... That is correct, we have not implemented keeping all line breaks in LaTeX. I've searched around a bit, and to my big surprise, I cannot find a LaTeX package pr

Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-28 Thread Thomas S. Dye
On Oct 28, 2009, at 7:15 AM, Eric Schulte wrote: "Thomas S. Dye" writes: On Oct 28, 2009, at 6:10 AM, Dan Davison wrote: Am I right in thinking that one issue remaining in this thread is that we currently have no means of tangling the output of org-babel- latex? Thus the

Re: [babel] Re: [Orgmode] org-babel: Meta-LaTeX-Python-Environment

2009-10-28 Thread Thomas S. Dye
On Oct 28, 2009, at 12:19 PM, Eric Schulte wrote: "Thomas S. Dye" writes: [...] Eric, I think Torsten has a clearer idea than I do about what kinds of programming structures might be appropriate here, but your suggestion looks to me like an elegant replacement for the file based

[Orgmode] [babel] noweb syntax

2009-10-31 Thread Thomas S. Dye
e % [[file:~/Public/projects/903_adzes/org-babel/test-babel.org::*test] [block-1]] This is tangled 1, but so this is. This is tangled 1, and so is this 2. % block-1 ends here All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (8

[Orgmode] [babel] noweb expansion in latex source blocks

2009-10-31 Thread Thomas S. Dye
Aloha all, Noweb expansion in latex source blocks inserts spaces that can introduce unwanted paragraph breaks in LaTeX. The outer-block in this org file looks like something that should be set as one paragraph in LaTeX. * noweb expansion #+srcname: outer-block #+begin_src latex :tangle n

Re: [Orgmode] [babel] noweb expansion in latex source blocks

2009-11-01 Thread Thomas S. Dye
On Nov 1, 2009, at 9:47 AM, Dan Davison wrote: "Thomas S. Dye" writes: Aloha all, Noweb expansion in latex source blocks inserts spaces that can introduce unwanted paragraph breaks in LaTeX. Hi Tom, I've just fixed this issue and the other one you posted, regarding multipl

[Orgmode] [babel] noweb expansion of LaTeX output from R

2009-11-01 Thread Thomas S. Dye
Aloha all, Is it possible to use the noweb syntax to pass LaTeX output from R into a latex source block? I thought this would work, but the noweb expansion yields nil. Please note that this is just a question and not a request for a change to org-babel. In this particular case, the best

Re: [Orgmode] [babel] noweb expansion of LaTeX output from R

2009-11-01 Thread Thomas S. Dye
On Nov 1, 2009, at 1:42 PM, Dan Davison wrote: "Thomas S. Dye" writes: On Nov 1, 2009, at 12:24 PM, Dan Davison wrote: "Thomas S. Dye" writes: Aloha all, Is it possible to use the noweb syntax to pass LaTeX output from R into a latex source block? I thought this

Re: [Orgmode] [babel] noweb expansion of LaTeX output from R

2009-11-01 Thread Thomas S. Dye
On Nov 1, 2009, at 1:42 PM, Dan Davison wrote: "Thomas S. Dye" writes: On Nov 1, 2009, at 12:24 PM, Dan Davison wrote: "Thomas S. Dye" writes: Aloha all, Is it possible to use the noweb syntax to pass LaTeX output from R into a latex source block? I thought this

[Orgmode] [babel] Uses for :session buffers

2009-11-04 Thread Thomas S. Dye
fully. I'm wondering: do other org-babelers use the :session buffer? How? For what purpose? Any tips or advice will be appreciated. All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http:/

Re: [Orgmode] [babel] Uses for :session buffers

2009-11-04 Thread Thomas S. Dye
On Nov 4, 2009, at 10:44 AM, Stephan Schmitt wrote: Thomas S. Dye wrote: Aloha all, I'm trying to comprehend the possibilities created by org-babel, and would like to draw on the experience of others if I could. I recently discovered the buffer created by :session. In my case, this

Re: [Orgmode] [babel] Uses for :session buffers

2009-11-04 Thread Thomas S. Dye
On Nov 4, 2009, at 12:02 PM, Dan Davison wrote: Stephan Schmitt writes: Thomas S. Dye wrote: Aloha all, I'm trying to comprehend the possibilities created by org-babel, and would like to draw on the experience of others if I could. I recently discovered the buffer created by :session

[Orgmode] [babel] :noweb

2009-11-08 Thread Thomas S. Dye
aise a warning or an error in this circumstance? All the best, Tom - * noweb #+begin_src R :noweb :session noweb <> <> #+end_src #+resname: : 2 #+srcname: bar #+begin_src R 2 #+end_src ------------- Thomas S. Dye, Ph.D. T. S

Re: [Orgmode][babel] noweb does not work (as expected)

2009-11-08 Thread Thomas S. Dye
moment. But, it looks to me as if you might want to :noweb instead of :tangle and perhaps establish a :session in case your source blocks need to communicate with one another. HTH, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-08

Re: [Orgmode][babel] noweb does not work (as expected)

2009-11-09 Thread Thomas S. Dye
On Nov 8, 2009, at 9:38 PM, Torsten Wagner wrote: Hi Tom, If I try to use the noweb way, I always got error messages which tells me that org-babel can not read the result correctly #+srcname: r-load-libraries #+begin_src R library(RMySQL) library(reshape) library(xtable) #+end_src

Re: [Orgmode] latex export and beamer columns

2009-11-21 Thread Thomas S. Dye
On Nov 21, 2009, at 2:49 AM, Eric S Fraga wrote: Recently, in September, there was a discussion about exporting org files to latex using the beamer class and generating slides with multiple columns: http://article.gmane.org/gmane.emacs.orgmode/17546 No solution was presented at that time but I

[Orgmode] [babel] editing LaTeX source code blocks

2009-11-23 Thread Thomas S. Dye
ser could be given a choice of which one to search for label definitions. There are easy workarounds for this, so it isn't a big deal. It would be deluxe to leverage the full power of reftex while editing org-babel LaTeX source code blocks, though. All the best, Tom Thoma

Re: [Orgmode] Beamer support in Org-mode

2009-11-26 Thread Thomas S. Dye
Hi Carsten, On Nov 26, 2009, at 1:17 AM, Carsten Dominik wrote: Hi, this is in response to the discussions about beamer export from Org-mode. Yesterday I had a long train ride during which I scanned the beamer documentation (smoking hot stuff!). Then I made the attached draft for Org-mode su

[Orgmode] beamer columns

2009-11-29 Thread Thomas S. Dye
Aloha all, Would it make sense to implement Beamer columns with Org-mode tables? All the best, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com ___ Emacs-org

Re: [Orgmode] beamer columns

2009-11-29 Thread Thomas S. Dye
On Nov 29, 2009, at 11:23 AM, Carsten Dominik wrote: On Nov 29, 2009, at 7:31 PM, Thomas S. Dye wrote: Aloha all, Would it make sense to implement Beamer columns with Org-mode tables? Hi Thomas, I cannot see how this would make sense. Maybe you'd like to elaborate? - Carsten

Re: [Orgmode] org-babel-tangle tangles too much !

2009-12-01 Thread Thomas S. Dye
-doc/test.org::*Nicolas %20Girard][b]] (a) (b) ;; b ends here Is this what you're after? HTH, Tom Thomas S. Dye, Ph.D. T. S. Dye & Colleagues, Archaeologists, Inc. Phone: (808) 529-0866 Fax: (808) 529-0884 http://www.tsdye.com ___ Emacs-

Re: [Orgmode] Re: org-babel-tangle tangles too much !

2009-12-01 Thread Thomas S. Dye
Hi Nicolas, On Dec 1, 2009, at 7:55 AM, Nicolas Girard wrote: On Tue, 01 Dec 2009 05:43:38 -1000, Thomas S. Dye wrote : Your code snippet doesn't tangle at all here. Perhaps you have a setting somewhere that has an effect on tangling? I'm intending my file (username.org) to be

Re: [Orgmode] Re: [babel] R questions

2009-12-08 Thread Thomas S. Dye
Aloha Sebasien, On Dec 7, 2009, at 11:50 PM, Sébastien Vauban wrote: But what's a "NA" value in general? Is 0 always a meaningful value as numeric? Context-sensitive.. NA is a logical constant of length 1 which contains a missing value indicator. Whether or not 0 is a meaningful value a

Re: [Orgmode] [Babel] - importing a data file- missing header row

2009-12-08 Thread Thomas S. Dye
Hi Graham, On Dec 8, 2009, at 6:41 AM, Graham Smith wrote: I need a bit of help importing a data file into orgmode/babel. The import doesn't seem to know about having a header row #+srcname:woodland #+begin_src R read.table("/home/graham/Dropbox/College/BY4001/WoodlandData/ BY4001WoodlandDat

Re: [Orgmode] Re: [babel] R questions

2009-12-08 Thread Thomas S. Dye
Hi Sebastien, On Dec 8, 2009, at 11:37 AM, Sébastien Vauban wrote: Hi Thomas, "Thomas S. Dye" wrote: On Dec 7, 2009, at 11:50 PM, Sébastien Vauban wrote: [2] I guess one could potentially think about dealing with missing values more explicitly in org-babel. E.g. there

Re: [Orgmode] [babel] R - variable names in summary

2009-12-09 Thread Thomas S. Dye
Hi Graham, On Dec 9, 2009, at 10:33 AM, Graham Smith wrote: Dan, That's great, I am beginning to grasp how this works But I would never have figured out the :results output method, however. OK, it would be really helpful if you could let us know how we should improve the documentation of

Re: [Orgmode] Beamer support in Org-mode

2009-12-10 Thread Thomas S. Dye
Hi Mark, On Dec 10, 2009, at 10:49 AM, Mark Elston wrote: I have been following this discussion with some interest as it may provide the basis for something I am interested in doing as well. I hope my discussion doesn't muddy the waters too much... Nick Dokos wrote: Darlan Cavalcante Moreira

[Orgmode] [babel] Idiomatic handling of quotes

2009-12-17 Thread Thomas S. Dye
etas) #+begin_src R :session str(x) x #+end_src #+results: test-list | "theta-1.csv" | | "theta-2.csv" | ... tdye> str(x) 'data.frame': 8 obs. of 1 variable: $ V1: chr "\"theta-1.csv\"" "\"theta-2.csv\"&q

Re: [Orgmode] [babel] Idiomatic handling of quotes

2009-12-18 Thread Thomas S. Dye
Hi Francesco, On Dec 17, 2009, at 11:20 PM, Francesco Pizzolante wrote: Hi Thomas, In the example below, note that the R representation of the directory listing escapes the quotes in the original and encloses it all in a second set of quotes, e.g. "\"theta-1.csv\"". This must come up a

<    1   2   3   4   5   6   7   8   9   10   >