[Orgmode] [babel] babel creating corrupt pdf and png

2010-08-26 Thread Graham Smith
PDFs created by Babel are giving a file corrupt message when trying to open them and a format not recognised message if I try pngs, Same files created directly from R are fine. This is with Ubuntu 10.04 and Org-mode version 6.36trans (release_7.01h.94.g25ac Example of code I am using is below.

[Orgmode] Org-beamer and beamer overlays

2010-08-26 Thread Glyn Millington
Good Morning :-) I'm having trouble getting beamer overlays to work properly when producing slides via org-mode. This may well be due to my not understanding the documentation!! I can only get this to work by dropping down into LaTeX - which on this scale is pretty painless - but feel sure

[Orgmode] [PATCH] Latest git pull has bug in (org-babel-remove-temporary-directory)

2010-08-26 Thread Noorul Islam
Latest pull is throwing error while quitting emacs. Here is the patch to fix this. ob.el: Fix minor bug * lisp/ob.el (org-babel-remove-temporary-directory) : Pass correct number of arguments to (delete-directory) Thanks and Regards Noorul diff --git a/lisp/ob.el b/lisp/ob.el index

[Orgmode] [Ann] Updates to org-drill (org topics as interactive flashcards using spaced repetition)

2010-08-26 Thread Paul Sexton
Org-Drill has recently been added to the contrib directory of the org repository. Latest version is in repository at: http://bitbucket.org/eeeickythump/org-drill I have made a couple of major updates recently. Changelogs are below. Reports of user experiences are welcome. Version 1.0 Added

Re: [Orgmode] [PATCH] Latest git pull has bug in (org-babel-remove-temporary-directory)

2010-08-26 Thread Eric Schulte
Hi Noorul, Can I ask what error the directory deletion is causing for you? I have the following delete-directory in my Emacs (latest from Git) ,[delete-directory] | delete-directory is an interactive compiled Lisp function in | `files.el'. | | (delete-directory DIRECTORY optional RECURSIVE

[Orgmode] [Windows] Quick guide on installing Emacs + OrgMode?

2010-08-26 Thread Gilles Ganault
Hello I'd like to take a quick look at Emacs in order to use its OrgMode add-on to get an outliner. Is there a HOWTO somewhere that would get me up and running quickly on Windows? Thank you. ___ Emacs-orgmode mailing list Please use `Reply All' to

Re: [Orgmode] [babel] babel creating corrupt pdf and png

2010-08-26 Thread Eric Schulte
Hi Graham, These pdf and png images are being created by R, Babel is simply passing commands to the R process setting the output device according to the :file argument, so for example :file fig1.pdf would result in wrapping your code in pdf(file=fig1.pdf) your-code-here dev.off I'd suggest

Re: [Orgmode] [PATCH] Latest git pull has bug in (org-babel-remove-temporary-directory)

2010-08-26 Thread Noorul Islam
On Thu, Aug 26, 2010 at 5:44 PM, Eric Schulte schulte.e...@gmail.com wrote: Hi Noorul, Can I ask what error the directory deletion is causing for you? I have the following delete-directory in my Emacs (latest from Git) ,[delete-directory] | delete-directory is an interactive compiled

[Orgmode] Re: Trouble syncing files to mobile-org.

2010-08-26 Thread Jason Schadel
With help from Richard Moreland, I found my MobileOrg settings were wrong. I had 'Index File' set to Mobileorg/index.org when it should have been just index.org. Thanks for the help. On Wed, Aug 25, 2010 at 11:29 AM, Jason Schadel jason.scha...@gmail.comwrote: I set it up using the Dropbox

[Orgmode] Re: [PATCH] Latest git pull has bug in (org-babel-remove-temporary-directory)

2010-08-26 Thread Detlef Steuer
Hi Eric, I have to confirm that bug. Org-mode as of today, emacs 23.1.1. Here is, what my *MESSAGES* buffer tells: CONTENTS...done (No files need saving) org-babel-remove-temporary-directory: Wrong number of arguments: delete-directory, 2 When done with a buffer, type C-x # Auto-saving...done

Re: [Orgmode] [babel] babel creating corrupt pdf and png

2010-08-26 Thread Graham Smith
Eriic, Thanks, I'd suggest looking at the R session (bats in your case) to see what errors if any are being thrown by R during execution of the boxplot command. Will do, but sidetracked somewhere else now. Its strange because some are now being produced fine, and other not. They are all

[Orgmode] Re: [babel] support plantuml

2010-08-26 Thread zwz
Mike Gauland mikely...@gmail.com writes: Mike Gauland mikelygee at gmail.com writes: I can get an image if I evaluate the block manually (e.g., via 'C-c C-c' with the cursor on the BEGIN block), but when I export the file the image is invalid. I figured it out. I was getting extra

[Orgmode] Re: [babel] support plantuml

2010-08-26 Thread zwz
Eric Schulte schulte.e...@gmail.com writes: Hi, I agree plantuml certainly makes sense as a new code block type. I'd like to include your ob-plantuml.el file into Org-mode/Babel, would you be willing to complete the FSF assignment process for contributing to Org-mode as described at

Re: [Orgmode] Re: [babel] support plantuml

2010-08-26 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 plantuml looks great - and it could save me quite a bit of work! Could you announce on the list as soon as it is uploaded to git so that I could try it? Cheers, Rainer On 26/08/10 16:26, zwz wrote: Eric Schulte schulte.e...@gmail.com writes:

Re: [Orgmode] Table of Contents in html export

2010-08-26 Thread Sebastian Rose
Andrei Jirnyi a-jir...@northwestern.edu writes: Hi all, Are there any options to modify the table of contents in the exported html files (other than whether to show it and to what level)? Or, if there are no such options, perhaps I could modify some elisp functions? Specifically, what I

Re: [Orgmode] [Windows] Quick guide on installing Emacs + OrgMode?

2010-08-26 Thread Sebastian Rose
Gilles Ganault gilles.gana...@free.fr writes: Hello I'd like to take a quick look at Emacs in order to use its OrgMode add-on to get an outliner. Is there a HOWTO somewhere that would get me up and running quickly on Windows? Thank you. Welcome Gilles, I'm not a windows user, but

Re: [Orgmode] Re: [babel] support plantuml

2010-08-26 Thread Eric Schulte
zwz zhangwe...@gmail.com writes: Eric Schulte schulte.e...@gmail.com writes: Hi, I agree plantuml certainly makes sense as a new code block type. I'd like to include your ob-plantuml.el file into Org-mode/Babel, would you be willing to complete the FSF assignment process for contributing

Re: [Orgmode] Re: problem with babel and R

2010-08-26 Thread Eric Schulte
Hi, A fix to this issue has been pushed up to the repository. As can now be read in the documentation of the `org-babel-insert-result' function [1], there is now a subtle distinction between :results org and :results raw, where :results org will wrap code block results in a begin_src org block.

[Orgmode] Re: [Windows] Quick guide on installing Emacs + OrgMode?

2010-08-26 Thread Richard Riley
Gilles Ganault gilles.gana...@free.fr writes: Hello I'd like to take a quick look at Emacs in order to use its OrgMode add-on to get an outliner. Is there a HOWTO somewhere that would get me up and running quickly on Windows? Thank you. ___

[Orgmode] Examples in numbered lists

2010-08-26 Thread Andrei Jirnyi
Hi -- Is there any way to make a numbered list preserve its' numbering when there are intervening code or example blocks? For example, if I have smth like this: * testing auto numbering 1. First do something #+begin_example here is an example how to do something #+end_example 2. Then do

Re: [Orgmode] Examples in numbered lists

2010-08-26 Thread Neil Hepburn
you could revert to raw latex code in your document and use \begin{enumerate}..\end{enumerate} with something like this: * testing auto numbering \begin{enumerate} \item First do something #+begin_example here is an example how to do something #+end_example \item Then do something else

Re: [Orgmode] Re: [babel] support plantuml

2010-08-26 Thread Eric Schulte
Rainer M Krug r.m.k...@gmail.com writes: plantuml looks great - and it could save me quite a bit of work! Could you announce on the list as soon as it is uploaded to git so that I could try it? This is now in the Org repository. For setup and usage information see

[Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Erik Iverson
Hello, I'm wondering if anyone can 1) reproduce what I'm seeing 2) help in understanding what's going on. If I export an Org file to LaTeX, the resulting .tex file contains the following in its header: \usepackage[T1]{fontenc} \usepackage{t1enc} Long story short: The resulting .PDF file

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread John Hendy
I know this is old, but check here? http://ubuntuforums.org/archive/index.php/t-557746.html http://ubuntuforums.org/archive/index.php/t-557746.htmlThey don't really solve the problem except by doing what you did -- remove the encoding lines. Perhaps you should try verifying your LaTeX fonts

[Orgmode] [BUG] export to latex breaks

2010-08-26 Thread Puneeth
Hi All, I'm on Org-mode version 7.01trans (release_7.01h.205.ge3d2) The LaTeX export of document test.org breaks. The headings Day 1 and Day 2 and content under them is not visible. [I have org-odd-levels-only set] Git bisect says - bb0a1f190be361ce1d717d79d411b88406d74c33 is the first bad

[Orgmode] Re: [Windows] Quick guide on installing Emacs + OrgMode?

2010-08-26 Thread Gilles Ganault
On Thu, 26 Aug 2010 18:09:07 +0200, Richard Riley rile...@gmail.com wrote: I dont use it myself but I have heard good things about Lennarts version. http://ourcomments.org/cgi-bin/emacsw32-dl-latest.pl Thanks guys for the tips. ___ Emacs-orgmode

[Orgmode] Bug: export aborts if ':eval query/never' in source code blocks

2010-08-26 Thread Paul Sexton
#+BEGIN_SRC R :eval query ... #+END_SRC If the above is in an org file, the user runs an export (C-c C-e), and the user types 'no' when asked whether to evaluate the code block, then the whole export process is aborted (no further blocks are processed and no export output is produced). The same

Re: [Orgmode] Bug: export aborts if ':eval query/never' in source code blocks

2010-08-26 Thread Erik Iverson
Which version of org-mode? I can't replicate on git version from minutes ago.. Paul Sexton wrote: #+BEGIN_SRC R :eval query ... #+END_SRC If the above is in an org file, the user runs an export (C-c C-e), and the user types 'no' when asked whether to evaluate the code block, then the whole

Re: [Orgmode] Re: problem with babel and R

2010-08-26 Thread David Hajage
I am so sorry to bother you again, but I must miss something. When I write: #+begin_src R :results output org :exports both library(ascii) options(asciiType = org) ascii(head(esoph)) #+end_src The results is: #+results: #+BEGIN_SRC org | | agegp | alcgp | tobgp| ncases | ncontrols |

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Erik Iverson
John, Thank you for your reply. For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is automatically telling latex to use T1 encoding, perhaps we should somewhere document to the user that Type 1 fonts should be available to get the best

Re: [Orgmode] Bug: export aborts if ':eval query/never' in source code blocks

2010-08-26 Thread Eric Schulte
Hi Paul, This is on the top of the stack for Babel bug fixes (see [1]), and I hope to have a solution pushed up to the git repository soon. I'll reply to this email when this issue is resolved. Thanks -- Eric Paul Sexton psex...@xnet.co.nz writes: #+BEGIN_SRC R :eval query ... #+END_SRC

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Erik Iverson
Alan, Hi Erik, I'm on Debian Squeeze, and I don't seem to have this problem. The fonts reported in the Properties are LMRoman and they look ok in Evince. I have all the latex extras installed. If you've seen my recent follow-up, that makes sense to me. So you are somehow getting LMRoman as

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents - oops

2010-08-26 Thread Erik Iverson
Alan L Tyree wrote: On Thu, 26 Aug 2010 12:34:08 -0500 Erik Iverson er...@ccbr.umn.edu wrote: Hello, I'm wondering if anyone can 1) reproduce what I'm seeing 2) help in understanding what's going on. If I export an Org file to LaTeX, the resulting .tex file contains the following in its

[Orgmode] Re: a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Markus Heller
Erik Iverson er...@ccbr.umn.edu writes: John, Thank you for your reply. For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is automatically telling latex to use T1 encoding, perhaps we should somewhere document to the user that Type 1

Re: [Orgmode] Re: problem with babel and R

2010-08-26 Thread David Hajage
Oups, I forgot ob-org in my .emacs... OK, now, really sorry for this. David On Thu, Aug 26, 2010 at 22:20, David Hajage dhaj...@gmail.com wrote: I am so sorry to bother you again, but I must miss something. When I write: #+begin_src R :results output org :exports both library(ascii)

Re: [Orgmode] Examples in numbered lists

2010-08-26 Thread Nicolas Goaziou
Hello, Andrei Jirnyi writes: Is there any way to make a numbered list preserve its' numbering when there are intervening code or example blocks? For example, if I have smth like this: * testing auto numbering 1. First do something #+begin_example here is an example how to do something

Re: [Orgmode] Bug: export aborts if ':eval query/never' in source code blocks

2010-08-26 Thread Erik Iverson
Eric, As a follow-up on a related issue: What if I want to eval a code block for some side-effect, but *not* include code or results in export. This assumes I'm using :session. Is there a way to currently do that? Setting :exports none seems to block evaluating of the code, can the :eval

Re: [Orgmode] Re: problem with babel and R

2010-08-26 Thread David Hajage
One comment: When I execute all the buffer (org-babel-execute-buffer), the result is: #+begin_src R :results output org :exports both library(ascii) options(asciiType = org) ascii(head(esoph, 3)) #+end_src #+results: #+BEGIN_SRC org | | agegp | alcgp | tobgp| ncases | ncontrols |

Re: [Orgmode] Re: a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Erik Iverson
Markus Heller wrote: Erik Iverson er...@ccbr.umn.edu writes: John, Thank you for your reply. For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is automatically telling latex to use T1 encoding, perhaps we should somewhere document to

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread John Hendy
On Thu, Aug 26, 2010 at 4:14 PM, Erik Iverson er...@ccbr.umn.edu wrote: John, Thank you for your reply. No problem -- nice report and I'm glad you got things fixed!! John For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is

[Orgmode] Re: [PATCH] Latest git pull has bug in (org-babel-remove-temporary-directory)

2010-08-26 Thread Seweryn
Hi Noorul, Thanks for pointing out the above, I guess files.el can't be assumed to be loaded. I've pushed up a fix. I have also: --- delete-directory is an interactive compiled Lisp function in `files.el'. (delete-directory DIRECTORY optional RECURSIVE) Delete the

Re: [Orgmode] a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Nick Dokos
Erik Iverson er...@ccbr.umn.edu wrote: For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is automatically telling latex to use T1 encoding, perhaps we should somewhere document to the user that Type 1 fonts should be available to get

[Orgmode] Re: a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Markus Heller
Erik Iverson er...@ccbr.umn.edu writes: Markus Heller wrote: Erik Iverson er...@ccbr.umn.edu writes: John, Thank you for your reply. For those that don't want to read all that follows, please note my conclusion, given here: Since orgmode is automatically telling latex to use T1

Re: [Orgmode] Re: problem with babel and R

2010-08-26 Thread Eric Schulte
Oh no! It appears this solution may have been too clever for it's own good. Thanks for suggesting :results silent as an additional default header argument, that appears to fixed this weird behavior. I've just pushed up that fix. Cheers -- Eric David Hajage dhaj...@gmail.com writes: One

Re: [Orgmode] Re: a bit offtopic, fonts in exported PDF documents

2010-08-26 Thread Nick Dokos
Nick Dokos nicholas.do...@hp.com wrote: the original Knuth fonts were Type3, That, of course, is nonsense: the original Knuth fonts were born before Adobe existed. They were in a format that Knuth invented (PK?). They could just naturally be mapped into Adobe Type3 fonts by dvips, so they

[Orgmode] Re: Bug: export aborts if ':eval query/never' in source code blocks

2010-08-26 Thread Paul Sexton
Eric Schulte schulte.eric at gmail.com writes: I've just pushed up a fix for this issue. For more information see http://eschulte.github.com/babel-dev/DONE-eval-and-noeval.html Wow, that was fast! Thanks very much. Paul ___ Emacs-orgmode