Re: [O] [POLL] Syntax change: make \[...\] non-inline (+1)
Hi, Federico Beffa be...@ieee.org writes: The problem with that is that a displayed equation should NOT start a new paragraph (in the generated LaTeX file). This is because if it does then LaTeX puts more (vertical) space than desirable. If this is always the case for you, you can fix this behavior by always putting it in a new paragraph and using a filter. Example: paragraph 1 \[math 1\] paragraph 2 Use a final filter to convert this to paragraph 1 \[math 1\] paragraph 2 Perhaps you want to have some finer control over whether there should be a newline between math 1 and paragraph 2, e.g. exploiting the fact that \n\n is exported as \n\n. Thus, paragraph 1 \[math 1\] paragraph 2 would become paragraph 1 \[math 1\] paragraph 2 Cheers, Rasmus
[O] numbering figure in html ?
Hello everybody,
In org-mode exporting
\begin{figure}
\begin{tikzpicture}
\draw[-, =latex][thick] (0,0) -- (1.6,0) node[right] {Subcontrary};
...
end{tikzpicture}
\caption{Square of opposition}
\end{figure}
works well with LateX, but fails with html: each Figure has the same
number, i.e. 1.
What is the best solution to get numbered Figure in html?
Regards
Jo.
Re: [O] Multi-line links
Hello Nicolas, On Sa, 2014-07-26 at 15:32 +0200, Nicolas Goaziou wrote: In the long run, I'm pretty sure the project will benefit more if you bring in your own, temporary, inexperience and start hacking from there. I’ll definitely look into this once I get a hang of Elisp. When I (unsuccessfully) tried to figure out how links are handled, it occurred to me some more inline docs would be useful; but then again maybe once one is used to Elisp the code becomes more transparent. When I have some time for another attempt to wrap my head around the code, maybe I could try adding in some comments as I go along. since multi-line descriptions seemed to be working (though only for 3 lines) and since the raw-path seemed to contain the needed line-breaks already. But if I understand you correctly, the complication is that the path parsing is the same across different link types, and so one cannot simply fix it up so that :path is equivalent to :raw-path, just with the link prefix stripped of? I fixed it in maint. org-element.el used an inadequate regexp to analyze the path. Could you confirm it? If I understand correctly, this change addresses the issue of truncated «path» and «raw-link»? These seem to return the expected results for multi-line links now. Wonderful! Thank you very much for this! The syntax highlighting seems to also work, though it requires refreshing the buffer display. The only remaining issue would be that these links can only be triggered from the first line. Clicking on another line will yield «No link found», so I cannot get org-ref to return the BibTeX entry appropriate for the line from which the action is triggered. Strangely, when I inspect the other lines using org-element-context, the link type is correctly shown, even though it’s a few lines before point. But when issuing org-open-at-point, it seems no handler is found when point is not on the first line of a multi-line link. Best regards, Tobias
[O] R code block produces only partial output
Hi all, I've been using Org mode (latest version - see my set up below) to perform some data analysis and have come across a problem evaluating R code blocks. I usually use a session when working and when evaluating a code block with describe (R package rms) and a quantitative variable the results in .org buffer and the *R* buffer (output) differ. However, it's not the describe function, but something about the output of that function. The following is a minimal example (both with and without the describe function) to illustrate the problem. I think it has something to do with a number of spaces followed by a '.' in the output buffer. Any thoughts or guidance would be greatly appreciated. Thanks in advance. Andreas --- test.org - #+STARTUP: showall indent hidestars #+PROPERTY: header-args:R :session *R* #+PROPERTY: header-args :results output graphics :exports both #+BEGIN_SRC R require(rms) x - rnorm(100) describe(x) #+END_SRC #+RESULTS: : 75 .90 .95 : 0.69261 1.38170 1.71468 : : lowest : -2.270 -1.878 -1.705 -1.525 -1.423 : highest: 1.739 2.032 2.061 2.150 2.480 #+BEGIN_SRC R x - rnorm(100) y - quantile(x, probs=seq(0,1,0.1)) names(y) - as.character(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)) y #+END_SRC #+RESULTS: : 6 .7 .8 .9 1 : 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 --- end test.org - The actual output for the first code block in the *R* buffer was: describe(x) x n missing unique Mean .05 .10 .25 .50 1000 100 0.1118 -1.39404 -1.02732 -0.45899 0.03756 .75 .90 .95 0.69261 1.38170 1.71468 lowest : -2.270 -1.878 -1.705 -1.525 -1.423 highest: 1.739 2.032 2.061 2.150 2.480 Similarly, the second code block resulted in: y 0 .1 .2 .3 .4 .5 -2.23303584 -1.31137871 -0.69424743 -0.48689155 -0.16973865 0.09289862 .6 .7 .8 .9 1 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 And finally my set up is: Emacs : GNU Emacs 24.3.1 (i386-mingw-nt6.2.9200) of 2013-03-18 on MARVIN Package: Org-mode version 8.2.7c (8.2.7c-elpa @ c:/Users/andre_000/Documents/.emacs.d/elpa/org-20140730/) current state: == (setq org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-latex-format-headline-function 'org-latex-format-headline-default-function org-src-fontify-natively t org-html-format-inlinetask-function 'ignore org-completion-use-iswitchb t org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-confirm-babel-evaluate nil org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-babel-pre-tangle-hook '(save-buffer) org-occur-hook '(org-first-headline-recenter) org-src-lang-modes '((r . ess-mode) (ocaml . tuareg) (elisp . emacs-lisp) (ditaa . artist) (asymptote . asy) (dot . fundamental) (sqlite . sql) (calc . fundamental) (C . c) (cpp . c++) (C++ . c++) (screen . shell-script)) org-shiftdown-final-hook '(windmove-down) org-html-format-headline-function 'ignore org-log-done 'time org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-catch-invisible-edits 'smart org-default-notes-file ~/.org//notes.org org-latex-format-drawer-function '(lambda (name contents) contents) org-src-tab-acts-natively t org-export-backends '(ascii html icalendar latex md) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-completion-use-ido t org-use-speed-commands t org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5] org-babel-result-hide-spec org-babel-hide-all-hashes org-mode-reftex-setup (lambda nil (flyspell-mode 1) (auto-fill-mode 1) (local-set-key \220 (quote outline-previous-visible-heading)) (local-set-key \225 (quote outline-up-heading)) (local-set-key \227 (quote org-table-copy-region)) (local-set-key \231 (quote org-table-paste-rectangle)) (local-set-key \214 (quote org-table-sort-lines)) (local-set-key \311 (quote org-toggle-iimage-in-org))) ) org-shiftup-final-hook '(windmove-up) org-ascii-format-drawer-function '(lambda (name contents width) contents) org-directory ~/.org/ org-html-format-drawer-function '(lambda (name contents) contents)
Re: [O] hiding intrusive target-markups-brackets ++ Re: org-special-keyword face not showing in sublevels anymore since commit 69700e1
Bastien bzg at gnu.org writes: Hi, mc mc at aiguphonie.com writes: Please allow me to shortly direct your attention to an open, still uncommented 'feature request’ addressing an optional ‘fontification' or ‘hiding' of the some kind of intrusive target-markups-brackets (), just like this is done with the org-link brackets ( [[ ]] ). I agree this would be useful, I gave it a try at the time but could not finish the code. I will have a look again at the end of august. Don't hesitate to raise this up again in september if nothing happens. Thanks, Bastien, thank you very much indeed for looking into this! I was also wondering if it was possible to hide the brackets and I fully second Martin's request. radio links become a lot more useful with this reduction of clutter in the file. Best Gaston
Re: [O] mathjax vs. imagemagick
You wrote:
Hello,
In order to convert a tikzpicture into html webpage, one needs
#+OPTIONS: tex:imagemagick
and it means that the other equations are no more converted via
Mathjax.
Is there a mean to combine the use of imagemagick only for
tikzpicture, and keeping the use of Mathjax to read the other
equations in the html file?
Hi,
You don't need to set the tex:imagemagick option globally. With the
example bellow, the HTML export should use Mathjax to render math
fragments:
#+begin_src org
,#+TITLE: Test
,#+AUTHOR: Blah
,#+LATEX_CLASS: article
,#+LATEX_CLASS_OPTIONS: [american]
#
# Setup tikz package for both LaTeX and HTML export:
,#+LATEX_HEADER: \usepackage{tikz}
,#+PROPERTY: header-args:latex+ :packages '(( tikz))
#
,#+PROPERTY: header-args:latex+ :imagemagick (by-backend (latex nil) (t
yes))
,#+PROPERTY: header-args:latex+ :exports results :fit yes
,* One Diamond
,#+name: diamond
,#+header: :iminoptions -density 600 -resample 100x100
,#+header: :file (by-backend (latex diamond.tikz) (t diamond.png))
,#+begin_src latex :results raw file
\begin{tikzpicture}
\draw (1,0) -- (0,1) -- (-1,0) -- (0,-1) -- cycle;
\end{tikzpicture}
,#+end_src
,#+attr_latex: :float nil :width
,#+results: diamond
,* LaTeX
Inline math follows \(\left\{ x \right\}\)…
,* COMMENT setup
,#+name: setup
,#+begin_src emacs-lisp :results silent :exports none
(defmacro by-backend (rest body)
`(case (if (boundp 'backend) (org-export-backend-name backend) nil)
,@body))
,#+end_src
# Local variables:
# eval: (org-sbe setup)
# End:
#+end_src
Regards,
--
Nicolas BerthierFSF Member #7975
Re: [O] R code block produces only partial output
Hi Andreas, Why are you setting the output type to graphics when you are trying to return text? I think that may be the source of your problem. Best, Eric Andreas Kiermeier andreas.kierme...@gmail.com writes: Hi all, I've been using Org mode (latest version - see my set up below) to perform some data analysis and have come across a problem evaluating R code blocks. I usually use a session when working and when evaluating a code block with describe (R package rms) and a quantitative variable the results in .org buffer and the *R* buffer (output) differ. However, it's not the describe function, but something about the output of that function. The following is a minimal example (both with and without the describe function) to illustrate the problem. I think it has something to do with a number of spaces followed by a '.' in the output buffer. Any thoughts or guidance would be greatly appreciated. Thanks in advance. Andreas --- test.org - #+STARTUP: showall indent hidestars #+PROPERTY: header-args:R :session *R* #+PROPERTY: header-args :results output graphics :exports both #+BEGIN_SRC R require(rms) x - rnorm(100) describe(x) #+END_SRC #+RESULTS: : 75 .90 .95 : 0.69261 1.38170 1.71468 : : lowest : -2.270 -1.878 -1.705 -1.525 -1.423 : highest: 1.739 2.032 2.061 2.150 2.480 #+BEGIN_SRC R x - rnorm(100) y - quantile(x, probs=seq(0,1,0.1)) names(y) - as.character(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)) y #+END_SRC #+RESULTS: : 6 .7 .8 .9 1 : 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 --- end test.org - The actual output for the first code block in the *R* buffer was: describe(x) x n missing unique Mean .05 .10 .25 .50 1000 100 0.1118 -1.39404 -1.02732 -0.45899 0.03756 .75 .90 .95 0.69261 1.38170 1.71468 lowest : -2.270 -1.878 -1.705 -1.525 -1.423 highest: 1.739 2.032 2.061 2.150 2.480 Similarly, the second code block resulted in: y 0 .1 .2 .3 .4 .5 -2.23303584 -1.31137871 -0.69424743 -0.48689155 -0.16973865 0.09289862 .6 .7 .8 .9 1 0.31144890 0.63292642 0.87168950 1.17596547 1.96212110 And finally my set up is: Emacs : GNU Emacs 24.3.1 (i386-mingw-nt6.2.9200) of 2013-03-18 on MARVIN Package: Org-mode version 8.2.7c (8.2.7c-elpa @ c:/Users/andre_000/Documents/.emacs.d/elpa/org-20140730/) current state: == (setq org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-latex-format-headline-function 'org-latex-format-headline-default-function org-src-fontify-natively t org-html-format-inlinetask-function 'ignore org-completion-use-iswitchb t org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-confirm-babel-evaluate nil org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-babel-pre-tangle-hook '(save-buffer) org-occur-hook '(org-first-headline-recenter) org-src-lang-modes '((r . ess-mode) (ocaml . tuareg) (elisp . emacs-lisp) (ditaa . artist) (asymptote . asy) (dot . fundamental) (sqlite . sql) (calc . fundamental) (C . c) (cpp . c++) (C++ . c++) (screen . shell-script)) org-shiftdown-final-hook '(windmove-down) org-html-format-headline-function 'ignore org-log-done 'time org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-catch-invisible-edits 'smart org-default-notes-file ~/.org//notes.org org-latex-format-drawer-function '(lambda (name contents) contents) org-src-tab-acts-natively t org-export-backends '(ascii html icalendar latex md) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-completion-use-ido t org-use-speed-commands t org-mode-hook '(#[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil \300\301\302\303\304$\207 [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5] org-babel-result-hide-spec org-babel-hide-all-hashes org-mode-reftex-setup (lambda nil (flyspell-mode 1) (auto-fill-mode 1) (local-set-key \220 (quote outline-previous-visible-heading)) (local-set-key \225 (quote outline-up-heading)) (local-set-key \227 (quote org-table-copy-region)) (local-set-key \231 (quote
Re: [O] [PATCH] ob-shell
Alan Schmitt alan.schm...@polytechnique.org writes: Hello, On 2014-06-22 14:50, Eric Schulte schulte.e...@gmail.com writes: If this maintains existing functionality, please go ahead and apply it. Has this been applied? I'm still seeing a failing test for ob-shell. 1 unexpected results: FAILED ob-shell/bash-uses-assoc-arrays Best, Alan It looks like Achim is part way through making the required changes. Achim Gratz strom...@nexgo.de writes: Eric Schulte writes: If this maintains existing functionality, please go ahead and apply it. Done on master. The tests are left untouched, I will not have time to do anything there for the next few days. Any helping hand is welcome. Regards, Achim. Best, Eric -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw)
Re: [O] R code block produces only partial output
On 4 August 2014 21:23, Eric Schulte schulte.e...@gmail.com wrote: Why are you setting the output type to graphics when you are trying to return text? I think that may be the source of your problem. Hi Eric, thanks for the quick response. I've had 'graphics' from my main data analysis file ... I think I got that from WORG. I've removed it, reloaded the file, but same outcome. Any other thoughts? Cheers, Andreas
Re: [O] R code block produces only partial output
Andreas Kiermeier andreas.kierme...@gmail.com writes: On 4 August 2014 21:23, Eric Schulte schulte.e...@gmail.com wrote: Why are you setting the output type to graphics when you are trying to return text? I think that may be the source of your problem. Hi Eric, thanks for the quick response. I've had 'graphics' from my main data analysis file ... I think I got that from WORG. I've removed it, reloaded the file, but same outcome. Any other thoughts? Cheers, Andreas Hi Andreas, I can't reproduce your problem. I get the following from your minimal example when run in an Org-mode file, and from the command line. They are identical. Are you using the latest version of Org-mode? Best, Eric #+BEGIN_SRC R :results output x - rnorm(100) y - quantile(x, probs=seq(0,1,0.1)) names(y) - as.character(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)) y #+END_SRC #+RESULTS: : 0 .1 .2 .3 .4 .5 .6 : -2.5388527 -1.7039145 -1.0586655 -0.4892375 -0.2083433 0.0669765 0.2674644 : .7 .8 .9 1 : 0.6065544 1.0985117 1.5376634 3.2423323 $ R R version 3.1.0 (2014-04-10) -- Spring Dance Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] x - rnorm(100) y - quantile(x, probs=seq(0,1,0.1)) names(y) - as.character(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)) y 0 .1 .2 .3 .4 .5 -2.53624773 -1.30846042 -0.70659822 -0.43565010 -0.24318346 -0.01034625 .6 .7 .8 .9 1 0.24125644 0.49945059 0.92032314 1.36423669 2.83357915 -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw)
Re: [O] A way to show time effort estimates in the org-clock-report
Alexander Artemenko wrote:
Is there a way to show time effort estimates in the org-clock-report?
I found only that :properties (Effort) could be specified, but it does
not work
neither for one level, nor for summing children nodes' estimations.
#+COLUMNS: %66ITEM(Task) %6CLOCKSUM(Time) %6Effort(Estim.){:}
Best regards,
Seb
--
Sebastien Vauban
Re: [O] mathjax vs. imagemagick
Many thanks for this help Nicolas. I do not succeed to adapt your example
to my file. I am afraid that it is too complicated for me.
I meet always difficulties with html export, and now it is a failure of
bibtex2html...
Thanks again
Best regards
Jo.
2014-08-04 13:32 GMT+02:00 Nicolas Berthier nberth...@gmail.com:
You wrote:
Hello,
In order to convert a tikzpicture into html webpage, one needs
#+OPTIONS: tex:imagemagick
and it means that the other equations are no more converted via
Mathjax.
Is there a mean to combine the use of imagemagick only for
tikzpicture, and keeping the use of Mathjax to read the other
equations in the html file?
Hi,
You don't need to set the tex:imagemagick option globally. With the
example bellow, the HTML export should use Mathjax to render math
fragments:
#+begin_src org
,#+TITLE: Test
,#+AUTHOR: Blah
,#+LATEX_CLASS: article
,#+LATEX_CLASS_OPTIONS: [american]
#
# Setup tikz package for both LaTeX and HTML export:
,#+LATEX_HEADER: \usepackage{tikz}
,#+PROPERTY: header-args:latex+ :packages '(( tikz))
#
,#+PROPERTY: header-args:latex+ :imagemagick (by-backend (latex nil) (t
yes))
,#+PROPERTY: header-args:latex+ :exports results :fit yes
,* One Diamond
,#+name: diamond
,#+header: :iminoptions -density 600 -resample 100x100
,#+header: :file (by-backend (latex diamond.tikz) (t diamond.png))
,#+begin_src latex :results raw file
\begin{tikzpicture}
\draw (1,0) -- (0,1) -- (-1,0) -- (0,-1) -- cycle;
\end{tikzpicture}
,#+end_src
,#+attr_latex: :float nil :width
,#+results: diamond
,* LaTeX
Inline math follows \(\left\{ x \right\}\)…
,* COMMENT setup
,#+name: setup
,#+begin_src emacs-lisp :results silent :exports none
(defmacro by-backend (rest body)
`(case (if (boundp 'backend) (org-export-backend-name backend) nil)
,@body))
,#+end_src
# Local variables:
# eval: (org-sbe setup)
# End:
#+end_src
Regards,
--
Nicolas BerthierFSF Member #7975
Re: [O] [RFC] Rewrite `org-entry-properties' using parser
At Mon, 04 Aug 2014 00:07:46 -0400,
Aaron Ecay wrote:
Hi Erik,
2014ko abuztuak 3an, Erik Hetzner-ek idatzi zuen:
[…]
This allows me to search with subject={Bar}, which is very helpful.
But it would be nice if org supported multi-valued properties.
It does, at least to a first approximation. Look at the functions
described in:
(info (org) Using the property API)
I’m not sure how well this feature is integrated with agenda
search/filtering, though – maybe you should give it a try.
Hi Aaron,
Unfortunately those functions (org-entry-get-multivalued-property,
etc.) are completely isolated from all other property related code, so
search and filtering does not recognize them. Furthermore, they simply
split properties string on whitespace.
best, Erik
--
Sent from my free software system http://fsf.org/.
Re: [O] How to call org-display-inline-images so that after a graphviz block is evaluated the image is refreshed?
Hello Bastien, Still far from keeping up with missed postings, because of holiday time... ;-) Bastien wrote: Sebastien Vauban writes: Rick Frankel wrote: (add-hook 'org-babel-after-execute-hook (lambda () (org-display-inline-images nil t))) I simply had: (add-hook 'org-babel-after-execute-hook 'org-display-inline-images) Anyway, for me, this should clearly be made a *default*, nope? I don't think so, displaying inline images can be perceived as intrusive, it's good as an option. I (can) share your POV regarding having inline images on by default. But, re-displaying the inline images should still be a default, IMO, when these are enabled? Best regards, Seb -- Sebastien Vauban
Re: [O] how to hide titles marked with DONE
Hi Bastien, Sebastien Vauban writes: As I do suffer from the same problem, and do not take the time to archive all DONE subtrees, I think that an alternative approach would be that DONE subtrees wouldn't be expanded (by default) in the S-TAB cycles. Does that sound reasonable? Not to me, as there would be no real difference between DONE and ARCHIVED tasks then. You're of course right. Though, without archiving manually the DONE items, the current view is confusing, see http://screencast.com/t/AdVMyOJge32Z. It'd be good that the `org-headline-done' face would be propagated to the DONE subtrees, and not only to the main headline. That would improve a lot the readability of Org tasks lists. Best regards, Seb -- Sebastien Vauban
Re: [O] Collecting unique selling proposition (USP) of Org-mode
M wrote: Von: Karl Voit devn...@karl-voit.at I was wondering if there are people out there who also need Org-mode features that are *not part of any other software solution*. For the usual question why should I learn Emacs/Org-mode? I'd like to have a list of cool Org-mode features that demonstrate the benefit. So, how about a short brainstorming here and a new Worg-page collecting those things? * seamlessly integrating notes, spreadsheet calculations, tasks, and more at one single place * being able to pipe results of program written in language A to another script in language B (babel) * quick and simple defining dependencies between tasks such as doing groceries is required for cooking fancy dinner (org-depend) Some more key selling points form someone who still tries to learn emacs just for using org-mode: * platform independent - available for Windows, UNIX and MacOS * free * tagging * powerful filtering and creation of views (agendas) from different perspectives * 110% customizable with scripting and keybindings * built on a very robust and well developed application (Emascs) * many other modules and extensions thanks to Emacs * all the above with simple plain text format - easy to save, DIFF and version control * defining custom templates for new notes/tasks/projects... * tasks and projects can be broken down hierarchically into subtasks with no limit in depth * powerful and customizable export * time clocking + Literate Programming capabilities + Reproducible Research capabilities, thank to Org Babel Best regards, Seb -- Sebastien Vauban
Re: [O] some lisp help (for complete 0-knowledge lisp emacs user :))
Xebar Saram wrote: Hi list so i know i should start to really learn lisp but real life (uni work, family etc) doesn't really allow me so im marking my 1st year anniversary of using emacs without grasping lisp (plus i am in generally coding inept :)) in any case :) i have this handy lisp snippet that i find very useful and maybe some others in the list will find as well. it allows to quick convert lines of text into org src/example blocks: (defun z-wrap-cblock-lisp () Wrap region in quote block (interactive) (save-excursion (save-restriction (and (region-active-p) (use-region-p) (narrow-to-region (region-beginning) (region-end))) (goto-char (point-min)) (insert #+BEGIN_SRC emacs-lisp :results none\n) (goto-char (point-max)) (insert #+END_SRC\n) (deactivate-mark this works well but has some annoying flaws like you have to first manually mark the region you want to convert etc i was wondering: a)can some lisp coding master show me how to make this function auto select the line//X user defined lines/smart paragraph selection before it wraps it in the org block b)any improvement ideas from the community? FYI, there's already C-c C-v C-d (`org-babel-demarcate-block')... Best regards, Seb -- Sebastien Vauban
[O] babel: ob-C with Visual C++ and compilation-mode
Hi, I am using ob-C with gcc and Microsoft Visual C++. These two compilers have two different behaviours for outputting errors. Gcc uses the standard error output and Visual C++ uses the regular output. Under Windows, errors are not displayed because of the way org-babel-eval is coded. To work on both platforms, the standard output must be concatenated with the standard error. I modified the org-babel-eval in the following way. diff --git a/lisp/ob-eval.el b/lisp/ob-eval.el index 057590f..1a93460 100644 --- a/lisp/ob-eval.el +++ b/lisp/ob-eval.el @@ -53,12 +53,20 @@ STDERR with `org-babel-eval-error-notify'. (setq exit-code (org-babel--shell-command-on-region (point-min) (point-max) cmd err-buff)) - (if (or (not (numberp exit-code)) ( exit-code 0)) - (progn - (with-current-buffer err-buff - (org-babel-eval-error-notify exit-code (buffer-string))) - nil) - (buffer-string) + (let ((temp-buffer-str (buffer-string))) ;;temp-buffer-str holds standard output + body + (if (or (not (numberp exit-code)) ( exit-code 0)) + (progn + (with-current-buffer err-buff + (org-babel-eval-error-notify exit-code (format %s%s temp-buffer-str (buffer-string))) + ) + (save-excursion + (when (get-buffer org-babel-error-buffer-name) + (with-current-buffer org-babel-error-buffer-name + (compilation-mode) + (read-only-mode 0) + ))) + nil) + temp-buffer-str) One suggestion. It will be nice to put the error buffer in compilation-mode, this way errors are highlighted and we can jump directly into the source code. I modified org-babel-eval to launch the compilation mode in case of errors. I also removed the read-only attribute, else the buffer content of org-babel-error-buffer-name cannot be erased. Clearly, it's not a good patch because org-babel-eval seems to be a core function in babel. Maybe for ob-C, this function should be replaced by a new function. Thanks to everyone for orgmode and babel to exist. Best Ernesto
Re: [O] How to disable block evaluation results being wrapped with a single character like =?
That is what I was thinking. I had set it to 0. What happened is that instead of a block showing up, the results were delimited with a prepended '=' instead of a ':'. Unfortunately I forgot how this occurred, as I manually wrapped the result with a block instead, so org was happy to use that instead. Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson On Sun, Aug 3, 2014 at 7:24 PM, Ista Zahn istaz...@gmail.com wrote: I'm somewhat confused by the wrapped in = part, but I think you are looking for 'C-h v org-babel-min-lines-for-block-output'. Best, Ista On Sun, Aug 3, 2014 at 3:03 PM, Grant Rettke g...@wisdomandwonder.com wrote: Hi, Sometimes block evaluation results are wrapped with a single character like =. When exporting to latex, the results block is lost. How may one force block evaluation always to be wrapped properly for export to latex? org 8.2.7a Kind regards, Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson
Re: [O] How to disable block evaluation results being wrapped with a single character like =?
Hi Grant, I cannot reproduce. Here is what I see: #+BEGIN_SRC emacs-lisp (setq org-babel-min-lines-for-block-output 10) (print 1) #+END_SRC #+RESULTS: : 1 #+BEGIN_SRC emacs-lisp (setq org-babel-min-lines-for-block-output 0) (print 1) #+END_SRC #+RESULTS: #+begin_example 1 #+end_example Perhaps try with emacs -q and see what you get. Best, Ista On Mon, Aug 4, 2014 at 1:23 PM, Grant Rettke g...@wisdomandwonder.com wrote: That is what I was thinking. I had set it to 0. What happened is that instead of a block showing up, the results were delimited with a prepended '=' instead of a ':'. Unfortunately I forgot how this occurred, as I manually wrapped the result with a block instead, so org was happy to use that instead. Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson On Sun, Aug 3, 2014 at 7:24 PM, Ista Zahn istaz...@gmail.com wrote: I'm somewhat confused by the wrapped in = part, but I think you are looking for 'C-h v org-babel-min-lines-for-block-output'. Best, Ista On Sun, Aug 3, 2014 at 3:03 PM, Grant Rettke g...@wisdomandwonder.com wrote: Hi, Sometimes block evaluation results are wrapped with a single character like =. When exporting to latex, the results block is lost. How may one force block evaluation always to be wrapped properly for export to latex? org 8.2.7a Kind regards, Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson
[O] Highlighting text for HTML mark tag export?
Just been looking around and I have not come across a way to highlight text in org-mode to be HTML exported as the mark.../mark tags? Anyone know if this exists? Thanks, -- 'Mash
[O] [feature request] Matching tags and properties
Hi all, ATM, it is possible to look for date in properties using special keywords such as now, today and tomorrow. Unfortunately, the last two keywords doesn't match on timestamps that include time information. e.g. [2014-08-04 Mon] can be matched, but not [2014-08-04 Mon 21:20]. I think it would make sense to allow the later to be matched with today, that is, to ignore time information. WDYT? -- Daimrod/Greg
Re: [O] HTML lists are including paragraphs (lip…/p/li)
Daniel Clemente n142...@gmail.com writes: Hi. With latest org I'm getting lip…/p/li, which makes no sense; it should be li…/li Aren't there tests to find this type of breakages in export? Example: - hola - uno - dos - tres Is exported to: ul class=org-ul lip hola /p /li lip uno /p ul class=org-ul lidos /li /ul /li lip tres /p /li /ul Confirmed. Bisection fingers this commit: , | 1c3bdbb80a143664ca719a8a8b439390c42e28a2 is the first bad commit | commit 1c3bdbb80a143664ca719a8a8b439390c42e28a2 | Author: Eric Schulte schulte.e...@gmail.com | Date: Mon Jun 23 17:33:18 2014 -0400 | | inhibit p wraps on a whole-list basis | | * lisp/ox-html.el (org-html-paragraph): Extend the special case of | inhibiting p wrappers to only perform such inhibition when *every* | element of the list is a single paragraph long. Otherwise unsightly | spacing results. ` -- Nick
[O] Archive subtrees hierarchical (keep the parent structure)
Dear all, some of my org-mode files are getting bigger and bigger. So, I decided to use the archive feature to remove old stuff. However, I was not happy with the current archive feature, because it just puts subtrees unorganized in the archive file. I was more looking for a way to archive a subtree, but keep the parent structure. Means, if the point is at the subtree *** FOO in the following example: * A ** B *** FOO then it should copy the heading * A and ** B to the archive file and then move *** Foo to it. The only thing that I found was a feature request from Florian Lindner [fn:1]. A couple of days I was given it a shot and tried to implement that myself. Attached you'll find my attempt. It is a bit hackish, but it works for me. I think the attached code misses two features: 1. it only copies the parent headings with tags, but ignores properties and stuff like that 2. it ignores org-reverse-note-order, but that should not be too hard to add. Before I work on it again, I would like to hear your comments. Have I implemented functions that are already in org-mode? Is this feature useful for other people? Does it in more complicated org-mode files? Best regards Footnotes: [fn:1] https://lists.gnu.org/archive/html/emacs-orgmode/2014-05/msg01214.html -- Florian Adamsky http://florian.adamsky.it/ org-archive-subtree-hierarchical.el Description: application/emacs-lisp
Re: [O] numbering figure in html ?
Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:
Hello everybody,
In org-mode exporting
\begin{figure}
\begin{tikzpicture}
\draw[-, =latex][thick] (0,0) -- (1.6,0) node[right] {Subcontrary};
...
end{tikzpicture}
\end{tikzpicture}
\caption{Square of opposition}
\end{figure}
works well with LateX, but fails with html: each Figure has the same number,
i.e. 1.
What is the best solution to get numbered Figure in html?
[Please provide complete examples whenever possible.]
How do you produce the figure for HTML export?
Perhaps
#+caption: Square of opposition
on the figure?
--
Nick
Re: [O] [PATCH] ob-shell
Alan Schmitt writes: Has this been applied? I'm still seeing a failing test for ob-shell. 1 unexpected results: FAILED ob-shell/bash-uses-assoc-arrays That's to be expected if you use a version of bash that doesn't support assoc arrays. WHat is the backtrace from the test? Babel (and the tests) blindly assume that these things work when they see you using bash. Regards, Achim. -- +[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+ Samples for the Waldorf Blofeld: http://Synth.Stromeko.net/Downloads.html#BlofeldSamplesExtra
[O] [Babel] Weaving noweb chunks
Hi all, When weaving with noweb style chunks is there a way for the noweb references to become links back to the chunk in the exported HTML? For example when the following is woven: ** weaving :PROPERTIES: :tangle: yes :END: #+name: foo#+begin_src emacs-lisp (foo) #+end_src#+begin_src emacs-lisp :noweb tangle foo#+end_src I'd like the `foo` in the HTML output to be a link to the `foo` source block. Thanks! -deech
[O] Org-mode extensions used to publish a dissertation
Hi List,
I thoroughly enjoyed using Org-mode to write my dissertation. I was
happy to be able to export (mostly) equivalent versions of the document
to HTML and PDF. I'd recommend using Org-mode for such a complex
writing task to those who are either willing to hack the exporter, or
are willing to accept an Org-mode document with inline LaTeX which only
/really/ works with the LaTeX backend.
As I fall in the former category, here are the small extensions to the
Org-mode exporter which I found necessary. Thanks to the new exporting
backend they were uniformly easy to implement. They are included in the
attached elisp file. Each pagefeed (^L) in the file marks a new section
of functionality, the sections are as follows...
1. Ignore Headlines and keep content (discussed here recently)
2. Multi-column Table Cells
3. Wide tables extend into the margins.
4. Wide tables squeezed within the margins
5. sc links for the \sc{} latex command
6. gls links for the \gls{} family of Glossary commands
7. color links
8. TIKZ figure links
9. Tie certain latex commands to the preceding word.
10. Fix emphasis in text export
A simplified version of my Makefile is also attached. I hope someone
finds this useful.
Best,
Eric
init.el
Description: application/emacs-lisp
Makefile
Description: Binary data
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)
Re: [O] R code block produces only partial output
Hi Eric, I'm running Org 8.2.7c (via ELPA) and ESS 14.05. I've tried to run with a minimal Org setup using only the following in my init file. The shortcut I use to start Emacs (on Windows 8.1) is: C:\emacs\bin\runemacs.exe -Q -l C:\emacs\bin\minimal-org.el However, the results are the same as before. Any thoughts on what else I could try? - ;;; Minimal setup to load latest `org-mode' ;; activate debugging (setq debug-on-error t debug-on-signal nil debug-on-quit nil) ;; add latest org-mode to load path (add-to-list 'load-path (expand-file-name C:/Users/andre_000/Documents/.emacs.d/elpa/org-20140804/)) (add-to-list 'load-path (expand-file-name C:/Users/andre_000/Documents/.emacs.d/elpa/ess-20140716.2033/lisp/)) (require 'ess-site) (setq org-babel-R-command C:/Progra~1/R/R-3.1.1/bin/x64/R --slave --no-save) (org-babel-do-load-languages 'org-babel-load-languages '((emacs-lisp . nil) (R . t))) Thanks, Andreas -- Dr Andreas Kiermeier | Director Statistical Process Improvement Consulting and Training Pty Ltd Mbl: +61 (4)23 028 565 | Email: andreas.kierme...@gmail.com Australia On 4 August 2014 22:40, Eric Schulte schulte.e...@gmail.com wrote: Andreas Kiermeier andreas.kierme...@gmail.com writes: On 4 August 2014 21:23, Eric Schulte schulte.e...@gmail.com wrote: Why are you setting the output type to graphics when you are trying to return text? I think that may be the source of your problem. Hi Eric, thanks for the quick response. I've had 'graphics' from my main data analysis file ... I think I got that from WORG. I've removed it, reloaded the file, but same outcome. Any other thoughts? Cheers, Andreas Hi Andreas, I can't reproduce your problem. I get the following from your minimal example when run in an Org-mode file, and from the command line. They are identical. Are you using the latest version of Org-mode? Best, Eric $ R R version 3.1.0 (2014-04-10) -- Spring Dance Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] x - rnorm(100) y - quantile(x, probs=seq(0,1,0.1)) names(y) - as.character(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)) y 0 .1 .2 .3 .4 .5 -2.53624773 -1.30846042 -0.70659822 -0.43565010 -0.24318346 -0.01034625 .6 .7 .8 .9 1 0.24125644 0.49945059 0.92032314 1.36423669 2.83357915 -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw)
Re: [O] cant get org-protocol right
wow found a solution. I dont understand why I have to do that, but it seems firefox fucks up some path or other variables and because of that it doesnt find the standard server socket file so when I explizitly specifiy that in the org-protocol.desktop file, it works: [Desktop Entry] Name=org-protocol Exec=emacsclient -s /tmp/emacs1000/server %u Type=Application Terminal=false Categories=System; MimeType=x-scheme-handler/org-protocol; I have on suspition what else could be the problem here, I use psd, profile-sync-daemon: https://wiki.archlinux.org/index.php/Profile-sync-daemon so maybe that causes the problems with finding the server file in tmp, on the other hand epiphany doesnt has this problem, and psd is also activated on epiphany, so I am not shure happy that it works with firefox now. Would be nice if somebody could update the http://orgmode.org/worg/org-contrib/org-protocol.html site, the gnome instructions are for gnome 2, most people today use gnome 3, so u need such a desktop file and then call this command, u maybe dont need the -s /tmp/emacs1000/server part for other setups, but with or without it, both would be better than having nothing, I think with the -s... cant hurt, if u need it or not, in most cases it should work. btw I use i3, so its not only a gnome3 issue, I think even kde uses now this mechanism. When I look at teh kde setup instructions they used a similar desktop file at that time already. So I think thats no standardised with this desktop files.
Re: [O] Archive subtrees hierarchical (keep the parent structure)
Florian Adamsky fa-orgm...@haktar.org writes: Dear all, some of my org-mode files are getting bigger and bigger. So, I decided to use the archive feature to remove old stuff. However, I was not happy with the current archive feature, because it just puts subtrees unorganized in the archive file. I was more looking for a way to archive a subtree, but keep the parent structure. Means, if the point is at the subtree *** FOO in the following example: * A ** B *** FOO then it should copy the heading * A and ** B to the archive file and then move *** Foo to it. The only thing that I found was a feature request from Florian Lindner [fn:1]. A couple of days I was given it a shot and tried to implement that myself. Attached you'll find my attempt. Thanks for this work -- I think this is a nice feature. One concern about the above is that, if you're archiving many FOOs, then you'll get a whole bunch of duplicate A/B parent structures. There are several places in my agenda files where I have the exact structure in your example, and a *whole* lot of FOOs going in and getting archived out. How hard would it be to look for an existing A/B parent structure in the archive file, and put FOO there if it's found? Not a perfect solution, since you might have more than one A/B, but seems like it would help in a majority of cases... Thanks again, Eric It is a bit hackish, but it works for me. I think the attached code misses two features: 1. it only copies the parent headings with tags, but ignores properties and stuff like that 2. it ignores org-reverse-note-order, but that should not be too hard to add. Before I work on it again, I would like to hear your comments. Have I implemented functions that are already in org-mode? Is this feature useful for other people? Does it in more complicated org-mode files? Best regards Footnotes: [fn:1] https://lists.gnu.org/archive/html/emacs-orgmode/2014-05/msg01214.html -- Florian Adamsky http://florian.adamsky.it/
[O] column view uses non-existent org-whitespace face
I started using column view (finally), and noticed two things I thought were odd: 1. The %ITEM specification is zero-width by default, while the other special properties default to being as big as they need to be. This just seems a little odd. A column spec of %ITEM %TODO will show the TODO properly, but just a dot for the item. Shouldn't it default to fully-visible? 2. The text for %ITEM has the face org-whitespace applied to the leading stars, which doesn't exist anymore. I assume the intended effect was that the stars take up space, emulating indentation, but not themselves be visible. I guess that would be done by replacing the org-whitespace face with whatever's being used as the column background color but I don't know enough about faces to make that work. I also tried switching 'org-whitespace to 'invisible, but that didn't do anything. This is in org-columns-cleanup-item. The first one's not a big deal. The second would be nice to resolve -- it's ugly! Thanks, Eric
[O] [PATCH] Couple of small fixes in exporting node.js and css content.
I've got a toy paper I'm writing where I ran into a couple of issues exporting to html. The first issue is related to exporting the source of a css block that contains proprietary properties. In short, it looks like a list is generated for the font face, where a single value was expected. The second issue may be my fault, so if there is a setting I should change on my end, apologies and I'll set said setting. Basically, there is a cutoff value whereby node.js will insert newlines into the results. This was incredibly frustrating as what was turning into a decent looking table would suddenly become garbage. In both cases, I did not add a test file. If it is enough to just copy an existing test file and trim it down to just these two items, I can certainly do that. Finally, apologies if I am doing this incorrectly. I tried following the directions on how to contribute as well as I could. Thanks! -josh From 0441982a9457f9bbd953a06ab4fa830c6ffc967b Mon Sep 17 00:00:00 2001 From: Josh Berry tae...@gmail.com Date: Mon, 4 Aug 2014 22:45:43 -0400 Subject: [PATCH 1/2] Fix css export when proprietary properties are used * htmlize.el (htmlize-face-size): Check for a list instead of a single font face. `face-attribute' does not act kindly to being given a list of faces. TINYCHANGE --- contrib/lisp/htmlize.el | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/lisp/htmlize.el b/contrib/lisp/htmlize.el index 3bf5949..6654f40 100644 --- a/contrib/lisp/htmlize.el +++ b/contrib/lisp/htmlize.el @@ -1079,7 +1079,7 @@ If no rgb.txt file is found, return nil. (let ((size-list (loop for f = face then (face-attribute f :inherit) - until (or (not f) (eq f 'unspecified)) + until (or (not f) (eq f 'unspecified) (listp f)) for h = (face-attribute f :height) collect (if (eq h 'unspecified) nil h (reduce 'htmlize-merge-size (cons nil size-list -- 1.9.1 From 792b89a0922ee21bd0155f68adb0ce07c2558a51 Mon Sep 17 00:00:00 2001 From: Josh Berry tae...@gmail.com Date: Mon, 4 Aug 2014 22:46:46 -0400 Subject: [PATCH 2/2] Fix javascript exporting of results from node.js * ob-js.el (org-babel-js-read): Expand regexps to account for newlines in output from node.js It may be possible to instruct node.js to not insert line breaks automatically. Was not difficult to fix the regular expressions to account for newlines, though. I did *not* add a test file that goes over this, as I did not see one already for ob-js.el. I can certainly add one, if desired. TINYCHANGE --- lisp/ob-js.el | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lisp/ob-js.el b/lisp/ob-js.el index 7789449..9d956cc 100644 --- a/lisp/ob-js.el +++ b/lisp/ob-js.el @@ -97,13 +97,13 @@ This function is called by `org-babel-execute-src-block' If RESULTS look like a table, then convert them into an Emacs-lisp table, otherwise return the results as a string. (org-babel-read - (if (and (stringp results) (string-match ^\\[.+\\]$ results)) + (if (and (stringp results) (string-match ^\\[[\0-\377[:nonascii:]]*\\]$ results)) (org-babel-read (concat ' (replace-regexp-in-string \\[ ( (replace-regexp-in-string \\] ) (replace-regexp-in-string - ,(replace-regexp-in-string + ,\\W (replace-regexp-in-string ' \ results)) results))) -- 1.9.1
Re: [O] R code block produces only partial output
On Mon, Aug 4, 2014 at 7:46 PM, Andreas Kiermeier andreas.kierme...@gmail.com wrote: Hi Eric, I'm running Org 8.2.7c (via ELPA) and ESS 14.05. I've tried to run with a minimal Org setup using only the following in my init file. The shortcut I use to start Emacs (on Windows 8.1) is: C:\emacs\bin\runemacs.exe -Q -l C:\emacs\bin\minimal-org.el However, the results are the same as before. Any thoughts on what else I could try? [snip] I can reproduce with a minimal config and on Linux (to toss in a confirmation). I *also* accidentally just stumbled on a way I can toggle the behavior between correct and incorrect! It arose because my file was not able to use the #+PROPERTY settings you have -- my results were not obeying what I had set. I looked around and believe the syntax is correct per this page: - http://orgmode.org/manual/Header-arguments-in-Org-mode-properties.html However, I guarantee that the results weren't updating to :results output drawer as I had them set. I also noticed that the header-args:R :session *R* also didn't seem to be working, as if I changed the name, Emacs wouldn't ask me if I wanted to create a new R session upon block execution. Here's what I've found: Correct results: #+begin_src org #+STARTUP: showall indent hidestars #+PROPERTY: header-args:R :session r #+BEGIN_SRC R :results output drawer require(rms) set.seed(123) x - rnorm(100) describe(x) #+END_SRC #+RESULTS: :RESULTS: x n missing unique Mean .05 .10 .25 .50 1000 100 0.09041 -1.26508 -1.06822 -0.49385 0.06176 .75 .90 .95 0.69182 1.26450 1.56653 lowest : -2.309 -1.967 -1.687 -1.549 -1.265 highest: 1.715 1.787 2.050 2.169 2.187 :END: #+end_src Incorrect results: #+begin_src org #+STARTUP: showall indent hidestars #+BEGIN_SRC R :session r :results output drawer require(rms) set.seed(123) x - rnorm(100) describe(x) #+END_SRC #+RESULTS: :RESULTS: 75 .90 .95 0.69182 1.26450 1.56653 lowest : -2.309 -1.967 -1.687 -1.549 -1.265 highest: 1.715 1.787 2.050 2.169 2.187 :END: #+end_src The reason, I think, is this (also correct): #+begin_src org #+STARTUP: showall indent hidestars #+BEGIN_SRC R :results output drawer require(rms) set.seed(123) x - rnorm(100) describe(x) #+END_SRC #+RESULTS: :RESULTS: x n missing unique Mean .05 .10 .25 .50 1000 100 0.09041 -1.26508 -1.06822 -0.49385 0.06176 .75 .90 .95 0.69182 1.26450 1.56653 lowest : -2.309 -1.967 -1.687 -1.549 -1.265 highest: 1.715 1.787 2.050 2.169 2.187 :END: #+end_src So, session settings in the #+PROPERTY config *or* no session set at all yields correct results. Again, on a fresh start the #+PROPERTY method does not ask to start a new R session. Last confirmation is that if one leaves the session #+PROPERTY line (with none in the code block) and comments out the require(rms) line after already having run the block, you get the error Could not find the function 'describe'. So, there's no session activity finding the already-loaded library. The remaining questions for me is why would results differ depending on whether or not it's going through a session? Eric: this also explains why your minimal .org file couldn't reproduce: there's no setting of the session (again, not sure why that matters... but it seems to). John
[O] MobileOrg documentation?
There is not much to the MobileOrg documentation. For instance, how do you 'add' a new heading to an outline? Any examples around on how to use MobileOrg? -- David Masterson Programmer At Large
Re: [O] R code block produces only partial output
On 5 August 2014 13:30, John Hendy jw.he...@gmail.com wrote: I can reproduce with a minimal config and on Linux (to toss in a confirmation). I *also* accidentally just stumbled on a way I can toggle the behavior between correct and incorrect! It arose because my file was not able to use the #+PROPERTY settings you have -- my results were not obeying what I had set. I looked around and believe the syntax is correct per this page: - http://orgmode.org/manual/Header-arguments-in-Org-mode-properties.html Thanks for confirming this John! I couldn't see how the #+PROPERTY settings I had differed from those in the link ... I recall getting them from there (but maybe I mistyped something?). So I copied what you provided for the rest of my testing. Getting rid of :session all together did produce the correct results for me, too. However, including a :session in either #+PROPERTY or at the beginning of the code block did not - irrespective of whether I used *R* or simply r. Correct results: #+begin_src org #+STARTUP: showall indent hidestars #+PROPERTY: header-args:R :session r #+BEGIN_SRC R :results output drawer require(rms) set.seed(123) x - rnorm(100) describe(x) #+END_SRC [snip] So, this example did *not* work for me. The reason, I think, is this (also correct): #+begin_src org #+STARTUP: showall indent hidestars #+BEGIN_SRC R :results output drawer require(rms) set.seed(123) x - rnorm(100) describe(x) #+END_SRC Yes, without a session it seems to work fine. Thanks, Andreas
