[O] Bug: [patch] Fixes behavior of org-agenda-tree-to-indirect-buffer [7.8.02 (release_7.7.796.gc512)]
Remember to cover the basics, that is, what you expected to happen and what in fact did happen. You don't know how to make a good report? See http://orgmode.org/manual/Feedback.html#Feedback Your bug report will be posted to the Org-mode mailing list. This function was misbehaving in a number of ways. The enclosed patch represents the changes necessary to make it work properly, accumulated over several weeks of testing. Sorry if the description is a bit vague. From c5128d1666e5fbe29a2fdfd6ee51622f05c42e9b Mon Sep 17 00:00:00 2001 From: Dave Abrahams d...@boostpro.com Date: Fri, 17 Feb 2012 22:44:13 -1000 Subject: [PATCH] Fix behavior of org-agenda-tree-to-indirect-buffer --- lisp/org-agenda.el | 11 +++ 1 files changed, 7 insertions(+), 4 deletions(-) diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el index 780794e..0c32b48 100644 --- a/lisp/org-agenda.el +++ b/lisp/org-agenda.el @@ -7202,16 +7202,19 @@ use the dedicated frame). (if (and current-prefix-arg (listp current-prefix-arg)) (org-agenda-do-tree-to-indirect-buffer) (let ((agenda-window (selected-window)) - (indirect-window (get-buffer-window org-last-indirect-buffer))) + (indirect-window + (and org-last-indirect-buffer + (get-buffer-window org-last-indirect-buffer (save-window-excursion (org-agenda-do-tree-to-indirect-buffer)) (unwind-protect - (progn -(unless indirect-window + (progn +(unless (and indirect-window (window-live-p indirect-window)) (setq indirect-window (split-window agenda-window))) (select-window indirect-window) (switch-to-buffer org-last-indirect-buffer :norecord) + (org-set-visibility-according-to-property) (fit-window-to-buffer indirect-window)) -(select-window agenda-window) + (select-window agenda-window) (defun org-agenda-do-tree-to-indirect-buffer () Same as `org-agenda-tree-to-indirect-buffer' without saving window. -- 1.7.5.4 Emacs : GNU Emacs 24.0.92.1 (x86_64-apple-darwin, NS apple-appkit-1038.36) of 2011-12-22 on bob.porkrind.org Package: Org-mode version 7.8.02 (release_7.7.796.gc512) -- Dave Abrahams BoostPro Computing http://www.boostpro.com
Re: [O] Limit todo window
Nick Dokos nicholas.do...@hp.com writes: Richard Riley rile...@gmail.com wrote: Whats the best way to limit the window that agendas use to show open todo items? e.g when I do C-c a a I dont want to see TODOs set for a years time - generally I might only want things in the current week or so. is there something built and instantly configurable to achieve this? org-agenda-span - also make sure to get rid of any settings of the obsolete variable org-agenda-ndays. The default is week however, so unless you've customized something, you should not see a year's worth of TODOS (I shudder at the thought...) Nick Hi Nick, I was being dense. I wasnt seeing the TODOs per se, but the creation of them! (I tag all items with a created date so they appear in a journal and I easily track creation of all org items). So yes, the span is the correct variable that I had previously thought not working... cheers r.
Re: [O] Bug: Remote state change of repeating TODO fails with calendar open [7.8.03]
Hi Thomas, At Fri, 17 Feb 2012 14:28:39 +0100, Thomas Morgan wrote: Changing a repeating TODO's state to DONE remotely from the agenda fails to change the date when the calendar is open in another window. The reason is that `org-recenter-calendar' selects the agenda window after doing its work, also making the agenda the current buffer, but caller `org-auto-repeat-maybe' expects the current buffer to be the Org file that contains the TODO item. Here's how to reproduce it: Run `emacs -Q -l setup.el'. Type `M-x calendar'. Type `M-x org-agenda', then `a' for weekly agenda. Move point to first TODO. Press `t' to try to change TODO state to DONE. The result is that `Note stored' appears in the echo area but there is no change in the agenda view or in the scheduled date in `test-case.org'. Thanks for the report and the detailed analysis. I pushed a fix for this problem, could you pull and check if the problem is fixed for you? Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgpCnXKGZRebK.pgp Description: PGP signature
Re: [O] using variables in org text
On 16 February 2012 17:05, Thomas S. Dye t...@tsdye.com wrote: Rainer M Krug r.m.k...@gmail.com writes: Hi I have defined a variable as follow #+property: var DC=/home/rkrug/tmp/CLUSTER and I am using this path quite often in source blocks (works nicely as expected) but also in org directly, e.g. * DC path is $DC$ The DC path $DC$ is pointing to a directory. Is it possible to use the variable DC in the text as well, so that $DC$ is replaced with the value of the variable DC as defined above? In other words: how can I tell org that on export, $DC$ stands for the value of the variable DC? Cheers, Rainer PS: I know that $...$ is for LaTeX math mode Aloha Rainer, Here is a way that works for me. * Krug How to have a variable show up in text. #+name: printDC #+BEGIN_SRC emacs-lisp :results silent raw :exports none (print DC) #+END_SRC In the text call_printDC() is shown. Great idea - I will try it as soon as I am back at work. Cheers, Rainer hth, Tom -- Thomas S. Dye http://www.tsdye.com -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax (F): +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug
[O] worg wrong link?
In http://orgmode.org/worg/org-tutorials/non-beamer-presentations.html#sec-3 the 'here' (emacs code available here under Code and usage for org-export-as-s5) points to http://gitweb.adaptive.cs.unm.edu/org-S5.git/blob_plain/HEAD:/org-export-as-s5.el (where theres nothing about emacs/org mode) Should probably point here https://github.com/eschulte/org-S5??
Re: [O] anyway to create link to a line number in a file
On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html
Re: [O] Freemind export and import question/suggestion (newlines problem)
Johnny yggdra...@gmx.co.uk writes: Hi, I am trying out the excellent freemind exporter/importer and am running into issues with long node names and newlines. 1) Exporting org to freemind (node name length limitation?) In org-mode, none of the headlines can contain newlines, so occasionaly they get a bit long. This is not a (big) issue in org, but when exorting to freemind, I would like to limit the names to a maximum length, as the mindmap display in freemind need reasonably short node names to give a clear overview. It would be great to be able to do this with the exporter by setting a variable / giving a prefix number. 2) Importing freemind to org (remove newlines?) For now, I have manually split some lines in freemind to get a good mindmap, but then the issue is that when re-importing to org, the headlines are including the newline, hence the org-mode headings are broken. This may be easily done by replacing all newlines in the node name when importing, but being Lisp challenged I cannot find where in org-freemind.el this replacement should be done. 3) Importing freemind to org (centered nodes) I noticed also that nodes in freemind that were centered broke the org import fairly bad by splitting the node name over several lines with blank lines in between. And none of the textual lines were actually displayed as a headline. I don't really have an issue with this, as I can do without changing from the default alignment in freeming, but thought I'd include it in this writeup. If anyone has an idea of how to solve this or could point me in the right direction that would be great! Of course, right after posting I found the setting in freemind to limit node length [1]. The solution for now is to avoid using newlines altogether in the node names. This means all node levels will have the same length, but this is ok for me. Sorry for the noise! Footnotes: [1] Under 'Tools - Preferences' under the tab 'Defaults' there's a 'Max Node Width' that can be set. -- Johnny
Re: [O] bug / regression: C-x C-s is broken in org-edit-special
Thanks for posting this workaround. I've just pushed up a change which rebinds this key in org-src-mode. I don't know why the binding was ever removed in the first place. Best, Leo Alekseyev dnqu...@gmail.com writes: In case anyone is curious, C-x C-s functionality in org-edit-special can be easily restored via (define-key org-src-mode-map \C-x\C-s 'org-edit-src-save) On Thu, Feb 9, 2012 at 4:49 PM, Leo Alekseyev dnqu...@gmail.com wrote: Previously, C-x C-s in an org-edit-special buffer (invoked via C-') would save the underlying org buffer (provided (setq org-src-window-setup (quote current-window)) was set; it was buggy with other settings, see http://thread.gmane.org/gmane.emacs.orgmode/50979 for discussion). Currently, C-x C-s prompts to save the temporary source edit buffer in a new file, which is almost certainly not what the user intends. I hope someone can look into this, C-x C-s shouldn't be broken in any context. This broke some time between commit fc93b6f34071703d5a154a51540f3f4e3f15b8a2 (Jan. 18) and this week, _possibly_ as a result of the change ensuring that buffer-file-name is nil in temporary org-src buffers. Buffer-file-name not being nil in a temp buffer is incorrect behavior, but in this context having C-x C-s not working is a much worse behavior, so perhaps that change ought to be reverted if it's the culprit. --Leo -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] requesting help debugging tangle on windows
Unfortunately I don't have access to a windows machine for testing of tangle behavior. Before we delve deeper, could you confirm two things. 1. It sounds as though you are not using the latest version of Org-mode from git. Please upgrade to the latest -- which should also get you the latest ob-clojure.el so you don't have to evaluate the snippet posted below. There are instructions for keeping current with org development at http://orgmode.org/worg/org-faq.html#Keeping-current. 2. Try to reproduce the problem using emacs -Q which will launch emacs without any personal configuration. That way we can see if this windows issue is someone related to your config, or is general. Thanks, Andrew Cheng ache...@gmail.com writes: Tangle works in my linux environment but doesn't quite work in my windows environment. Here's my org file. It defines a code snippet named block and then has a tangle section that refers to block. Tangle results in a file with two blank lines in my windows environment. #+name: block #+begin_src clojure :results silent (+ 2 3) #+end_src #+begin_src clojure :tangle ../src/tmp.clj :results silent :exports none :noweb yes block #+end_src But --- If my tangle section has regular code in it instead of referring to other named blocks then the resulting file after tangle has the code you'd expect. Below is my org setup. The *Messages* buffer doesn't contain any interesting error messages. What can I do to find out what's going on? I did evaluate the following snippet to get C-c C-c to properly evaluate a clojure code block successfully on my machine. It didn't affect the issue of tangling. Just thought I'd mention it to be thorough. The snippet is from Eric Schulte. I thought that by deleting my elpa org folder and starting emacs again I'd get the latest (with his fix) but I discovered that I still needed to run this snippet to get C-c C-c to work. Thanks in advance for any help! (defun org-babel-execute:clojure (body params) Execute a block of Clojure code with Babel. (require 'slime) (with-temp-buffer (insert (org-babel-expand-body:clojure body params)) ((lambda (result) (let ((result-params (cdr (assoc :result-params params (if (or (member scalar result-params) (member verbatim result-params)) result (condition-case nil (org-babel-script-escape result) (error result) (slime-eval `(swank:eval-and-grab-output ,(buffer-substring-no-properties (point-min) (point-max))) (cdr (assoc :package params)) Emacs : GNU Emacs 24.0.50.1 (i386-mingw-nt5.1.2600) of 2011-09-03 on SHAN-PC Package: Org-mode version 7.7 current state: == (setq org-export-blocks '((src org-babel-exp-src-block nil) (comment org-export-blocks-format-comment t) (ditaa org-export-blocks-format-ditaa nil) (dot org-export-blocks-format-dot nil)) org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code) org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-babel-pre-tangle-hook '(save-buffer) org-occur-hook '(org-first-headline-recenter) org-export-interblocks '((lob org-babel-exp-lob-one-liners) (src org-babel-exp-inline-src-blocks)) org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-elisp-link-function 'yes-or-no-p org-export-latex-format-toc-function 'org-export-latex-format-toc-default org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-export-first-hook '(org-beamer-initialize-open-trackers) 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-from-is-user-regexp nil org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc org-beamer-auto-fragile-frames org-beamer-place-default-actions-for-lists) org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars) org-metadown-hook '(org-babel-pop-to-session-maybe) org-src-mode-hook '(org-src-babel-configure-edit-buffer
Re: [O] Setting multiple variables for code blocks in one property drawer
Viktor Rosenfeld listuse...@googlemail.com writes: Hi Eric, thanks for your input. I just pulled the latest code from git and while my original example works, the following does not: :PROPERTIES: :var: foo=1 :var+: bar=2 :var+: baz=3 :END: #+BEGIN_SRC sh echo foo: $foo echo bar: $bar echo baz: $baz #+END_SRC Thanks for reporting, I've just pushed up a fix for this bug. There also appears to be a difference between quoted and unquoted values and commatas. E.g. the following works :PROPERTIES: :var: foo=1 :var+: bar=2, baz=3 :END: #+BEGIN_SRC sh echo foo: $foo echo bar: $bar echo baz: $baz #+END_SRC If I remove the quotes around 2 I get the following error: ad-Orig-error: reference '2,' not found in this buffer On the other hand, the following version does not produce an error, but the value of $baz is not set. :PROPERTIES: :var: foo=1 :var+: bar=2, :var+: baz=3 :END: #+BEGIN_SRC sh echo foo: $foo echo bar: $bar echo baz: $baz #+END_SRC Yes, the comma results in the 2 not being parsed as a number, which means that it will then try to be understood by Babel (which thinks first of a reference unless the value is wrapped in quotes indicating it is a string). The moral is to not give references purely numerical names. Best, Cheers, Viktor Eric Schulte wrote: Viktor Rosenfeld listuse...@googlemail.com writes: Hi, after following the discussion about the new BABEL syntax I was under the impression that the following should work to set two variables in one PROPERTIES drawer: :PROPERTIES: :var: foo=1 :var+: bar=2 :END: However, the definition of bar is ignored. It turns out that there can only be one :var: or :var+: entry in a drawer and the latter can only be used to append to inherited entries, but not to those defined in the same drawer. Is this the intended behavior? How would I define multiple variables in a drawer (except for putting them all on one line)? Thanks, Viktor You are correct, I believe this is a bug. I've just pushed up a fix, so your example above should now work as expected. Thanks, -- Eric Schulte http://cs.unm.edu/~eschulte/ -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] Incomplete syntax highlight for C++ code
Hi Zhiqiu,
First, I would look at the actual text of the exported html code
example. It likely contains css code specifying how to fontify many
elements of the code block (e.g., on my system your example exports to
the following html [1]). You can then add css to your org-mode file
specifying what colors to use for each code class.
Also, see the `org-export-htmlize-output-type' variable.
Best,
Zhiqiu Kong breaddaw...@gmail.com writes:
Hi,
I am a new org-mode user and am trying to take notes with it. As I put
source code into my codes a lot, I love the integration with htmlize pretty
much. However, I found the syntax highlight on exported html file is not
as what I see in Emacs. To be more specific, only comments and string
literals are colored, which is shown in http://img.ly/dXTK. And here is
what is looks like in Emacs: http://img.ly/dXU6.
Actually, what I expected is the keywords such as int, return should at
least be colored, which is as introduced by emacs-fu (
http://emacs-fu.blogspot.com/2009/05/writing-and-blogging-with-org-mode.html
).
I checked out the latest org-mode (Org-mode version 7.8.03
(release_7.8.03.336.gdf0a9) ) and htmlize (for git repository), but the
problem remains. Moreover, here is my project setting:
(setq org-publish-project-alist
'((note-org
:base-directory ~/Docs/notes/org/
:publishing-directory ~/Docs/notes/html/
:htmlized-source t
:base-extension org
:sub-superscript nil
:recursive t
:publishing-function org-publish-org-to-html
;; :org-export-htmlize-output-type css
:html-extension html
:auto-index t
:index-filename index.org
:index-title My Notes
:link-home index.html
;; :section-numbers nil
:style link rel=\stylesheet\
href=\css/worg.css\
type=\text/css\/)
(note-static
:base-directory ~/Docs/notes/org/
:publishing-directory ~/Docs/notes/html/
:recursive t
:base-extension
css\\|js\\|png\\|jpg\\|gif\\|pdf\\|mp3\\|swf\\|zip\\|gz\\|txt\\|el
:publishing-function org-publish-attachment)
(My Notes
:components (note-org note-static)
:auto-sitemap t
:auto-index t
)))
Any suggestion on how to debug and fix this problem? Or this is normal?
Thanks a lot!!
Thanks,
-Zhiqiu
Footnotes:
[1] pre class=src src-c++span style=color: #ff;int/span span
style=color: #ffc66d;main/span(){
span style=color: #6d9cbe;std/span::cout lt;lt; span style=color:
#a5c261;hello/span lt;lt; span style=color:
#6d9cbe;std/span::endl;
}
/pre
--
Eric Schulte
http://cs.unm.edu/~eschulte/
Re: [O] Babel add comma in front of my '*'
Daniel Dehennin daniel.dehen...@baby-gnu.org writes: Hello, I tryed to babelize an iptables-save file and file to restore it. Babel put a comma in front of my '*', in the following, the '*mangle' became ',*mangle': #+begin_src text # Generated by iptables-save v1.4.4 on Wed Feb 15 10:16:05 2012 ,*mangle :PREROUTING ACCEPT [0:0] :INPUT ACCEPT [0:0] :FORWARD ACCEPT [0:0] :OUTPUT ACCEPT [0:0] :POSTROUTING ACCEPT [0:0] COMMIT #+end_src Regards. Yes, Org-mode does the above to protect the rest of the file from the possible Org-mode syntax in the code block. However if you then use this text (e.g., through tangling or reference from another code block) the comma will be automatically removed, so it shouldn't cause you any problems. Best, -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] How to activate pre.src in org-babel html output? Can only get class=example
Hi Giovanni, When I export the following code block , | #+begin_src emacs-lisp :exports both | :foo | #+end_src ` it generates the following HTML. , | pre class=src src-emacs-lispspan style=color: #d0d0ff;:foo/span | /pre | | | pre class=example | :foo | /pre ` My guess is that during export you get a message along the lines of htmlize is required for export. Try explicitly loading htmlize.el (in the contrib/lisp directory of org) and then re-exporting and you should get the desired output. Best, Giovanni Moretti g.more...@massey.ac.nz writes: Using org-babel, I'm wanting to output Python fragments along with the resultant output to HTML. That bit's easy, and the following works as expected: #+options: toc:nil num:nil * Using Python interactively Any commands typed into the console executed immediately. #+begin_src python :results output :exports both print 355/113 print 17/2 print 17/2.0 #+end_src python However, although I find references to various styling mechanisms (e.g *pre.src*) in the orgmode documentation, I can't find any way to get any more CSS selectors on both the src and output blocks. The only one that ever appears is example as shown here: pre class=exampleprint 355/113 print 17/2 print 17/2.0 /pre pre class=example 3 8 8.5 /pre /div If I can find out how to make pre.src appear (hopefully only on the source block) , then I can change the background colours or fonts to make the output visibly distinct from the source code. The full HTML output I get is at http://dl.dropbox.com/u/2671560/org-py-babel.html contains lots of CSS selectors, and I can easily include my my own using #+STYLE lines, but I need some way to differentiate the two blocks. I'm using Emacs 23.1.50.1 and the lastest orgmode commit b5082974c83a3a4838db86025edce857b11e5847 (Fri Feb 3 15:18:05 2012 +0100) Any tips? Thanks Giovanni -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] [PATCH] org-capture, removing whitespace from new captures
Hi Bastien, Hi Paul, At Sat, 29 Oct 2011 14:08:52 +0200, Bastien wrote: Hi Paul, Paul emacs-orgm...@lookmumnohands.net writes: In fact adding whitespace-cleanup to org-capture-before-finalize-hook was what I tried first, but it didn't do what I wanted. This hook is called _after_ the buffer is widened - making whitespace-cleanup operate on the _entire_ buffer, not just the newly added capture. I believe the patch is still required - I should have explained org-capture-before-finalize-hook's behaviour more explicitly in my original submission. I'm willing to apply this patch -- could you provide it with a well-formatted ChangeLog entry? Instead of adding the :whitespace-cleanup property to the template definition (what requires you to specify e.g. whitespace-cleanup in every single template) why not define a new hook that is run before the finalization starts? I.e. with capture buffer current and still narrowed. See attached patch that such a hook called `org-capture-prepare-finalize-hook'. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de From f737fbdc6ed1d45d8629eb1347e8c8d828f77e32 Mon Sep 17 00:00:00 2001 From: David Maus dm...@ictsoc.de Date: Sat, 18 Feb 2012 16:41:30 +0100 Subject: [PATCH] New hook: Run before the finalization process starts * org-capture.el (org-capture-prepare-finalize-hook): New hook. Run before the finalization process starts. (org-capture-finalize): Run new hook. --- lisp/org-capture.el |9 + 1 files changed, 9 insertions(+), 0 deletions(-) diff --git a/lisp/org-capture.el b/lisp/org-capture.el index d77415b..e3bd9f7 100644 --- a/lisp/org-capture.el +++ b/lisp/org-capture.el @@ -347,6 +347,13 @@ widened to the entire buffer. :version 24.1 :type 'hook) +(defcustom org-capture-prepare-finalize-hook nil + Hook that is run before the finalization starts. +The capture buffer is current and still narrowed. + :group 'org-capture + :version 24.1 + :type 'hook) + ;;; The property list for keeping information about the capture process (defvar org-capture-plist nil @@ -530,6 +537,8 @@ captured item after finalizing. (buffer-base-buffer (current-buffer))) (error This does not seem to be a capture buffer for Org-mode)) + (run-hooks 'org-capture-prepare-finalize-hook) + ;; Did we start the clock in this capture buffer? (when (and org-capture-clock-was-started org-clock-marker (marker-buffer org-clock-marker) -- 1.7.2.5 pgpnFSAWSudo2.pgp Description: PGP signature
[O] [PATCH] manual: fix references to Calc manual
* doc/org.texi: Decapitalize file name in references to Calc manual.
On a case sensitive file system the references from the HTML Org
manual (e. g. the link href=Calc.html#Embedded-Mode or
href=../Calc/Embedded-Mode.html#Embedded-Mode) to the HTML Calc
manual (e. g. the file calc.html or calc/Embedded-Mode.html) do not
match.
The info browser did not suffer from this doc bug in org.texi,
it seems to be case-insensitive regarding link target file name.
Michael
From d4bbda362fe1efc3dd36e5612f9749d91db27e08 Mon Sep 17 00:00:00 2001
From: Michael Brand michael.ch.br...@gmail.com
Date: Sat, 18 Feb 2012 17:03:36 +0100
Subject: [PATCH] manual: fix references to Calc manual
* doc/org.texi: Decapitalize file name in references to Calc manual.
On a case sensitive file system the references from the HTML Org
manual (e. g. the link href=Calc.html#Embedded-Mode or
href=../Calc/Embedded-Mode.html#Embedded-Mode) to the HTML Calc
manual (e. g. the file calc.html or calc/Embedded-Mode.html) do not
match.
---
doc/org.texi | 13 +++--
1 files changed, 3 insertions(+), 10 deletions(-)
diff --git a/doc/org.texi b/doc/org.texi
index 4bc912c..7a727c5 100644
--- a/doc/org.texi
+++ b/doc/org.texi
@@ -1967,13 +1967,7 @@ @section The Orgstruct minor mode
Org comes with a fast and intuitive table editor. Spreadsheet-like
calculations are supported using the Emacs @file{calc} package
-@ifinfo
-(@pxref{Top,Calc,,Calc,Gnu Emacs Calculator Manual}).
-@end ifinfo
-@ifnotinfo
-(see the Emacs Calculator manual for more information about the Emacs
-calculator).
-@end ifnotinfo
+(@pxref{Top, Calc, , calc, Gnu Emacs Calculator Manual}).
@menu
* Built-in table editor:: Simple tables
@@ -2533,9 +2527,8 @@ @subsection Formula syntax for Calc
non-standard convention that @samp{/} has lower precedence than
@samp{*}, so that @samp{a/b*c} is interpreted as @samp{a/(b*c)}.} Before
evaluation by @code{calc-eval} (@pxref{Calling Calc from
-Your Programs,calc-eval,Calling Calc from Your Lisp Programs,Calc,GNU
+Your Programs, calc-eval, Calling Calc from Your Lisp Programs, calc, GNU
Emacs Calc Manual}),
-@c FIXME: The link to the Calc manual in HTML does not work.
variable substitution takes place according to the rules described above.
@cindex vectors, in table calculations
The range vectors can be directly fed into the Calc vector functions
@@ -14897,7 +14890,7 @@ @subsection Packages that Org cooperates with
been installed properly. As of Emacs 22, Calc is part of the Emacs
distribution. Another possibility for interaction between the two
packages is using Calc for embedded calculations. @xref{Embedded Mode,
-, Embedded Mode, Calc, GNU Emacs Calc Manual}.
+, Embedded Mode, calc, GNU Emacs Calc Manual}.
@item @file{constants.el} by Carsten Dominik
@cindex @file{constants.el}
@cindex Dominik, Carsten
--
1.7.4.2
Re: [O] [PATCH] Fix old Babel syntax in library-of-babel.org
Applied, Thanks Sebastien Vauban wxhgmqzgw...@spammotel.com writes: From 3569c16e1d4270e6004441d8cdcc92801b3a01cd Mon Sep 17 00:00:00 2001 From: Sebastien Vauban s...@mygooglest.com Date: Thu, 16 Feb 2012 15:50:17 +0100 Subject: [PATCH] Fix old Babel syntax --- contrib/babel/library-of-babel.org |2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diff --git a/contrib/babel/library-of-babel.org b/contrib/babel/library-of-babel.org index ecad0fe..0098e72 100644 --- a/contrib/babel/library-of-babel.org +++ b/contrib/babel/library-of-babel.org @@ -143,7 +143,7 @@ normal document. #+end_src example usage -: #+source: fibs +: #+name: fibs : #+begin_src emacs-lisp :var n=8 : (flet ((fib (m) (if ( m 2) 1 (+ (fib (- m 1)) (fib (- m 2)) : (mapcar (lambda (el) (list el (fib el))) (number-sequence 0 (- n 1 -- 1.7.5.1 Best regards, Seb -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] [0][babel][R] Undesired conversion of integers to floats in R code block output
Daniel Drake silopho...@gmail.com writes:
Hi All,
I'm using R in org-mode/babel to analyze data from a psychological
study. The subjects in this study are identified by nine digit integers
(e.g., 987654321) that I treat as strings (or factors) in my R data
frames.
Tables output by an R code block that contain these subject IDs are
not formatted properly: the subject IDs seem to be treated as numbers
and a decimal point and a trailing zero are appended. For example,
what should be
| subj.id |
|---|
| 987654321 |
becomes
| subj.id |
| 987654321.0 |
(I've included real, self-contained code below.)
When I write the data frames directly to a file from within the R code
block (using a write.table function call that mimics the one in
ob-R.el), the integer IDs are preserved; but when code from ob-R.el
writes them out, the values get reformated as floats.
I've noticed that eight digit integers are not modified in the same
way, which makes me wonder if there is a 'digits' threshold I could
modify to prevent this from happening.
I've pretty much ruled out the possibility that this transformation
occurs in R; however I'm not proficient enough in elisp to follow the
operations that happen after the data frame is written to a file in
the org-babel-R-write-object-command.
Any pointers to help me figure this out would be very appreciated!
(I've seen this thread:
http://comments.gmane.org/gmane.emacs.orgmode/31373, but do not know
if the conversion to calc has been made already or if it is the source
of the problem.)
Hi Dan,
When I launch Emacs without any personal configuration (emacs -Q),
evaluate ob-R.el to add R support, and then execute your code blocks I
get the following behavior.
* Test
** table as generated by org-mode/babel
#+name: make
#+begin_src R :results value :colnames yes
temp - data.frame('A'=c('987654321'),'B'=c('98765432'))
## -- this call mimics the one in ob-R.el
write.table(temp,file='test_r.tsv',sep='\t',na='nil',row.names=FALSE,col.names=TRUE,quote=FALSE)
temp
#+end_src
#+RESULTS: make
| A |B |
|---+--|
| 987654321 | 98765432 |
** table as generated by R directly
#+name: read
#+begin_src sh :results output
cat test_r.tsv
#+end_src
#+RESULTS: read
: A B
: 987654321 98765432
I would recommend installing the latest version of Org-mode from source
as that tends to fix many problems, and will at least ensure that we are
both working from the same code base moving forward. See
http://orgmode.org/worg/org-faq.html#Keeping-current
Best,
--
Eric Schulte
http://cs.unm.edu/~eschulte/
Re: [O] Babel add comma in front of my '*'
Eric Schulte eric.schu...@gmx.com writes: [...] Yes, Org-mode does the above to protect the rest of the file from the possible Org-mode syntax in the code block. However if you then use this text (e.g., through tangling or reference from another code block) the comma will be automatically removed, so it shouldn't cause you any problems. What about removing it during org-edit-special? My use is to org-edit-special the block, and use that overlay by cutpast and so on. Regards. -- Daniel Dehennin Récupérer ma clef GPG: gpg --keyserver pgp.mit.edu --recv-keys 0x6A2540D1 pgpeb8wKTRyZE.pgp Description: PGP signature
Re: [O] sqlite3 in org-babel
Daniel Clemente n142...@gmail.com writes: Have you tried using a sqlite code block? See ob-sqlite.el I didn't notice there were both ob-sql and ob-sqlite. It would be useful to mention sqlite inside ob-sql. Done. Perhaps they should be united? I believe there were reasons for keeping them separate. I'd rather not combine them without a full overview of both code files. I still prefer ob-sql for sqlite because it lets me pass the parameter :init /dev/null. That makes it NOT load my ~/.sqliterc (where I have a very verbose .tables). ob-sqlite does not have :init and therefore always stuffs that output into the results. From looking at the man page of sqlite, it seems you can do the same with ob-sqlite. Simply pass --init /dev/null to the sqlite command. This could be done e.g. with something like (org-babel-sqlite3-command sqlite3 --init /dev/null) Best, Daniel Clemente n142...@gmail.com writes: Hi, org-babel works well with sqlite3 if you add this (which I propose for inclusion): -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] anyway to create link to a line number in a file
I looked that section carefully and the whole manual briefly. I haven't found anything yet. That's why I am asking on the mailing list to see if anyone has some workaround. On Sat, Feb 18, 2012 at 9:03 AM, Sean O'Halpin sean.ohal...@gmail.com wrote: On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html -- Best, Zhenjiang
Re: [O] anyway to create link to a line number in a file
Not To Miss not.to.m...@gmail.com writes: I looked that section carefully and the whole manual briefly. I haven't found anything yet. That's why I am asking on the mailing list to see if anyone has some workaround. [[file:filename.txt::6]] jumps to line 6 of filename.txt for me. I don't know if this is documented... if not a documentation patch would be appreciated. Best, On Sat, Feb 18, 2012 at 9:03 AM, Sean O'Halpin sean.ohal...@gmail.com wrote: On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html -- Eric Schulte http://cs.unm.edu/~eschulte/
[O] Tangle only code block body
Hi all, Is there a way to tangle just the body of code blocks, without any header argurments? For example when I tangle this file # begin example # * test #+name: testplot #+begin_src R :results output graphics :file tmp.png :tangle tmp.R plot(1:10) #+end_src # end example # I get png(filename=tmp.png) plot(1:10) dev.off() but I want just plot(1:10) I've tried removing the %flag setting in org-babel-exp-code-template but it didn't seem to have any effect. Thanks for any pointers, Ista
Re: [O] [PATCH] org-capture, removing whitespace from new captures
Hi David and Paul, David Maus dm...@ictsoc.de writes: Instead of adding the :whitespace-cleanup property to the template definition (what requires you to specify e.g. whitespace-cleanup in every single template) why not define a new hook that is run before the finalization starts? I.e. with capture buffer current and still narrowed. Yes, I think this is more general, feel free to commit this. Thanks to you and to Paul for his neat suggestion! Best, -- Bastien
Re: [O] [PATCH] manual: fix references to Calc manual
Michael Brand michael.ch.br...@gmail.com writes: * doc/org.texi: Decapitalize file name in references to Calc manual. On a case sensitive file system the references from the HTML Org manual (e. g. the link href=Calc.html#Embedded-Mode or href=../Calc/Embedded-Mode.html#Embedded-Mode) to the HTML Calc manual (e. g. the file calc.html or calc/Embedded-Mode.html) do not match. The info browser did not suffer from this doc bug in org.texi, it seems to be case-insensitive regarding link target file name. Applied, thanks! -- Bastien
Re: [O] anyway to create link to a line number in a file
Sorry, I didn't make it more clear. I want to create a link to a specific line automatically, just as the command C-c l (org-store-link) to automatically create a link to the text of current line. Sometimes line number is more important for me to record. On Sat, Feb 18, 2012 at 12:11 PM, Eric Schulte eric.schu...@gmx.com wrote: Not To Miss not.to.m...@gmail.com writes: I looked that section carefully and the whole manual briefly. I haven't found anything yet. That's why I am asking on the mailing list to see if anyone has some workaround. [[file:filename.txt::6]] jumps to line 6 of filename.txt for me. I don't know if this is documented... if not a documentation patch would be appreciated. Best, On Sat, Feb 18, 2012 at 9:03 AM, Sean O'Halpin sean.ohal...@gmail.com wrote: On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html -- Eric Schulte http://cs.unm.edu/~eschulte/ -- Best, Zhenjiang
Re: [O] anyway to create link to a line number in a file
Not To Miss not.to.m...@gmail.com wrote: I looked that section carefully and the whole manual briefly. I haven't found anything yet. That's why I am asking on the mailing list to see if anyone has some workaround. On Sat, Feb 18, 2012 at 9:03 AM, Sean O'Halpin sean.ohal...@gmail.com wrote: On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html *Following* a link with a line number is no problem: org does that out of the box with a link like [[file:foo.txt::NNN][desc]] That is actually documented: (info (org) External links) The problem is to make sure org-store-link will actually store the line number (along with everything else) so that then org-insert-link can insert the link in the proper format. I don't think there is a function to do that out of the box for line numbers, but you can easily (for some value of easily) write your own. Look in (info (org)Adding hyperlink types) for some hints. Briefly, you write a function that checks whether it wants to deal with the link or not, and you add it to org-store-link-functions. I don't have the time to try it out right now, but I believe this should work for what you want. Nick
Re: [O] [PATCH] org-capture, removing whitespace from new captures
At Sat, 18 Feb 2012 18:19:49 +0100, Bastien wrote: Hi David and Paul, David Maus dm...@ictsoc.de writes: Instead of adding the :whitespace-cleanup property to the template definition (what requires you to specify e.g. whitespace-cleanup in every single template) why not define a new hook that is run before the finalization starts? I.e. with capture buffer current and still narrowed. Yes, I think this is more general, feel free to commit this. Thanks to you and to Paul for his neat suggestion! And... done. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgpEgAWNlmHwq.pgp Description: PGP signature
Re: [O] Babel add comma in front of my '*'
Daniel Dehennin daniel.dehen...@baby-gnu.org writes: Eric Schulte eric.schu...@gmx.com writes: [...] Yes, Org-mode does the above to protect the rest of the file from the possible Org-mode syntax in the code block. However if you then use this text (e.g., through tangling or reference from another code block) the comma will be automatically removed, so it shouldn't cause you any problems. What about removing it during org-edit-special? My use is to org-edit-special the block, and use that overlay by cutpast and so on. Regards. I've just pushed up a fix so that commas will be stripped when org-edit-special is used. Best, -- Eric Schulte http://cs.unm.edu/~eschulte/
[O] get all todo items as lisp list
Hi, Given a todo list in an org file, is there already a function, that converts this list to an elisp list, that contains at least heading, deadline and properties? Example input: --8---cut here---start-8--- * TODO todo-test DEADLINE: 2012-04-19 Thu 13:33 :PROPERTIES: :notify: notify-test :END: * TODO todo-test2 DEADLINE: 2012-05-20 Sun 16:66 :PROPERTIES: :notify: notify-test2 :END: --8---cut here---end---8--- Example output: --8---cut here---start-8--- ((file test.org heading TODO todo-test deadline (111 222 333) properties (notify notify-test)) (file test.org heading TODO todo-test2 deadline (123 456 789) properties (notify notify-test2))) --8---cut here---end---8--- Or are there functions, that could help me, to do it myself? (I've tried with `org-agenda-get-day-entries', but without success...) TIA for any help! -- Peter
Re: [O] Temp files from testing are permanent...
Achim Gratz strom...@nexgo.de writes: Olaf Meeuwissen olaf.meeuwis...@avasys.jp writes: Successful tests can clean up after themselves but failed tests should not so you can debug. The decision to remove these files should be left to whoever runs the test suite. That implies that even successful tests don't really have to bother cleaning up after themselves. As hinted at in another post yesterday, I did browse the test suite code briefly. The tests try to clean up after themselves, sort-of Sorry to come late to this discussion. The tests should clean up all temporary files and buffers left during their execution. There has been some work on this in the last month or two so hopefully the situation has improved. — the trouble is that they leave tangled files and results produced during suceesful tests. It will be up to the authors of individual tests to remove tangled and exported files. Ideally we can patch each test to clean up after itself. Perhaps we should provide a test macro which accepts a list of file names and optionally removes them if the test exists successfully. e.g., (org-test-with-cleanup '(exported.html tangled.sh etc...) ...test body...) If you use `make check` to run the test suite, you can easily set TMPDIR via the TESTS_ENVIRONMENT Makefile variable (assuming that that variable is taken into account when making unique file names). Something like Yes, that's about the same conclusion I also reached. Not sure when I'll have time to implement and test it. Even if the above is implemented this sounds like a good safeguard. Thanks, Regards, Achim. -- Eric Schulte http://cs.unm.edu/~eschulte/
[O] Displaying or linking to definitions of terms?
I've done a fair amount of reading (and-rereading) the manual, and searching around, but my search skills are failing me and org-mode is flexible enough that I figure that someone has either done this, or there's something that makes it unnecessary that I don't know of. I'd like to be able to write a definition of a term, and then be able to jump to that definition, or see that definition in some way in buffers where the term occurs. Preferably on a file can specify a file with term definitions or a global scale, but even per-file period would be awesome. I imagine something like a block. In pseudo-org-code: #+begin_definition :term elegant pleasingly graceful and stylish in appearance or manner; pleasingly ingenious and simple. #+end_definition If there's a way for me to acheive the goal of find the definition for this term in a this is already idiomatic-org type of way, I'd love to hear it. If anyone has done something similar, I'd love to hear about it. If not, I'd love to implement it, and would be immensely grateful for any high-level pointers to entry-points for implementation, whether functions or code files or whatnot. Thanks for your time, and for all the collective effort put into this amazingly useful peice of software.
Re: [O] A manuscript on reproducible research introducing org-mode
Samuel Wales samolog...@gmail.com writes: As a followup to my last comment, this explains how Stapel fooled almost everybody and kept raw data hidden: http://chronicle.com/blogs/percolator/the-fraud-who-fooled-almost-everyone/27917 And NYT Fraud Case Seen as a Red Flag for Psychology Research which has a raw data take: http://www.nytimes.com/2011/11/03/health/research/noted-dutch-psychologist-stapel-accused-of-research-fraud.html Thanks for the videos, Stephen, I will check them out. I have been running across scads of fraud stories and interesting studies on conflict of interest, reliability of research results, etc. It's all over the place, just scattered and nobody pays much attention, perhaps not wanting to believe it. Reproducible research aims directly at this stuff. Chapeau! Samuel I just ran across this article on reproducible research that some of you might find interesting. http://journal.r-project.org/archive/2011-2/RJournal_2011-2_Lundholm.pdf All the best, Tom -- Thomas S. Dye http://www.tsdye.com
Re: [O] android mobile org question on capture
Hi Renato, I'm the maintainer of MobileOrg for Android. Regarding #1 this seems like an org-mode thing and I'm not too sure... usually I just look at these and file them manually, but this could get untenable if you have a lot of content on #2 I think we have it solved here: https://github.com/matburt/mobileorg-android/issues/168 and it will be available in the next version (0.8.4+) Thanks :) On Fri, Feb 17, 2012 at 9:24 AM, Renato renn...@gmail.com wrote: Hi, I have finally set up mobile org on my android phone, with calendar sync, and like it very much. Regarding the capture functionality, is it (or will it be) possible to: 1) define wich file and under which header the TODOs get written to. I have a notes.org file with Todo section where I store all my generic TODOs... alternativly I guess I could set up an automated refile when calling org-mobile-pull 2) define SCHEDULED and DEADLINE for the note. This would also be handy because captured notes would appear right away in my android calendar, without having to get to my pc, org-mobile-pull, add a deadline, refile, and finally org-mobile-push. I just upgraded from 0.8.0 to 0.8.3 cheers and a big thank you to who is writing this software, renato
Re: [O] android mobile org question on capture
On Sat, 18 Feb 2012 13:28:17 -0500 Matthew Jones bsdmatb...@gmail.com wrote: Hi Renato, I'm the maintainer of MobileOrg for Android. Hi, Regarding #1 this seems like an org-mode thing and I'm not too sure... usually I just look at these and file them manually, but this could get untenable if you have a lot of content uh yeah, having used it for a few days I realised it's no big fuss as I thought it would be on #2 I think we have it solved here: https://github.com/matburt/mobileorg-android/issues/168 and it will be available in the next version (0.8.4+) great!! Thanks :) thanks to you, again ;) cheers, renato
Re: [O] Temp files from testing are permanent...
Eric Schulte eric.schu...@gmx.com writes: It will be up to the authors of individual tests to remove tangled and exported files. Ideally we can patch each test to clean up after itself. Perhaps we should provide a test macro which accepts a list of file names and optionally removes them if the test exists successfully. e.g., (org-test-with-cleanup '(exported.html tangled.sh etc...) ...test body...) Currently those files would have inpredictable names AFAICS, which would defeat that purpose. I'm not sure where to do this, but it occurs to me that it would be easier if those files only had a unique prefix that didn't change for each invocation of the test suite (a timestamp would be OK, so it is easier to see which files you're looking at). If the files always had the same name, you would have to make sure that there was no collision, either with existing files or results from earlier tests, so that would be no good. If it is easier to always have the same names for the files, one could just make the test directory name unique. I think it is useful for debugging to be able to keep a few generation of tests around. Even if the above is implemented this sounds like a good safeguard. Safeguards are in place in my Makefile fork. Regards, Achim. -- +[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+ Waldorf MIDI Implementation additional documentation: http://Synth.Stromeko.net/Downloads.html#WaldorfDocs
[O] [PATCH] Avoid some warnings about `assignment to free variable'
* lisp/org.el, lisp/org-pcomplete.el: Add some `defvars' to avoid warnings about `assignment to free variable'. TINYCHANGE --- lisp/org-pcomplete.el |5 + lisp/org.el |2 ++ 2 files changed, 7 insertions(+), 0 deletions(-) diff --git a/lisp/org-pcomplete.el b/lisp/org-pcomplete.el index c475bcc..7a4dc0d 100644 --- a/lisp/org-pcomplete.el +++ b/lisp/org-pcomplete.el @@ -50,6 +50,9 @@ :tag Org :group 'org) +(defvar org-drawer-regexp) +(defvar org-property-re) + (defun org-thing-at-point () Examine the thing at point and let the caller know what it is. The return value is a string naming the thing at point. @@ -247,6 +250,8 @@ This needs more work, to handle headings with lots of spaces in them. lst)) (substring pcomplete-stub 1))) +(defvar org-drawers) + (defun pcomplete/org-mode/drawer () Complete a drawer name. (let ((spc (save-excursion diff --git a/lisp/org.el b/lisp/org.el index a81f7fc..45d4b6a 100644 --- a/lisp/org.el +++ b/lisp/org.el @@ -12778,6 +12778,7 @@ ACTION can be `set', `up', `down', or a character. Tags +(defvar tags-list) (defvar org-agenda-archives-mode) (defvar org-map-continue-from nil Position from where mapping should continue. @@ -14957,6 +14958,7 @@ So these are more for recording a certain time/date. (defvar org-ans2) ; dynamically scoped parameter (defvar org-plain-time-of-day-regexp) ; defined below +(defvar org-read-date-inactive) (defvar org-overriding-default-time nil) ; dynamically scoped (defvar org-read-date-overlay nil) -- 1.7.3.4
Re: [O] [PATCH] Avoid lisp error with (org-deadline nil +1d)
On Thu, Nov 24 2011, Nick Dokos wrote: Are they free variable warnings? If so, you now know how to fix them: go wild :-) All right, done so... ;) -- Peter
Re: [O] Bug: [Babel] sqlite if: End of file during parsing
Philip Rooke p...@yax.org.uk writes: Eric Schulte eric.schu...@gmx.com writes: Does the following work with the addition of :results scalar? Yes, there is no error although the format of the result is different to the one database line query or the equivalent shell command. This is what happens for me: #+begin_src sqlite :db ob-bug.db :results output scalar select f_name || || l_name from person; #+end_src #+results: : Joe Bloggs : Fred Smith Hi Phil, Thanks for the detailed reproduction information in your original email, it made this issue much easier to solve. I've just pushed up a fix, please let me know if the problem continues. Best, -- Eric Schulte http://cs.unm.edu/~eschulte/
Re: [O] Updating the Babel section of Worg
t...@tsdye.com (Thomas S. Dye) writes: Hi Eric, I pushed a draft of the revised LaTeX language section to Worg (http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html). Please take a look and edit as necessary. Too often I understand these things partially! Everything looks great to me. Thanks for the contribution! If Andreas Leha is reading this it would be good to take a look at my description of the ImageMagick facility. I tried to stick closely to the sources, but might have strayed. All the best, Tom Eric Schulte eric.schu...@gmx.com writes: t...@tsdye.com (Thomas S. Dye) writes: Hi Eric, I've attached a first draft of a template for review and revision. It is heavily influenced by John Hendy's terrific gnuplot page. I believe it incorporates the points in your outline. Feel free to edit as appropriate. Looks great to me. I made a small change, and I've just pushed it up to worg and linked to it from the languages page. We can continue to improve this template as needed on worg although I think it is already in very good shape and ready for use. Thanks, All the best, Tom Eric Schulte eric.schu...@gmx.com writes: Hi Tom, t...@tsdye.com (Thomas S. Dye) writes: Hi Eric, Yes, this is overdue. I think your plan is a good one. Perhaps a few of the individual use cases could be moved to FIXME, instead? I'm thinking here of Feiming Chen's R setup and some of my contributions when I was experimenting writing LaTeX inside source code blocks. The authors could resurrect these as they see fit. I don't know what FIXME is, but if there is a way to keep the page in the worg git repository but remove it from the exported HTML then that sounds ideal. Hopefully, others will contribute use examples. My sense from reading the list is there are many interesting ones. I'd like it if Org mode users designed a template for the language specific pages. Currently, these seem to me a mixed bag and it would be good to regularize them. The below is a modified version of a template which can be found in a couple of the existing language tutorials, I think it serves as a good starting point. - Install and Setup - Instillation and configuration of software (e.g., the language itself) - Configuration of Emacs (e.g., activate language, set command path) - Examples - Common ways to use the language in an Org-mode document - Special cases - are there any language-specific header arguments - does the language support session evaluation - does the language support all result types - is the language different from most babel languages (e.g., C is compiled before execution, ditaa returns files, etc...) It would also be nice to have one for each of the supported languages. There are 11 language specific pages now, which leaves quite a few languages under-documented. (length org-babel-load-languages) ;; = 27 ls org-contrib/babel/languages/ob-doc-*|wc -l # = 11 It looks like we have at least 16 more to go before we hit full language coverage. Perhaps we should use the empty cells in the documentation column in the languages table at [1] as a sign up space for volunteers who would be willing to write a brief tutorial demonstrating usage of Org-mode with their favorite language. Moving forward this is likely something we could request of the contributors of new languages. Also, once the template above is finalized it should be posted on worg and linked to through the languages page. I'll be happy to work on this as I can. Great, I don't anticipate having time to put towards this, although I'll be happy to help troubleshoot where I can. Cheers, All the best, Tom Eric Schulte eric.schu...@gmx.com writes: Thanks for raising this point. The bulk of the content in the Babel portion of worg is fairly old, predating the syntax standardization efforts this fall. I've just pushed some minor updates to the main babel pages, but updating the language-specific tutorials and the individual use cases will be a much larger effort. I'm not sure how to proceed. One option would be to go through and add a [uses deprecated syntax] tag to the top of each such page, which could be removed after the page has been checked and possibly updated to ensure consistency with the latest syntax. Given that the Babel syntax will not be changing significantly moving forward now would be a good time to do such a review. Ideally this could be completed before the release of Emacs 24 in a couple of months. Any other ideas for update/reorganization or volunteers? Cheers, t...@tsdye.com (Thomas S. Dye) writes: Hi Riccardo, Thanks for the URL. Org mode has evolved since this article was written. It should probably be revised or taken off Worg. I've copied Eric Schulte, who is better able than me to determine the correct course of action here. In the meantime, an up-to-date
Re: [O] anyway to create link to a line number in a file
Nick Dokos nicholas.do...@hp.com wrote: Not To Miss not.to.m...@gmail.com wrote: I looked that section carefully and the whole manual briefly. I haven't found anything yet. That's why I am asking on the mailing list to see if anyone has some workaround. On Sat, Feb 18, 2012 at 9:03 AM, Sean O'Halpin sean.ohal...@gmail.com wrote: On Fri, Feb 17, 2012 at 4:54 PM, Not To Miss not.to.m...@gmail.com wrote: Hi all, I am reading a long text file and want to write down my notes with org-mode. I extremely would like to put the line numbers down along with my notes. Although there is a way to store a link for text search for the current line, I haven't found a way to create a link to a line number in the current buffer. Is there anyway to do that? Thanks Take a look at org-capture: http://orgmode.org/manual/Capture.html The problem is to make sure org-store-link will actually store the line number (along with everything else) so that then org-insert-link can insert the link in the proper format. I don't think there is a function to do that out of the box for line numbers, but you can easily (for some value of easily) write your own. Look in (info (org)Adding hyperlink types) for some hints. Briefly, you write a function that checks whether it wants to deal with the link or not, and you add it to org-store-link-functions. I don't have the time to try it out right now, but I believe this should work for what you want. Following up on this, the following seems to work, although you probably want to tweak the criterion of when you want *this* function to take care of links - this particular implementation only applies the line number treatment to links generated in the file named /path/to/the.file.txt and only that file: --8---cut here---start-8--- (defun org-file-lineno-store-link() (when (string-equal (buffer-file-name) /path/to/the.file.txt) (let* ((link (format file:%s::%d (buffer-file-name) (line-number-at-pos (org-store-link-props :type file :link link (add-hook 'org-store-link-functions 'org-file-lineno-store-link) --8---cut here---end---8--- Nick
Re: [O] get all todo items as lisp list
On Sun, Feb 19 2012, Peter Münster wrote: Hi, Given a todo list in an org file, is there already a function, that converts this list to an elisp list, that contains at least heading, deadline and properties? Example input: * TODO todo-test DEADLINE: 2012-04-19 Thu 13:33 :PROPERTIES: :notify: notify-test :END: * TODO todo-test2 DEADLINE: 2012-05-20 Sun 16:66 :PROPERTIES: :notify: notify-test2 :END: Example output: ((file test.org heading TODO todo-test deadline (111 222 333) properties (notify notify-test)) (file test.org heading TODO todo-test2 deadline (123 456 789) properties (notify notify-test2))) Or are there functions, that could help me, to do it myself? (I've tried with `org-agenda-get-day-entries', but without success...) Hi, If you load org-element.el from contrib/, I think the function `org-element-parse-buffer' does what you want (and probably a whole lot more). Eric -- GNU Emacs 24.0.93.1 (i686-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-02-16 on pellet Org-mode version 7.8.03 (release_7.8.03.362.g1cc2)
Re: [O] A manuscript on reproducible research introducing org-mode
t...@tsdye.com (Thomas S. Dye) writes: I just ran across this article on reproducible research that some of you might find interesting. http://journal.r-project.org/archive/2011-2/RJournal_2011-2_Lundholm.pdf On reproducible research, are you guys aware of the relatively recent project Knitr? Basically, it is a new Sweave which integrate (i) Sweave, (ii) TiKZDevice, (iii) cacheSweave, and (iv) code highlight into one very well-functioning package. It kind of works with Org, but not ideally¹. It might be nice to integrate it closer with Babel-R, as it just-worksᵀᴹ. –Rasmus Footnotes: ¹ http://yihui.name/knitr/demo/org/ -- Enought with the bla bla!
Re: [O] get all todo items as lisp list
Hi, Given a todo list in an org file, is there already a function, that converts this list to an elisp list, that contains at least heading, deadline and properties? Create the following interactive function. This functions exports Org file to a *pretty* lisp file. --8---cut here---start-8--- (defun org-export-as-lisp () (interactive) (or (featurep 'pp) (require 'pp)) (let ((out-file (concat (file-name-sans-extension (buffer-file-name)) .el))) (pp-display-expression (org-element-parse-buffer) *Org Data*) (with-current-buffer *Org Data* (write-file out-file nil --8---cut here---end---8--- I am attaching sample todo.org and and the todo.el file created by the above command. * TODO todo-test DEADLINE: 2012-04-19 Thu 13:33 :PROPERTIES: :notify: notify-test :END: * TODO todo-test2 DEADLINE: 2012-05-20 Sun 16:66 :PROPERTIES: :notify: notify-test2 :END: todo.el Description: todo.el Example output: ((file test.org heading TODO todo-test deadline (111 222 333) properties (notify notify-test)) (file test.org heading TODO todo-test2 deadline (123 456 789) properties (notify notify-test2))) Or are there functions, that could help me, to do it myself? (I've tried with `org-agenda-get-day-entries', but without success...) TIA for any help! --
Re: [O] [0][babel][R] Undesired conversion of integers to floats in R code block output
On 02/18/2012 08:23 AM, Eric Schulte wrote: Daniel Drakesilopho...@gmail.com writes: Hi All, I'm using R in org-mode/babel to analyze data from a psychological study. The subjects in this study are identified by nine digit integers (e.g., 987654321) that I treat as strings (or factors) in my R data frames. Tables output by an R code block that contain these subject IDs are not formatted properly: the subject IDs seem to be treated as numbers and a decimal point and a trailing zero are appended. For example, what should be | subj.id | |---| | 987654321 | becomes | subj.id | | 987654321.0 | (I've included real, self-contained code below.) When I write the data frames directly to a file from within the R code block (using a write.table function call that mimics the one in ob-R.el), the integer IDs are preserved; but when code from ob-R.el writes them out, the values get reformated as floats. I've noticed that eight digit integers are not modified in the same way, which makes me wonder if there is a 'digits' threshold I could modify to prevent this from happening. I've pretty much ruled out the possibility that this transformation occurs in R; however I'm not proficient enough in elisp to follow the operations that happen after the data frame is written to a file in the org-babel-R-write-object-command. Any pointers to help me figure this out would be very appreciated! (I've seen this thread: http://comments.gmane.org/gmane.emacs.orgmode/31373, but do not know if the conversion to calc has been made already or if it is the source of the problem.) Hi Dan, When I launch Emacs without any personal configuration (emacs -Q), evaluate ob-R.el to add R support, and then execute your code blocks I get the following behavior. I would recommend installing the latest version of Org-mode from source as that tends to fix many problems, and will at least ensure that we are both working from the same code base moving forward. See http://orgmode.org/worg/org-faq.html#Keeping-current Best, Hi Eric, First of all, thanks for your reply. Just to be safe, I nuked my org-mode directory and re-cloned from the git repository: I'm now at release_7.8.03.386.g2239d (I was at release_7.8.03-351-g47eb3 previously). Is there a more recent version? I also removed the org directory that came with the packaged version of emacs, just in case. I start emacs with the following options: $ emacs -Q -eval '(setq load-path (cons ~/share/emacs/site-lisp/org-mode/lisp load-path))' -eval (require 'ob-R) test.org I get the same behavior as before. I was a little puzzled when I saw this happen, as I've been working on this study for over a year in org and it's the first time I've seen this behavior. I went back and tried previous versions (e.g., 7.4), and now I see the same thing. I wonder if Arch (a rolling release linux distribution that tries to be close to the leading edge) has updated an underlying library that impacts the babel code in some odd way. (Granted, I don't see how this could be, as the emacs environment seems pretty well insulated from the underlying OS; PEBKAC just as likely.) In any event, since you can't reproduce the behavior (thanks again for trying), I don't expect it's anything you can fix. Maybe it will show up in other distributions as they update to more current versions. In the mean time, I'll try to improve my elisp skills and figure out where the extraneous formatting occurs. Best, Dan - GNU Emacs 23.4.1 (i686-pc-linux-gnu, GTK+ Version 2.24.9) of 2012-02-01 on shirley.hoetzel.info - Org-mode version 7.8.03 (release_7.8.03.386.g2239d)
