Re: [O] Integration of RefTeX and LaTeX export
Hi Nick,
thanks for this, but i cannot get it to work ...
I have started a vanilla emacs without any init file
(emacs -q), have loaded your snippet from a file and
evaluated the buffer. Again, the export-handler does
not get called. I am running Debian 6.0.4 and my emacs
is the one coming with it (see below).
I feel so stupid :-))
Andreas
M-x emacs-version says: GNU Emacs 23.2.1 (i486-pc-linux-gnu, GTK+ Version
2.20.0) of 2010-12-12 on raven, modified by Debian
M-x org-version says: Org-mode version 6.33x
Debian version is 6.0.4 (/etc/debian_version)
-Original Message-
From: Nick Dokos [mailto:nicholas.do...@hp.com]
Sent: Fri 2/17/2012 6:31 PM
To: Andreas Willig
Cc: Thomas S.Dye; emacs-orgmode@gnu.org; nicholas.do...@hp.com
Subject: Re: [O] Integration of RefTeX and LaTeX export
Andreas Willig wrote:
>
> Hi Thomas,
>
> thanks for this hint. I have looked at this, the changed / added functions are
> below, everything else has not changed. I still have a problem.
>
> I have created a new link type as you suggested and have consulted google
> on how to do it (my emacs-lisp-fu is not good enough to sort out directly what
> this function is doing ...). In my understanding the third argument is a
> function
> that is called when an export process has started and a link is about to be
> exported. My first problem is: this handler function is never called, the
> error
> message that i have inserted below does never appear. I have seen that the
> variable "org-link-types" contains the defined link type, and the variable
> "org-link-protocols" shows my handler.
>
> My second problem is that the generated LaTeX output is
> "\texttt{\cite{key}}"
> but it should simply be "\cite{key}". I would guess that the second problem
> is a corollary of the first one ...
>
> Any ideas?
>
> Andreas
>
I'm pretty sure the second function is not quoted properly in your
org-add-link-type so it ends up actually getting called at the time of
the org-add-link-type is called.
Try the following:
--8<---cut here---start->8---
(defun rt-follow-handler (path)
(message "dummy handler called, path = %s" path)
(let ((arg (concat "\\cite{" path "}")))
(reftex-view-crossref arg)))
(defun rt-export-handler (path desc format)
(message "my handler is called")
(cond ((eq format 'latex)
(if (or (not desc) (equal 0 (search "rtcite:" desc)))
(format "\\cite{%s}" path)
(format "\\cite[%s]{%s}" desc path)
(require 'org)
(org-add-link-type "rtcite"
(function rt-follow-handler)
(function rt-export-handler))
--8<---cut here---end--->8---
By way of explanation:
I had this as part of a minimal .emacs and it seems to work more or
less OK: I replaced the error call with a message call, because it
actually triggered and blew up :-) The rt-export-handler needs tweaking
but you 'll know what to do better than I do when you see the latex
output.
I had to (require 'org) to pick up the definition of org-add-link-type:
that seems to be a missing autoload somewhere.
And finally I like to quote functions with function, not quote, for
compiled-code reasons, but in most cases, it won't make any difference:
use quotes if you prefer.
Nick
>
>
> (defun rt-handler (path)
> (message "dummy handler called, path = %s" path)
> (let ((arg (concat "\\cite{" path "}")))
> (reftex-view-crossref arg)))
>
> (org-add-link-type "rtcite"
> 'rt-handler
> (lambda (path desc format)
>(error "my handler is called")
>(cond ((eq format 'latex)
> (if (or (not desc) (equal 0 (search "rtcite:"
> desc)))
> (format "\\cite{%s}" path)
> (format "\\cite[%s]{%s}" desc path))
>
>
>
This email may be confidential and subject to legal privilege, it may
not reflect the views of the University of Canterbury, and it is not
guaranteed to be virus free. If you are not an intended recipient,
please notify the sender immediately and erase all copies of the message
and any attachments.
Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
information.
Re: [O] Integration of RefTeX and LaTeX export
Andreas Willig wrote:
>
> Hi Thomas,
>
> thanks for this hint. I have looked at this, the changed / added functions are
> below, everything else has not changed. I still have a problem.
>
> I have created a new link type as you suggested and have consulted google
> on how to do it (my emacs-lisp-fu is not good enough to sort out directly what
> this function is doing ...). In my understanding the third argument is a
> function
> that is called when an export process has started and a link is about to be
> exported. My first problem is: this handler function is never called, the
> error
> message that i have inserted below does never appear. I have seen that the
> variable "org-link-types" contains the defined link type, and the variable
> "org-link-protocols" shows my handler.
>
> My second problem is that the generated LaTeX output is
> "\texttt{\cite{key}}"
> but it should simply be "\cite{key}". I would guess that the second problem
> is a corollary of the first one ...
>
> Any ideas?
>
> Andreas
>
I'm pretty sure the second function is not quoted properly in your
org-add-link-type so it ends up actually getting called at the time of
the org-add-link-type is called.
Try the following:
--8<---cut here---start->8---
(defun rt-follow-handler (path)
(message "dummy handler called, path = %s" path)
(let ((arg (concat "\\cite{" path "}")))
(reftex-view-crossref arg)))
(defun rt-export-handler (path desc format)
(message "my handler is called")
(cond ((eq format 'latex)
(if (or (not desc) (equal 0 (search "rtcite:" desc)))
(format "\\cite{%s}" path)
(format "\\cite[%s]{%s}" desc path)
(require 'org)
(org-add-link-type "rtcite"
(function rt-follow-handler)
(function rt-export-handler))
--8<---cut here---end--->8---
By way of explanation:
I had this as part of a minimal .emacs and it seems to work more or
less OK: I replaced the error call with a message call, because it
actually triggered and blew up :-) The rt-export-handler needs tweaking
but you 'll know what to do better than I do when you see the latex
output.
I had to (require 'org) to pick up the definition of org-add-link-type:
that seems to be a missing autoload somewhere.
And finally I like to quote functions with function, not quote, for
compiled-code reasons, but in most cases, it won't make any difference:
use quotes if you prefer.
Nick
>
>
> (defun rt-handler (path)
> (message "dummy handler called, path = %s" path)
> (let ((arg (concat "\\cite{" path "}")))
> (reftex-view-crossref arg)))
>
> (org-add-link-type "rtcite"
> 'rt-handler
> (lambda (path desc format)
>(error "my handler is called")
>(cond ((eq format 'latex)
> (if (or (not desc) (equal 0 (search "rtcite:"
> desc)))
> (format "\\cite{%s}" path)
> (format "\\cite[%s]{%s}" desc path))
>
>
>
Re: [O] Integration of RefTeX and LaTeX export
Hi Thomas,
thanks for this hint. I have looked at this, the changed / added functions are
below, everything else has not changed. I still have a problem.
I have created a new link type as you suggested and have consulted google
on how to do it (my emacs-lisp-fu is not good enough to sort out directly what
this function is doing ...). In my understanding the third argument is a
function
that is called when an export process has started and a link is about to be
exported. My first problem is: this handler function is never called, the error
message that i have inserted below does never appear. I have seen that the
variable "org-link-types" contains the defined link type, and the variable
"org-link-protocols" shows my handler.
My second problem is that the generated LaTeX output is
"\texttt{\cite{key}}"
but it should simply be "\cite{key}". I would guess that the second problem
is a corollary of the first one ...
Any ideas?
Andreas
(defun rt-handler (path)
(message "dummy handler called, path = %s" path)
(let ((arg (concat "\\cite{" path "}")))
(reftex-view-crossref arg)))
(org-add-link-type "rtcite"
'rt-handler
(lambda (path desc format)
(error "my handler is called")
(cond ((eq format 'latex)
(if (or (not desc) (equal 0 (search "rtcite:"
desc)))
(format "\\cite{%s}" path)
(format "\\cite[%s]{%s}" desc path))
(defun org-mode-reftex-setup ()
(load-library "reftex")
(and (buffer-file-name) (file-exists-p (buffer-file-name))
(progn
;;enable auto-revert-mode to update reftex when bibtex file changes on
disk
(global-auto-revert-mode t)
(reftex-parse-all)
;;add a custom reftex cite format to insert links
(reftex-set-cite-format "[[rtcite:%l][\\cite{%l}]]")
))
(define-key org-mode-map (kbd "C-c )") 'reftex-citation)
(define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))
On 17/02/2012, at 11:08 AM, Thomas S. Dye wrote:
> Andreas Willig writes:
>
>> Hi,
>>
>> i am relatively new to org mode. Yesterday i have tried to use org mode for
>> the first time to write the beginnings of a paper, and found that i wanted to
>> insert literature references and a bibliography. I like RefTeX a lot and
>> google
>> provided me some links for proper integration. As a result, i have added the
>> stuff to my .emacs that you find below. The "org-latex-to-pdf-process" stuff
>> works.
>>
>> My problems are related to (reftex-set-cite-format ..). Right now i do not
>> use
>> it and get the default implementation by which RefTeX simply expands the
>> chosen reference to \cite{Key}, which is not highlighted in the org buffer.
>> I would
>> like to have this expanded into an org link with the [[][]] syntax. I have
>> tried
>> several variations of (reftex-set-cite-format ...) but i have never
>> succeeded in
>> creating the bibliography. After generating the LaTeX output into a buffer
>> (C-c C-e L) i found that org translates [[][]] type of stuff into
>> \hyperref{}s and not
>> into \cite{} commands.
>>
>> So, how can i change things so that in the org buffer the bib key gets
>> displayed
>> nicely and in the LaTeX output a \cite{} command is generated?
>>
>> Any help would be appreciated!!
>>
>> Best regards,
>>
>> Andreas
>>
>> --
>>
>> (require 'org-latex)
>> (unless (boundp 'org-export-latex-classes)
>> (setq org-export-latex-classes nil))
>>
>>
>> (add-to-list 'org-export-latex-classes
>> '("article"
>> "\\documentclass{article}"
>> ("\\section{%s}" . "\\section*{%s}")
>> ("\\subsection{%s}" . "\\subsection*{%s}")
>> ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>> ("\\paragraph{%s}" . "\\paragraph*{%s}")))
>>
>> (add-to-list 'org-export-latex-classes
>> '("komaarticle"
>> "\\documentclass{scrartcl}"
>> ("\\section{%s}" . "\\section*{%s}")
>> ("\\subsection{%s}" . "\\subsection*{%s}")
>> ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>> ("\\paragraph{%s}" . "\\paragraph*{%s}")))
>>
>>
>> (add-to-list 'org-export-latex-classes
>> '("komabook"
>> "\\documentclass{scrbook}"
>> ("\\chapter{%s}" . "\\chapter*{%s}")
>> ("\\section{%s}" . "\\section*{%s}")
>> ("\\subsection{%s}" . "\\subsection*{%s}")
>> ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>> ("\\paragraph{%s}" . "\\paragraph*{%s}")))
>>
>>
>> (defun org-mode-reftex-setup ()
>> (load-library "reftex")
>> (and (buffer-file-name) (file-exists-p (buffer-file-name))
>> (progn
>>
Re: [O] multilingual presentation with org
On Fri, Feb 17, 2012 at 4:29 AM, Daniel Clemente wrote: > > > El Wed, 15 Feb 2012 13:33:49 +0530 Rustom Mody va escriure: > > > Now I am exploring how I could 'zip' the two together. My requirements > are like this: > > > > Any thoughts/suggestions? > > > > I made a small markup language which lets you write it in this way: > > > --- > A song in English and Sanskrit: > Thanks Daniel -- that looks useful at some stage of the processing. I was thinking of concocting something like this myself. My (current main) use is a bit different however. Its not so much hand-translation as machine-transliteration. The below elisp code will apply whatever input-method you put into rpm-input-method and put the result into a new buffer. After that pasting the two together into something palatable/presentable is the question. For now Ive used paste -d'|' and then run it through org's table system to produce html ---elisp- (defvar rpm-input-method "devanagari-itrans") (defun rpm-apply-input-method () (interactive) (let* ((inp (buffer-substring-no-properties (point-min) (point-max))) (filename (file-name-nondirectory (buffer-file-name))) (outname (concat (file-name-sans-extension filename) "-hi" (file-name-extension filename t))) (p)) (switch-to-buffer-other-frame outname) (save-excursion (save-window-excursion (setq p (point)) (erase-buffer) (setq buffer-file-coding-system 'utf-8) (set-input-method rpm-input-method t) (execute-kbd-macro inp))) (goto-char p) (other-frame 1))) (global-set-key [f4] 'rpm-apply-input-method)
[O] Bug: Habit consistency graph redisplay bug involving filters [7.8.03 (release_7.4.2711.gc2c5.dirty)]
I've been noticing that some habit consistency graphs get wiped out
by clocking in; I'd like to offer this minimal test case and patch.
To reproduce the bug, save this Org file as `test-case.org':
* TODO Item One :random:
SCHEDULED: <2012-02-16 Thu .+1d>
:PROPERTIES:
:STYLE:
habit
:END:
* TODO Item Two
SCHEDULED: <2012-02-16 Thu .+1d>
:PROPERTIES:
:STYLE:
habit
:END:
* TODO Item Three:random:
SCHEDULED: <2012-02-16 Fri .+1d>
:PROPERTIES:
:STYLE:
habit
:END:
And save this file as `setup.el':
(add-to-list 'load-path "/src/org-mode/lisp")
(require 'org-install)
(setq org-modules (cons 'org-habit org-modules))
(setq org-habit-graph-column 51)
(setq org-agenda-files '("./test-case.org"))
Then start Emacs with `emacs -Q -l setup.el'.
Type `M-x org-agenda' and press `a' to make the agenda view.
Type `/ TAB random RET' to show only the tagged TODO items (1 and 3).
Move point to Item Three and press `I' to clock in.
Now Item One's consistency graph disappears.
The following patch fixes the problem, at least for me:
>From 93f16bc95a32f4bee2c07ca6da6f0b89c2bb6e4b Mon Sep 17 00:00:00 2001
From: Thomas Morgan
Date: Tue, 7 Feb 2012 19:10:09 -0500
Subject: [PATCH] * org-habit.el (org-habit-insert-consistency-graphs): Don't
let an overlay on the next line make the current line's
consistency graph invisible.
---
lisp/org-habit.el | 13 ++---
1 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/lisp/org-habit.el b/lisp/org-habit.el
index 67f8779..be0efff 100644
--- a/lisp/org-habit.el
+++ b/lisp/org-habit.el
@@ -344,13 +344,12 @@ current time."
(delete-char (min (+ 1 org-habit-preceding-days
org-habit-following-days)
(- (line-end-position) (point
- (insert (org-habit-build-graph
-habit
-(time-subtract moment
- (days-to-time org-habit-preceding-days))
-moment
-(time-add moment
- (days-to-time org-habit-following-days))
+ (insert-before-markers
+(org-habit-build-graph
+ habit
+ (time-subtract moment (days-to-time org-habit-preceding-days))
+ moment
+ (time-add moment (days-to-time org-habit-following-days))
(forward-line)
(defun org-habit-toggle-habits ()
--
1.7.5.4
Emacs : GNU Emacs 24.0.93.1 (i686-pc-linux-gnu, X toolkit, Xaw3d scroll bars)
of 2012-02-09 on tyl
Package: Org-mode version 7.8.03 (release_7.4.2711.gc2c5.dirty)
current state:
==
(setq
org-export-blocks '((src org-babel-exp-src-block nil) (export-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-modules '(org-habit org-bbdb org-bibtex org-docview org-gnus org-info
org-jsinfo org-irc org-mew org-mhe org-rmail org-vm org-w3m org-wl)
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 '((src org-babel-exp-non-block-elements))
org-habit-graph-column 51
org-metaup-hook '(org-babel-load-in-session-maybe)
org-confirm-elisp-li
Re: [O] Killing list and subtree?
On 2012-02-16 23:08 +0800, François Pinard wrote: > Is there an easy command to kill a list and its subtree hierarchy? > Something like `C-c C-x C-w' but which would work at the list level > rather than at the item level? fold the tree using TAB and then C-k? Leo
Re: [O] sqlite3 in org-babel
> 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. Perhaps they should be united? 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. > > Daniel Clemente writes: > > > Hi, > >org-babel works well with sqlite3 if you add this (which I propose for > > inclusion): > >
Re: [O] Controlling pagination on headings in Latex/PDF export?
Hi! Thanks for your kind words! ; - ) I did wrap the "mykeepwithnextpar" definition and I moved the call between the heading and the table as suggested, but it still doesn't seem to want to cooperate (heading on one page, table on the next). Since this seems to be strange behaviour, I will set up a minimal failing %.org file and send it tomorrow to demonstrate the problem. Thanks again! Jos'h ___ Jos'h Fuller, Production Programmer Arc Productions Ltd. p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com 230 Richmond Street East | Toronto, ON M5A 1P4 |
Re: [O] multilingual presentation with org
El Wed, 15 Feb 2012 13:33:49 +0530 Rustom Mody va escriure: > Now I am exploring how I could 'zip' the two together. My requirements are > like this: > > Any thoughts/suggestions? > I made a small markup language which lets you write it in this way: --- A song in English and Sanskrit: @en bhaja govindam bhaja govindam @sa भज गोविंदं भज गोविंदं @en govindam bhaja mUDhamate @sa गोविंदं भज मूढमते @en saMprApte sannihite kAle @sa संप्राप्ते सन्निहिते काले @en nahi nahi rakShati DukrinkaraNe @sa नहि नहि रक्षति डुकृंकरणे --- You run it through a script and you obtain two files, one with all the @en and the other with all the @sa. The common text goes to both. The script is at http://www.danielclemente.com/dislines/index.en.html How to integrate this approach with org's outline… is a challenge. One header per language? One property per language? Inline headers?… Daniel
Re: [O] Integration of RefTeX and LaTeX export
Andreas Willig writes:
> Hi,
>
> i am relatively new to org mode. Yesterday i have tried to use org mode for
> the first time to write the beginnings of a paper, and found that i wanted to
> insert literature references and a bibliography. I like RefTeX a lot and
> google
> provided me some links for proper integration. As a result, i have added the
> stuff to my .emacs that you find below. The "org-latex-to-pdf-process" stuff
> works.
>
> My problems are related to (reftex-set-cite-format ..). Right now i do not use
> it and get the default implementation by which RefTeX simply expands the
> chosen reference to \cite{Key}, which is not highlighted in the org buffer. I
> would
> like to have this expanded into an org link with the [[][]] syntax. I have
> tried
> several variations of (reftex-set-cite-format ...) but i have never succeeded
> in
> creating the bibliography. After generating the LaTeX output into a buffer
> (C-c C-e L) i found that org translates [[][]] type of stuff into
> \hyperref{}s and not
> into \cite{} commands.
>
> So, how can i change things so that in the org buffer the bib key gets
> displayed
> nicely and in the LaTeX output a \cite{} command is generated?
>
> Any help would be appreciated!!
>
> Best regards,
>
> Andreas
>
> --
>
> (require 'org-latex)
> (unless (boundp 'org-export-latex-classes)
> (setq org-export-latex-classes nil))
>
>
> (add-to-list 'org-export-latex-classes
> '("article"
>"\\documentclass{article}"
>("\\section{%s}" . "\\section*{%s}")
>("\\subsection{%s}" . "\\subsection*{%s}")
>("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>("\\paragraph{%s}" . "\\paragraph*{%s}")))
>
> (add-to-list 'org-export-latex-classes
> '("komaarticle"
>"\\documentclass{scrartcl}"
>("\\section{%s}" . "\\section*{%s}")
>("\\subsection{%s}" . "\\subsection*{%s}")
>("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>("\\paragraph{%s}" . "\\paragraph*{%s}")))
>
>
> (add-to-list 'org-export-latex-classes
> '("komabook"
>"\\documentclass{scrbook}"
>("\\chapter{%s}" . "\\chapter*{%s}")
>("\\section{%s}" . "\\section*{%s}")
>("\\subsection{%s}" . "\\subsection*{%s}")
>("\\subsubsection{%s}" . "\\subsubsection*{%s}")
>("\\paragraph{%s}" . "\\paragraph*{%s}")))
>
>
> (defun org-mode-reftex-setup ()
> (load-library "reftex")
> (and (buffer-file-name) (file-exists-p (buffer-file-name))
>(progn
>(global-auto-revert-mode t)
>(reftex-parse-all)
>;;(reftex-set-cite-format "\[cite][%l]]")
>))
> (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
> (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))
>
> (add-hook 'org-mode-hook 'org-mode-reftex-setup)
>
>
> (defun org-mode-reftex-search ()
> ;;jump to the notes for the paper pointed to at from reftex search
> (interactive)
> (org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t
>
> (setq org-latex-to-pdf-process
> '("pdflatex -interaction nonstopmode %b"
> "bibtex %b"
> "pdflatex -interaction nonstopmode %b"
> "pdflatex -interaction nonstopmode %b"))
>
>
> This email may be confidential and subject to legal privilege, it may
> not reflect the views of the University of Canterbury, and it is not
> guaranteed to be virus free. If you are not an intended recipient,
> please notify the sender immediately and erase all copies of the message
> and any attachments.
>
> Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
> information.
>
>
Aloha Andreas,
Welcome to Org Mode!
You might want to define a new link type. See
http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17-2 for
one example of how this might be done.
hth,
Tom
--
Thomas S. Dye
http://www.tsdye.com
Re: [O] Controlling pagination on headings in Latex/PDF export?
Jos'h Fuller wrote:
> OK, I'm an idiot. I forgot to put in the ":" after the "#+latex", so
> it didn't get processed correctly.
Indeed, I've *never* made such an idiotic mistake (well, at least not since
yesterday) - how could you? :-)
OTOH, I tend to forget the + routinely, but you know what they say: to
each his own blind spot.
On a more serious note, things that need to end up in the preamble should
be marked
#+LaTeX_HEADER: \def\mykeepwithnextpar{\par\nobreak\@afterheading}
(and note my other post about @).
The
#+LATEX: \foo
markup is for things that end up in the document environment.
Nick
>
> However, once I did put it in, it does work to keep the headings together
> with the table data. However... it also seems to embed the spurious word
> "afterheading" (in italics) after most (but not all) of the top level
> headings in the file.
>
> So, it totally works to keep the headings and tables together, but the
> /afterheading/ thing is very strange.
>
> I've probably still done something wrong. Any ideas?
>
> Thanks again!
>
> Jos'h
> ___
>
> Jos'h Fuller, Production Programmer
>
> Arc Productions Ltd.
>
> p: 416.682.5237 | f: 416.682.5209 |
> http://www.arcproductions.com
> 230 Richmond Street East | Toronto, ON M5A 1P4 |
>
>
> > -Original Message-
> > From: emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org
> > [mailto:emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org]
> > On Behalf Of Jos'h Fuller
> > Sent: Thursday, February 16, 2012 3:09 PM
> > To: Sebastien Vauban; emacs-orgmode@gnu.org
> > Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> > export?
> >
> > Hi Sebastien!
> >
> > I tried it, and it didn't work. However, I may not have set it up
> > right:
> >
> > --snip!--
> > #+latex \def\mykeepwithnextpar{\par\nobreak\@afterheading}
> >
> > #+latex: \newpage
> > * Period...
> > ** Asset
> > #+latex: \mykeepwithnextpar{}
> > *** DEPARTMENT
> > | Table | Data | Here |
> > --snip!--
> >
> > Did I do this correctly or does the "mykeepwithnextpar" definition have
> > to go into a different file?
> >
> > Thanks very much!
> > ___
> >
> >
> > Jos'h Fuller, Production Programmer
> >
> > Arc Productions Ltd.
> >
> > p: 416.682.5237 | f: 416.682.5209 |
> > http://www.arcproductions.com
> > 230 Richmond Street East | Toronto, ON M5A 1P4 |
> >
> >
> > > -Original Message-
> > > From: emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org
> > > [mailto:emacs-orgmode-
> > bounces+jos'h.fuller=arcproductions@gnu.org]
> > > On Behalf Of Sebastien Vauban
> > > Sent: Thursday, February 16, 2012 2:44 PM
> > > To: emacs-orgmode@gnu.org
> > > Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> > > export?
> > >
> > > Hi Jos'h,
> > >
> > > Jos'h Fuller wrote:
> > > > I am familiar with \newpage (and I especially like to put it at the
> > > front of
> > > > the document to keep my content out of my table of contents!), but
> > I
> > > was
> > > > hoping to be able to do this in some more automatic fashion, since
> > > these are
> > > > long reports and I want to be able to process them unattended.
> > > >
> > > > Is it possible to do something like this:
> > > >
> > > > * Period...
> > > > ** Asset
> > > > #+latex: \keepthisstufftogether{begin}
> > > > *** DEPARTMENT A
> > > > | Table | Data | Here. |
> > > > | Table | Data | Here. |
> > > > | Table | Data | Here. |
> > > > #+latex: \keepthisstufftogether{end}
> > > > *** DEPARTMENT B
> > > > ...
> > > >
> > > > I have no idea what /actual/ LaTeX call fills in for
> > > > "\keepthisstufftogether" though...
> > >
> > > I have written such a thing, years ago, first for LaTeX, now for Org:
> > >
> > > --8<---cut here---start->8---
> > > % how not to have a page break with what is following?
> > > \def\mykeepwithnextpar{\par\nobreak\@afterheading}
> > > --8<---cut here---end--->8---
> > >
> > > and I put whereever it's needed
> > >
> > > --8<---cut here---start->8---
> > > ** Asset
> > > #+latex: \mykeepwithnextpar{}
> > > *** DEPARTMENT A
> > > | Table | Data | Here. |
> > > | Table | Data | Here. |
> > > | Table | Data | Here. |
> > > *** DEPARTMENT B
> > > --8<---cut here---end--->8---
> > >
> > > Does it work for you?
> > >
> > > Best regards,
> > > Seb
> > >
> > > --
> > > Sebastien Vauban
> > >
> >
>
>
Re: [O] Controlling pagination on headings in Latex/PDF export?
Sebastien Vauban wrote:
> Jos'h,
>
> Jos'h Fuller wrote:
> > OK, I'm an idiot. I forgot to put in the ":" after the "#+latex", so it
> > didn't get processed correctly.
>
> That happens to everybody... No need to be an idiot ;-)
>
> > However, once I did put it in, it does work to keep the headings together
> > with
> > the table data. However... it also seems to embed the spurious word
> > "afterheading" (in italics) after most (but not all) of the top level
> > headings
> > in the file.
> >
> > So, it totally works to keep the headings and tables together, but the
> > /afterheading/ thing is very strange.
> >
> > I've probably still done something wrong. Any ideas?
>
> Strange. Maybe, you could send here an ECM (Minimal Complete Example) that
> shows the bug without the \mykeepwithnextpar and shows the afterheading
> problem with it...
>
> So that one can try to reproduce your problem without loosing too much time,
> in order to help you better and quicker.
>
> BTW, you should put \mykeepwithnextpar after the heading "DEPARTMENT A", not
> before (as I wrote)...
>
> >> > I have written such a thing, years ago, first for LaTeX, now for Org:
> >> >
> >> > --8<---cut here---start->8---
> >> > % how not to have a page break with what is following?
> >> > \def\mykeepwithnextpar{\par\nobreak\@afterheading}
> >> > --8<---cut here---end--->8---
> >> >
> >> > and I put whereever it's needed
> >> >
> >> > --8<---cut here---start->8---
> >> > ** Asset
> >> > #+latex: \mykeepwithnextpar{}
> >> > *** DEPARTMENT A
> >> > | Table | Data | Here. |
> >> > | Table | Data | Here. |
> >> > | Table | Data | Here. |
> >> > *** DEPARTMENT B
> >> > --8<---cut here---end--->8---
>
@ is a character that is reserved for .sty files: it's basically used as
a mechanism to manufacture private names that are not going to conflict
with other names. If you want to use @ in a macro in your .tex file,
then you have to do something like this:
#+LaTeX_HEADER: \makeatletter
#+LaTeX_HEADER: \def\mykeepwithnextpar{\par\nobreak\@afterheading}
#+LaTeX_HEADER: \makeatother
However the best thing is to put the definition in a .sty file:
--8<---keeper.sty---start->8---
\def\mykeepwithnextpar{\par\nobreak\@afterheading}
--8<---keeper.sty---end--->8---
and then use
--8<---cut here---start->8---
#+LaTeX_HEADER: \usepackage{keeper}
--8<---cut here---end--->8---
in your .org file.
However, I find it exceedingly difficult to manufacture an example that
will produce the bad break that the OP reports: LaTeX seems very
reluctant to break after the headline. E.g. in the appended file, I can
vary the number of foo lines from 0 to enough to fill the page and I
cannot split the DEPARTMENT headline from the table. I also tried
various lengths for the table (not very systematically, I must admit)
and I still cannot get the default settings to misbehave. This leads me
to believe that there are those "other" factors that affect badness:
LaTeX thinks that there is something so severely out of whack in the
"other" factors that it is willing to make the supreme sacrifice of
splitting the headline from the table.
So if the OP can provide a misbehaving example, that could help clarify
things.
Nick
PS. Note that the call to \mykeewithnextpar is disabled in the file
below. If I enable it, I actually get a foo line at the top of the
second page before the DEPARTMENT headline, so it certainly affects
the output, but not in a good way.
--8<---cut here---start->8---
#+LaTeX_HEADER: \usepackage{keeper}
* Period 2012-02-06 to 2012-02-12
** Asset
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
foo foo foo foo foo foo foo foo foo foo foo foo foo foofoo foo foo foo foo foo
##+LATEX: \mykeepwithnextpar{}
*** DEPARTMENT
| Data| Data | Data | Data |
|-+--+--+--|
| XX |1 |1 |0 |
| YY |5 |4 |0 |
|
[O] Integration of RefTeX and LaTeX export
Hi,
i am relatively new to org mode. Yesterday i have tried to use org mode for
the first time to write the beginnings of a paper, and found that i wanted to
insert literature references and a bibliography. I like RefTeX a lot and google
provided me some links for proper integration. As a result, i have added the
stuff to my .emacs that you find below. The "org-latex-to-pdf-process" stuff
works.
My problems are related to (reftex-set-cite-format ..). Right now i do not use
it and get the default implementation by which RefTeX simply expands the
chosen reference to \cite{Key}, which is not highlighted in the org buffer. I
would
like to have this expanded into an org link with the [[][]] syntax. I have tried
several variations of (reftex-set-cite-format ...) but i have never succeeded in
creating the bibliography. After generating the LaTeX output into a buffer
(C-c C-e L) i found that org translates [[][]] type of stuff into \hyperref{}s
and not
into \cite{} commands.
So, how can i change things so that in the org buffer the bib key gets displayed
nicely and in the LaTeX output a \cite{} command is generated?
Any help would be appreciated!!
Best regards,
Andreas
--
(require 'org-latex)
(unless (boundp 'org-export-latex-classes)
(setq org-export-latex-classes nil))
(add-to-list 'org-export-latex-classes
'("article"
"\\documentclass{article}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")))
(add-to-list 'org-export-latex-classes
'("komaarticle"
"\\documentclass{scrartcl}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")))
(add-to-list 'org-export-latex-classes
'("komabook"
"\\documentclass{scrbook}"
("\\chapter{%s}" . "\\chapter*{%s}")
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")))
(defun org-mode-reftex-setup ()
(load-library "reftex")
(and (buffer-file-name) (file-exists-p (buffer-file-name))
(progn
(global-auto-revert-mode t)
(reftex-parse-all)
;;(reftex-set-cite-format "\[cite][%l]]")
))
(define-key org-mode-map (kbd "C-c )") 'reftex-citation)
(define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
(defun org-mode-reftex-search ()
;;jump to the notes for the paper pointed to at from reftex search
(interactive)
(org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t
(setq org-latex-to-pdf-process
'("pdflatex -interaction nonstopmode %b"
"bibtex %b"
"pdflatex -interaction nonstopmode %b"
"pdflatex -interaction nonstopmode %b"))
This email may be confidential and subject to legal privilege, it may
not reflect the views of the University of Canterbury, and it is not
guaranteed to be virus free. If you are not an intended recipient,
please notify the sender immediately and erase all copies of the message
and any attachments.
Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
information.
Re: [O] A manuscript on "reproducible research" introducing org-mode
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 -- The Kafka Pandemic: http://thekafkapandemic.blogspot.com
Re: [O] Temp files from testing are permanent...
Achim Gratz writes: > Barring any setup or options I might have missed, it looks like I will > have to do two things: first, set TMPDIR to a newly created directory > during the test runs and second, remove that directory after the test > (with an option to keep it for inspection and removing only with > "clean"). Done and pushed to my Makefile fork on repo.or.cz. Temporary test files automatically vaporize when the test suite successfully runs and are left for inspection otherwise. If you need to keep them regardless of the test result, define TEST_NO_AUTOCLEAN non-empty. A new target cleantest can be used to remove the temporary test directory and all its content whenever necessary, this is also done when doing a "cleanall". The location of the temporary test directory follows $TMPDIR and can be overriden in local.mk via variable testdir. TMPDIR, if not already present in the environment, will default to /tmp, which incidentally should resolve a bug in my tricky build environment at work. Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ SD adaptations for Waldorf Q V3.00R3 and Q+ V3.54R2: http://Synth.Stromeko.net/Downloads.html#WaldorfSDada
Re: [O] Controlling pagination on headings in Latex/PDF export?
Jos'h,
Jos'h Fuller wrote:
> OK, I'm an idiot. I forgot to put in the ":" after the "#+latex", so it
> didn't get processed correctly.
That happens to everybody... No need to be an idiot ;-)
> However, once I did put it in, it does work to keep the headings together with
> the table data. However... it also seems to embed the spurious word
> "afterheading" (in italics) after most (but not all) of the top level headings
> in the file.
>
> So, it totally works to keep the headings and tables together, but the
> /afterheading/ thing is very strange.
>
> I've probably still done something wrong. Any ideas?
Strange. Maybe, you could send here an ECM (Minimal Complete Example) that
shows the bug without the \mykeepwithnextpar and shows the afterheading
problem with it...
So that one can try to reproduce your problem without loosing too much time,
in order to help you better and quicker.
BTW, you should put \mykeepwithnextpar after the heading "DEPARTMENT A", not
before (as I wrote)...
>> > I have written such a thing, years ago, first for LaTeX, now for Org:
>> >
>> > --8<---cut here---start->8---
>> > % how not to have a page break with what is following?
>> > \def\mykeepwithnextpar{\par\nobreak\@afterheading}
>> > --8<---cut here---end--->8---
>> >
>> > and I put whereever it's needed
>> >
>> > --8<---cut here---start->8---
>> > ** Asset
>> > #+latex: \mykeepwithnextpar{}
>> > *** DEPARTMENT A
>> > | Table | Data | Here. |
>> > | Table | Data | Here. |
>> > | Table | Data | Here. |
>> > *** DEPARTMENT B
>> > --8<---cut here---end--->8---
Best regards,
Seb
--
Sebastien Vauban
Re: [O] A manuscript on "reproducible research" introducing org-mode
Samuel Wales writes: > I applaud all of this. Raw data need to be made available by default > (with only a few exceptions). Org can help people reproduce all of > the succeeding steps also. Some people on the list might like to see the short (13 min) segment on Duke University's recent problems with reproducible research http://www.cbsnews.com/video/watch/?id=7398476n&tag=contentMain;contentAux and the heroic efforts to uncover what had been done (37 min): http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/ Stephen
Re: [O] Controlling pagination on headings in Latex/PDF export?
OK, I'm an idiot. I forgot to put in the ":" after the "#+latex", so it didn't
get processed correctly.
However, once I did put it in, it does work to keep the headings together with
the table data. However... it also seems to embed the spurious word
"afterheading" (in italics) after most (but not all) of the top level headings
in the file.
So, it totally works to keep the headings and tables together, but the
/afterheading/ thing is very strange.
I've probably still done something wrong. Any ideas?
Thanks again!
Jos'h
___
Jos'h Fuller, Production Programmer
Arc Productions Ltd.
p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com
230 Richmond Street East | Toronto, ON M5A 1P4 |
> -Original Message-
> From: emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org
> [mailto:emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org]
> On Behalf Of Jos'h Fuller
> Sent: Thursday, February 16, 2012 3:09 PM
> To: Sebastien Vauban; emacs-orgmode@gnu.org
> Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> export?
>
> Hi Sebastien!
>
> I tried it, and it didn't work. However, I may not have set it up
> right:
>
> --snip!--
> #+latex \def\mykeepwithnextpar{\par\nobreak\@afterheading}
>
> #+latex: \newpage
> * Period...
> ** Asset
> #+latex: \mykeepwithnextpar{}
> *** DEPARTMENT
> | Table | Data | Here |
> --snip!--
>
> Did I do this correctly or does the "mykeepwithnextpar" definition have
> to go into a different file?
>
> Thanks very much!
> ___
>
>
> Jos'h Fuller, Production Programmer
>
> Arc Productions Ltd.
>
> p: 416.682.5237 | f: 416.682.5209 |
> http://www.arcproductions.com
> 230 Richmond Street East | Toronto, ON M5A 1P4 |
>
>
> > -Original Message-
> > From: emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org
> > [mailto:emacs-orgmode-
> bounces+jos'h.fuller=arcproductions@gnu.org]
> > On Behalf Of Sebastien Vauban
> > Sent: Thursday, February 16, 2012 2:44 PM
> > To: emacs-orgmode@gnu.org
> > Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> > export?
> >
> > Hi Jos'h,
> >
> > Jos'h Fuller wrote:
> > > I am familiar with \newpage (and I especially like to put it at the
> > front of
> > > the document to keep my content out of my table of contents!), but
> I
> > was
> > > hoping to be able to do this in some more automatic fashion, since
> > these are
> > > long reports and I want to be able to process them unattended.
> > >
> > > Is it possible to do something like this:
> > >
> > > * Period...
> > > ** Asset
> > > #+latex: \keepthisstufftogether{begin}
> > > *** DEPARTMENT A
> > > | Table | Data | Here. |
> > > | Table | Data | Here. |
> > > | Table | Data | Here. |
> > > #+latex: \keepthisstufftogether{end}
> > > *** DEPARTMENT B
> > > ...
> > >
> > > I have no idea what /actual/ LaTeX call fills in for
> > > "\keepthisstufftogether" though...
> >
> > I have written such a thing, years ago, first for LaTeX, now for Org:
> >
> > --8<---cut here---start->8---
> > % how not to have a page break with what is following?
> > \def\mykeepwithnextpar{\par\nobreak\@afterheading}
> > --8<---cut here---end--->8---
> >
> > and I put whereever it's needed
> >
> > --8<---cut here---start->8---
> > ** Asset
> > #+latex: \mykeepwithnextpar{}
> > *** DEPARTMENT A
> > | Table | Data | Here. |
> > | Table | Data | Here. |
> > | Table | Data | Here. |
> > *** DEPARTMENT B
> > --8<---cut here---end--->8---
> >
> > Does it work for you?
> >
> > Best regards,
> > Seb
> >
> > --
> > Sebastien Vauban
> >
>
Re: [O] Controlling pagination on headings in Latex/PDF export?
Hi Sebastien!
I tried it, and it didn't work. However, I may not have set it up right:
--snip!--
#+latex \def\mykeepwithnextpar{\par\nobreak\@afterheading}
#+latex: \newpage
* Period...
** Asset
#+latex: \mykeepwithnextpar{}
*** DEPARTMENT
| Table | Data | Here |
--snip!--
Did I do this correctly or does the "mykeepwithnextpar" definition have to go
into a different file?
Thanks very much!
___
Jos'h Fuller, Production Programmer
Arc Productions Ltd.
p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com
230 Richmond Street East | Toronto, ON M5A 1P4 |
> -Original Message-
> From: emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org
> [mailto:emacs-orgmode-bounces+jos'h.fuller=arcproductions@gnu.org]
> On Behalf Of Sebastien Vauban
> Sent: Thursday, February 16, 2012 2:44 PM
> To: emacs-orgmode@gnu.org
> Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> export?
>
> Hi Jos'h,
>
> Jos'h Fuller wrote:
> > I am familiar with \newpage (and I especially like to put it at the
> front of
> > the document to keep my content out of my table of contents!), but I
> was
> > hoping to be able to do this in some more automatic fashion, since
> these are
> > long reports and I want to be able to process them unattended.
> >
> > Is it possible to do something like this:
> >
> > * Period...
> > ** Asset
> > #+latex: \keepthisstufftogether{begin}
> > *** DEPARTMENT A
> > | Table | Data | Here. |
> > | Table | Data | Here. |
> > | Table | Data | Here. |
> > #+latex: \keepthisstufftogether{end}
> > *** DEPARTMENT B
> > ...
> >
> > I have no idea what /actual/ LaTeX call fills in for
> > "\keepthisstufftogether" though...
>
> I have written such a thing, years ago, first for LaTeX, now for Org:
>
> --8<---cut here---start->8---
> % how not to have a page break with what is following?
> \def\mykeepwithnextpar{\par\nobreak\@afterheading}
> --8<---cut here---end--->8---
>
> and I put whereever it's needed
>
> --8<---cut here---start->8---
> ** Asset
> #+latex: \mykeepwithnextpar{}
> *** DEPARTMENT A
> | Table | Data | Here. |
> | Table | Data | Here. |
> | Table | Data | Here. |
> *** DEPARTMENT B
> --8<---cut here---end--->8---
>
> Does it work for you?
>
> Best regards,
> Seb
>
> --
> Sebastien Vauban
>
Re: [O] Controlling pagination on headings in Latex/PDF export?
Hi Jos'h,
Jos'h Fuller wrote:
> I am familiar with \newpage (and I especially like to put it at the front of
> the document to keep my content out of my table of contents!), but I was
> hoping to be able to do this in some more automatic fashion, since these are
> long reports and I want to be able to process them unattended.
>
> Is it possible to do something like this:
>
> * Period...
> ** Asset
> #+latex: \keepthisstufftogether{begin}
> *** DEPARTMENT A
> | Table | Data | Here. |
> | Table | Data | Here. |
> | Table | Data | Here. |
> #+latex: \keepthisstufftogether{end}
> *** DEPARTMENT B
> ...
>
> I have no idea what /actual/ LaTeX call fills in for
> "\keepthisstufftogether" though...
I have written such a thing, years ago, first for LaTeX, now for Org:
--8<---cut here---start->8---
% how not to have a page break with what is following?
\def\mykeepwithnextpar{\par\nobreak\@afterheading}
--8<---cut here---end--->8---
and I put whereever it's needed
--8<---cut here---start->8---
** Asset
#+latex: \mykeepwithnextpar{}
*** DEPARTMENT A
| Table | Data | Here. |
| Table | Data | Here. |
| Table | Data | Here. |
*** DEPARTMENT B
--8<---cut here---end--->8---
Does it work for you?
Best regards,
Seb
--
Sebastien Vauban
[O] [0][babel][R] Undesired conversion of integers to floats in R code block output
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.)
Thanks,
Dan
I'm running:
- Arch Linux (32 bit)
- GNU Emacs 23.4.1
- Org-mode version release_7.8.03-351-g47eb3
- R version 2.14.1 (2011-12-22)
* 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 |
|-+--|
| 987654321.0 | 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
Re: [O] Controlling pagination on headings in Latex/PDF export?
I often use newpage myself, and have wondered if there were a way to
ensure every first level (maybe second level too?) always had an
automatic newpage before it.
On Thu, Feb 16, 2012 at 06:25:40PM +, Jos'h Fuller wrote:
> Hi!
>
> I am familiar with \newpage (and I especially like to put it at the front of
> the document to keep my content out of my table of contents!), but I was
> hoping to be able to do this in some more automatic fashion, since these are
> long reports and I want to be able to process them unattended.
>
> Is it possible to do something like this:
>
> * Period...
> ** Asset
> #+latex: \keepthisstufftogether{begin}
> *** DEPARTMENT A
> | Table | Data | Here. |
> | Table | Data | Here. |
> | Table | Data | Here. |
> #+latex: \keepthisstufftogether{end}
> *** DEPARTMENT B
> ...
>
> I have no idea what /actual/ LaTeX call fills in for "\keepthisstufftogether"
> though...
>
> Thanks!
>
> ___
>
> Jos'h Fuller, Production Programmer
>
> Arc Productions Ltd.
>
> p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com
> 230 Richmond Street East | Toronto, ON M5A 1P4 |
>
>
> > -Original Message-
> > From: nicholas.do...@hp.com [mailto:nicholas.do...@hp.com]
> > Sent: Thursday, February 16, 2012 1:21 PM
> > To: Jos'h Fuller
> > Cc: emacs-orgmode@gnu.org; nicholas.do...@hp.com
> > Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> > export?
> >
> > Jos'h Fuller wrote:
> >
> > > Hi!
> > >
> > > I'm have an org-mode document something like this:
> > >
> > > * Period 2012-02-06 to 2012-02-12
> > > ** Asset
> > > *** DEPARTMENT
> > > | Data| Data | Data | Data |
> > > |-+--+--+--|
> > > | XX |1 |1 |0 |
> > > | YY |5 |4 |0 |
> > >
> > > (There are more "Assets", each with several DEPARTMENTS. The tables
> > are short, perhaps 10-15 rows.)
> > >
> > > When I go to export a PDF, I will often get "DEPARTMENT" at the
> > bottom of one page, with the actual data table at the start of the
> > next. Is there any way to keep the heading together with the table?
> > >
> >
> > Try adding
> >
> > #+LATEX: \newpage
> >
> > before the heading where you want the page break to occur:
> >
> > --8<---cut here---start->8---
> > Period 2012-02-06 to 2012-02-12
> > ** Asset
> > #+LATEX: \newpage
> > *** DEPARTMENT
> > | Data| Data | Data | Data |
> > |-+--+--+--|
> > | XX |1 |1 |0 |
> > | YY |5 |4 |0 |
> >
> > --8<---cut here---end--->8---
> >
> > You should probably do that as a last resort in the last editing
> > round, just to fix problematic spots.
> >
> > > I tried using the longtable environment, but that just splits the
> > > table itself, so that I might have the heading at the bottom of the
> > > page with one row of the table and a continued message. I also tried
> > > the LaTeX directives \goodbreak before the headings and \nobreak
> > > between the headings and tables but they didn't seem to affect
> > > anything.
> > >
> >
> > IIRC, these influence LaTeX's internal measures of whether this is a
> > good or bad place to do it, but there are several factors in
> > competition
> > and they probably lose in comparison to the other factors.
> >
> > \newpage otoh is Thor's hammer: no questions asked.
> >
> > Nick
>
--
Russell Adamsrlad...@adamsinfoserv.com
PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/
Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3
Re: [O] Controlling pagination on headings in Latex/PDF export?
Hi!
I am familiar with \newpage (and I especially like to put it at the front of
the document to keep my content out of my table of contents!), but I was hoping
to be able to do this in some more automatic fashion, since these are long
reports and I want to be able to process them unattended.
Is it possible to do something like this:
* Period...
** Asset
#+latex: \keepthisstufftogether{begin}
*** DEPARTMENT A
| Table | Data | Here. |
| Table | Data | Here. |
| Table | Data | Here. |
#+latex: \keepthisstufftogether{end}
*** DEPARTMENT B
...
I have no idea what /actual/ LaTeX call fills in for "\keepthisstufftogether"
though...
Thanks!
___
Jos'h Fuller, Production Programmer
Arc Productions Ltd.
p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com
230 Richmond Street East | Toronto, ON M5A 1P4 |
> -Original Message-
> From: nicholas.do...@hp.com [mailto:nicholas.do...@hp.com]
> Sent: Thursday, February 16, 2012 1:21 PM
> To: Jos'h Fuller
> Cc: emacs-orgmode@gnu.org; nicholas.do...@hp.com
> Subject: Re: [O] Controlling pagination on headings in Latex/PDF
> export?
>
> Jos'h Fuller wrote:
>
> > Hi!
> >
> > I'm have an org-mode document something like this:
> >
> > * Period 2012-02-06 to 2012-02-12
> > ** Asset
> > *** DEPARTMENT
> > | Data| Data | Data | Data |
> > |-+--+--+--|
> > | XX |1 |1 |0 |
> > | YY |5 |4 |0 |
> >
> > (There are more "Assets", each with several DEPARTMENTS. The tables
> are short, perhaps 10-15 rows.)
> >
> > When I go to export a PDF, I will often get "DEPARTMENT" at the
> bottom of one page, with the actual data table at the start of the
> next. Is there any way to keep the heading together with the table?
> >
>
> Try adding
>
> #+LATEX: \newpage
>
> before the heading where you want the page break to occur:
>
> --8<---cut here---start->8---
> Period 2012-02-06 to 2012-02-12
> ** Asset
> #+LATEX: \newpage
> *** DEPARTMENT
> | Data| Data | Data | Data |
> |-+--+--+--|
> | XX |1 |1 |0 |
> | YY |5 |4 |0 |
>
> --8<---cut here---end--->8---
>
> You should probably do that as a last resort in the last editing
> round, just to fix problematic spots.
>
> > I tried using the longtable environment, but that just splits the
> > table itself, so that I might have the heading at the bottom of the
> > page with one row of the table and a continued message. I also tried
> > the LaTeX directives \goodbreak before the headings and \nobreak
> > between the headings and tables but they didn't seem to affect
> > anything.
> >
>
> IIRC, these influence LaTeX's internal measures of whether this is a
> good or bad place to do it, but there are several factors in
> competition
> and they probably lose in comparison to the other factors.
>
> \newpage otoh is Thor's hammer: no questions asked.
>
> Nick
Re: [O] Controlling pagination on headings in Latex/PDF export?
Jos'h Fuller wrote: > Hi! > > I'm have an org-mode document something like this: > > * Period 2012-02-06 to 2012-02-12 > ** Asset > *** DEPARTMENT > | Data| Data | Data | Data | > |-+--+--+--| > | XX |1 |1 |0 | > | YY |5 |4 |0 | > > (There are more "Assets", each with several DEPARTMENTS. The tables are > short, perhaps 10-15 rows.) > > When I go to export a PDF, I will often get "DEPARTMENT" at the bottom of one > page, with the actual data table at the start of the next. Is there any way > to keep the heading together with the table? > Try adding #+LATEX: \newpage before the heading where you want the page break to occur: --8<---cut here---start->8--- Period 2012-02-06 to 2012-02-12 ** Asset #+LATEX: \newpage *** DEPARTMENT | Data| Data | Data | Data | |-+--+--+--| | XX |1 |1 |0 | | YY |5 |4 |0 | --8<---cut here---end--->8--- You should probably do that as a last resort in the last editing round, just to fix problematic spots. > I tried using the longtable environment, but that just splits the > table itself, so that I might have the heading at the bottom of the > page with one row of the table and a continued message. I also tried > the LaTeX directives \goodbreak before the headings and \nobreak > between the headings and tables but they didn't seem to affect > anything. > IIRC, these influence LaTeX's internal measures of whether this is a good or bad place to do it, but there are several factors in competition and they probably lose in comparison to the other factors. \newpage otoh is Thor's hammer: no questions asked. Nick
Re: [O] Temp files from testing are permanent...
Olaf Meeuwissen 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 — the trouble is that they leave tangled files and results produced during suceesful tests. > 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. Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ SD adaptations for KORG EX-800 and Poly-800MkII V0.9: http://Synth.Stromeko.net/Downloads.html#KorgSDada
[O] Controlling pagination on headings in Latex/PDF export?
Hi! I'm have an org-mode document something like this: * Period 2012-02-06 to 2012-02-12 ** Asset *** DEPARTMENT | Data| Data | Data | Data | |-+--+--+--| | XX |1 |1 |0 | | YY |5 |4 |0 | (There are more "Assets", each with several DEPARTMENTS. The tables are short, perhaps 10-15 rows.) When I go to export a PDF, I will often get "DEPARTMENT" at the bottom of one page, with the actual data table at the start of the next. Is there any way to keep the heading together with the table? I tried using the longtable environment, but that just splits the table itself, so that I might have the heading at the bottom of the page with one row of the table and a continued message. I also tried the LaTeX directives \goodbreak before the headings and \nobreak between the headings and tables but they didn't seem to affect anything. Thanks very much! ___ Jos'h Fuller, Production Programmer Arc Productions Ltd. p: 416.682.5237 | f: 416.682.5209 | http://www.arcproductions.com 230 Richmond Street East | Toronto, ON M5A 1P4 |
Re: [O] hidestarsfile: "hidestars" for file
Hi all
For the case that anyone should be interested in this, still only a
monolog:
On Thu, Feb 9, 2012 at 19:57, Michael Brand wrote:
> Now I see that for testing how a hidestarsfile looks like in a file
> viewer or simple editor, preferred over switching the major mode is:
> Just stay in Org mode and with org-hide-leading-stars still enabled
> from before, temporarily change only the look:
>
> #+BEGIN_SRC emacs-lisp
> (visible-mode 1)
> (my-disable-font-lock-except-org-hide)
> #+END_SRC
>
> I have not yet much of an idea how to do this: Disable font lock for
> all faces except the face org-hide. What possibilities are there?
After an adventurous, instructive and funny "proof of concept" to
backup, overwrite with the face "default" and restore again one of the
Org faces (extensible to all) with the help of "copy-face",
"symbol-name" and "intern" I decided to study font-lock and now am
starting to use this simple possibility to disable all faces except
org-hide:
#+BEGIN_SRC emacs-lisp
(defun my-org-lookout-face-defaults ()
"Reset font lock of faces back to `org-set-font-lock-defaults'.
Derived from `font-lock-add-keywords'."
(interactive)
(if (eq major-mode 'org-mode)
(progn
(setq font-lock-keywords
(font-lock-compile-keywords org-font-lock-keywords))
(font-lock-fontify-buffer))
(message "ERR: not in Org mode")
(ding)))
(defun my-org-lookout-face-hide ()
"Leave `org-hide' for leading stars and disable all other faces.
Derived from `font-lock-add-keywords' and
`org-set-font-lock-defaults'. Does not adapt font-lock-defaults and
sets font-lock-keywords directly"
(interactive)
(if (eq major-mode 'org-mode)
(progn
(setq font-lock-keywords
(font-lock-compile-keywords
'(("^\\(\\**\\)\\(\\* \\)\\(.*\\)"
(1 (if org-hide-leading-stars
'org-hide
'org-default))
(font-lock-fontify-buffer))
(message "ERR: not in Org mode")
(ding)))
#+END_SRC
Michael
Re: [O] understanding column groups
Rustom Mody writes: > I am trying to make (and understand!) column groups for html export > According to http://orgmode.org/manual/Column-groups.html having a > line starting / and then showing < for group start and group end > makes column groups. > > When I make and org file containing these 4 lines: > > * head > | / | < > | | < > | > | some text | and some more | d e | fg | > | | | | | > > all that happens on export is that the / < > etc literally appear in > the export! > > Is there something else I should study? Not this < > but this <>. i.e., no spaces between the angle brackets. Seems to work. > Org-mode version 7.8.02 > > --
Re: [O] understanding column groups
Hi Rustom, I think the issue is that you have missed assigning a column (the 3rd) to a group. Also, to simplify things, as stated no the link you gave, you can just specify the start of column groups. Something like the following should work as expected: * head | / | < |<| < | | some text | and some more | d e | fg | | | | | | Chris On Feb 16, 2012, at 9:27 AM, Rustom Mody wrote: > I am trying to make (and understand!) column groups for html export > According to http://orgmode.org/manual/Column-groups.html having a line > starting / and then showing < for group start and group end makes column > groups. > > When I make and org file containing these 4 lines: > > * head > | / | < > | | < > | > | some text | and some more | d e | fg | > | | | | | > > all that happens on export is that the / < > etc literally appear in the > export! > > Is there something else I should study? > > Org-mode version 7.8.02 - Chris Malone (mal...@ucolick.org) Dept. of Astronomy and Astrophysics UC Santa Cruz 1156 High Street Santa Cruz, CA 95064-1077 phone: 831-459-3809 -
[O] understanding column groups
I am trying to make (and understand!) column groups for html export According to http://orgmode.org/manual/Column-groups.html having a line starting / and then showing < for group start and group end makes column groups. When I make and org file containing these 4 lines: * head | / | < > | | < > | | some text | and some more | d e | fg | | | | | | all that happens on export is that the / < > etc literally appear in the export! Is there something else I should study? Org-mode version 7.8.02
Re: [O] Table formulas: Cannot use column names on the left hand side
Hi Yu On Thu, Feb 16, 2012 at 16:56, Yu wrote: > I tried today to use named columns for calculations. While this works > on the right hand side of the equation, names don't seem to work for > the left hand side -- Named columns are not supported on the left hand side. > which is a problem, because a change in column > arrangement, that isn't caused by org functions (e.g. manually > inserting a column with rectangle-copying) may cause an input column > to be overwritten accidentially (e.g. having a formula $4=$3*$2+$1 and > then manually inserting a column for line markers as described in > "Advanced Features"). If one uses M- and M- instead of rectangle edit to move around columns then it is much faster and Org takes care of adapting the formulas so that they still match the new coordinates. Michael
Re: [O] using variables in org text
Rainer M Krug 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. hth, Tom -- Thomas S. Dye http://www.tsdye.com
[O] Table formulas: Cannot use column names on the left hand side
Hello! I tried today to use named columns for calculations. While this works on the right hand side of the equation, names don't seem to work for the left hand side -- which is a problem, because a change in column arrangement, that isn't caused by org functions (e.g. manually inserting a column with rectangle-copying) may cause an input column to be overwritten accidentially (e.g. having a formula $4=$3*$2+$1 and then manually inserting a column for line markers as described in "Advanced Features"). Exactly this happened to me recently, forcing me to redo some by-hand evaluation. Here some examples to clarify the problem: - Recalculation attempts done each with C-u C-c C-c in the table and with C-c C-c in the formula line, and with C-u C-c *. Works fine: | a | b | a+b | |-+-+-| | 1.0 | 1.0 | 2.0 | | 1.5 | 0.5 | 2.0 | | 0.5 | 0.0 | 0.5 | #+TBLFM: $3=$1+$2;%.1f Doesn't Work: | | a | b | a+b | |---+-+-+-| | | 1.0 | 1.0 | | | | 1.5 | 0.5 | | | | 0.5 | 0.0 | | | ! | a | b | ab | #+TBLFM: $ab=$a+$b Doesn't Work: | | a | b | a+b | |---+-+-+-| | | 1.0 | 1.0 | | | | 1.5 | 0.5 | | | | 0.5 | 0.0 | | | ! | a | b | ab | #+TBLFM: $4=$a+$b Even this doesn't work | | a | b | a+b | |---+-+-+-| | | 1.0 | 1.0 | | | | 1.5 | 0.5 | | | | 0.5 | 0.0 | | | ! | a | b | ab | #+TBLFM: $4=$2+$3 This works again; This is sort of consistent with the specification, that "Unmarked lines are exempt from recalculation with C-u C-c *", but there was no mention, that it affects other methods of causing recalculation too in `(info "(org)")'. | | a | b | a+b | |---+-+-+-| | * | 1.0 | 1.0 | 2. | | * | 1.5 | 0.5 | 2. | | * | 0.5 | 0.0 | 0.5 | | ! | a | b | ab | #+TBLFM: $4=$2+$3 This again does NOT work. | | a | b | a+b | |---+-+-+-| | * | 1.0 | 1.0 | | | * | 1.5 | 0.5 | | | * | 0.5 | 0.0 | | | ! | a | b | ab | #+TBLFM: $ab=$2+$3 Works again. | | a | b | a+b | |---+-+-+-| | * | 1.0 | 1.0 | 2. | | * | 1.5 | 0.5 | 2. | | * | 0.5 | 0.0 | 0.5 | | ! | a | b | ab | #+TBLFM: $4=$a+$b
[O] Killing list and subtree?
Hi, Org friends. Is there an easy command to kill a list and its subtree hierarchy? Something like `C-c C-x C-w' but which would work at the list level rather than at the item level? For now, I'm either repeating a string of `C-k' or setting a region to cut, and it happens that neither is very efficient, human-wise :-). François
[O] [PATCH] Add "Time-stamp: <>" in (first 8 lines of) export template
>From 74f376c12cceae196f5a856eac1a39cdbcc8e360 Mon Sep 17 00:00:00 2001 From: Sebastien Vauban Date: Thu, 16 Feb 2012 15:48:37 +0100 Subject: [PATCH] Add Time-stamp in export template --- lisp/org-exp.el |1 + 1 files changed, 1 insertions(+), 0 deletions(-) diff --git a/lisp/org-exp.el b/lisp/org-exp.el index d9b5adc..2333bf0 100644 --- a/lisp/org-exp.el +++ b/lisp/org-exp.el @@ -3139,6 +3139,7 @@ Does include HTML export options as well as TODO and CATEGORY stuff." #+AUTHOR:%s #+EMAIL: %s #+DATE: %s +#+Time-stamp: <> #+DESCRIPTION: #+KEYWORDS: #+LANGUAGE: %s -- 1.7.5.1 Best regards, Seb -- Sebastien Vauban
[O] [PATCH] Fix old Babel syntax in library-of-babel.org
>From 3569c16e1d4270e6004441d8cdcc92801b3a01cd Mon Sep 17 00:00:00 2001 From: Sebastien Vauban 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 -- Sebastien Vauban
[O] using variables in org text
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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 - -- 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 : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk89FEYACgkQoYgNqgF2egrBVACeOd98IOFf/WkxnIO7FJPJ+D6i ptsAn1pmhPihT2OgZlRpZ/PfL2En1lUp =JQCJ -END PGP SIGNATURE-
Re: [O] Archiving old instances of repeating todos
On Wed, Feb 15, 2012 at 5:33 AM, Bernt Hansen wrote: > lbml...@hethcote.com writes: > >> How do you archive old instances of repeating todos, C-c C-x C-s archives >> the whole thing. I'd like to have something that would take the following: >> >> ** TODO Mutter an oath >>DEADLINE: <2012-02-13 Mon ++1d -0d> >>- State "DONE" from "TODO" [2012-02-12 Sun 16:25] I also note that you do not keep your state messages inside of a logbook drawer. If you are just concerned with seeing the data and not with it accumulating there, you could stuff it inside a LOGBOOK drawer. (setq org-clock-into-drawer t) or the equivalent configuration options should configure this. --Brian
Re: [O] Weirdness re: inclusion of figures
Hello! The behaviour is actually as expected. To understand this, you have to consider, that org-mode currently only seems to recognize the relation between source block and #+result paragraph if one of these two conditions holds: o The "#+result:" line follows the source code without any text in between. o Both code block and "#+result:" line are labeled with the same name. Also consider, as said by Nick Dokos, the significance of the ":exports" header argument: o By default the result is computed but not exported. o If the (unnamed) result is delimited from the source code by intervening text, it is no longer considered any source blocks result: The exporter just ignores the "#+result:" line and includes the image into the exported file. Labelling a source code block can be done with a "#+NAME:" line preceding the code block. When evaluating the code block, the "#+results"-line automatically gets named too. When reevaluating a code block then the contents of this "#+results" entry is correctly refreshed even after intervening code. What you want thus probably is: : #+name: code-block : #+begin_src R :file z.png :results output graphics : plot(matrix(rnorm(100), ncol=2), type="l") : #+end_src : : Intervening text : : #+results: code-block : [[file:z.png]] I did some tests to verify I'm right about this though, having installed a recent version from git (at most 2 days since the last pull): o No intervening text, no ":exports": Image is not exported. o No intervening text, ":exports both": Image is exported once; When exporting the code is rerun. o Intevening text, no ":exports": The image is exported once. The code block is not rerun on export. o Intervening text, ":exports both": The code is run twice (!), the image is exported both before and after the text. king regards, Yu 2012/2/16 Paul Magwene : > Hi All, > > I'm trying to get up to speed with org-mode and babel for doing > reproducible computational research. I'm just starting to play around > with simple examples, and I'm baffled by the following. > > This first example, when exported to HTML or LaTeX produces the > expected result -- a simply code block with one embedded figure. > > # Example 1. > > This is my R example: > > #+begin_src R :file z.png :results output graphics > plot(matrix(rnorm(100), ncol=2), type="l") > #+end_src > > Some intervening text... > > #+results: > [[file:z.png]] > > > However, this almost identical example, minus the intervening text > between the code and the results, doesn't include the figure: > > # Example 2 > > This is my R example: > > #+begin_src R :file z.png :results output graphics > plot(matrix(rnorm(100), ncol=2), type="l") > #+end_src > > #+results: > [[file:z.png]] > > > What gives here? Do I always need to have intervening text between the > source code and results in order to get a figure in the exported > document? > > Thanks, > Paul >
Re: [O] A manuscript on "reproducible research" introducing org-mode
Hello Jambunathan,
The ODT version was prepared "by hand" using LibreOffice. This was
written (last May) before your org-odt functions became part of org-mode
(if I'm right). I would now also do it with org-mode.
Christophe
Jambunathan K writes:
> Christophe
>
> I see an ODT file in there - LFPdetection_in.odt
> http://hal.archives-ouvertes.fr/hal-00591455/
>
> May I ask how the document was produced.
>
> Do you have any insights on how the Org's ODT exporter performs wrt your
> input Org file. Just curious.
>
>> @article{Delescluse2011,
>> title = "Making neurophysiological data analysis reproducible: Why and how?",
>> journal = "Journal of Physiology-Paris",
>> volume = "",
>> number = "0",
>> pages = " - ",
>> year = "2011",
>> note = "",
>> issn = "0928-4257",
>> doi = "10.1016/j.jphysparis.2011.09.011",
>> url = "http://www.sciencedirect.com/science/article/pii/S0928425711000374";,
>> author = "Matthieu Delescluse and Romain Franconville and Sébastien Joucla
>> and Tiffany Lieury and Christophe Pouzat",
>> keywords = "Software",
>> keywords = "R",
>> keywords = "Emacs",
>> keywords = "Matlab",
>> keywords = "Octave",
>> keywords = "LATEX",
>> keywords = "Org-mode",
>> keywords = "Python",
>> abstract = "Reproducible data analysis is an approach aiming at
>> complementing classical printed scientific articles with everything required
>> to independently reproduce the results they present. “Everything” covers
>> here: the data, the computer codes and a precise description of how the code
>> was applied to the data. A brief history of this approach is presented
>> first, starting with what economists have been calling replication since the
>> early eighties to end with what is now called reproducible research in
>> computational data analysis oriented fields like statistics and signal
>> processing. Since efficient tools are instrumental for a routine
>> implementation of these approaches, a description of some of the available
>> ones is presented next. A toy example demonstrates then the use of two open
>> source software programs for reproducible data analysis: the “Sweave family”
>> and the org-mode of emacs. The former is bound to R while the latter can be
>> used with R, Matlab, Python and many more “generalist” data processing
>> software. Both solutions can be used with Unix-like, Windows and Mac
>> families of operating systems. It is argued that neuroscientists could
>> communicate much more efficiently their results by adopting the reproducible
>> research paradigm from their lab books all the way to their articles, thesis
>> and books."
>> }
--
Most people are not natural-born statisticians. Left to our own
devices we are not very good at picking out patterns from a sea of
noisy data. To put it another way, we are all too good at picking out
non-existent patterns that happen to suit our purposes.
Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap
--
Christophe Pouzat
MAP5 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France
tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
Re: [O] A manuscript on "reproducible research" introducing org-mode
Christophe
I see an ODT file in there - LFPdetection_in.odt
http://hal.archives-ouvertes.fr/hal-00591455/
May I ask how the document was produced.
Do you have any insights on how the Org's ODT exporter performs wrt your
input Org file. Just curious.
> @article{Delescluse2011,
> title = "Making neurophysiological data analysis reproducible: Why and how?",
> journal = "Journal of Physiology-Paris",
> volume = "",
> number = "0",
> pages = " - ",
> year = "2011",
> note = "",
> issn = "0928-4257",
> doi = "10.1016/j.jphysparis.2011.09.011",
> url = "http://www.sciencedirect.com/science/article/pii/S0928425711000374";,
> author = "Matthieu Delescluse and Romain Franconville and Sébastien Joucla
> and Tiffany Lieury and Christophe Pouzat",
> keywords = "Software",
> keywords = "R",
> keywords = "Emacs",
> keywords = "Matlab",
> keywords = "Octave",
> keywords = "LATEX",
> keywords = "Org-mode",
> keywords = "Python",
> abstract = "Reproducible data analysis is an approach aiming at complementing
> classical printed scientific articles with everything required to
> independently reproduce the results they present. “Everything” covers here:
> the data, the computer codes and a precise description of how the code was
> applied to the data. A brief history of this approach is presented first,
> starting with what economists have been calling replication since the early
> eighties to end with what is now called reproducible research in
> computational data analysis oriented fields like statistics and signal
> processing. Since efficient tools are instrumental for a routine
> implementation of these approaches, a description of some of the available
> ones is presented next. A toy example demonstrates then the use of two open
> source software programs for reproducible data analysis: the “Sweave family”
> and the org-mode of emacs. The former is bound to R while the latter can be
> used with R, Matlab, Python and many more “generalist” data processing
> software. Both solutions can be used with Unix-like, Windows and Mac families
> of operating systems. It is argued that neuroscientists could communicate
> much more efficiently their results by adopting the reproducible research
> paradigm from their lab books all the way to their articles, thesis and
> books."
> }
--
[O] short section titles in TOC
Hi,
Is it possible to have a short version of a section title in the table
of contents? Eg in LaTeX, one can use
\section[Suggestions]{Suggestions for discussion}
and the first one would show up in the TOC. I was wondering if one
can do this in org-mode.
Best,
Tamas
