For some reason ob-R refuses to compile when it requires ob-comint.
When (require 'ob-comint) is not included in ob-R.el everything
compiles without error, but warnings are thrown because the
arguments to a macro defined in ob-comint are mis-interpreted as
functions.
When (require 'ob-comint) is added to ob-R.el then it throws errors
complaining that the last argument to a function is nil and should
be a string. I don't understand this error at all and can't fix it.
* lisp/org.el (org-babel-load-languages): this variable controls which
languages will be loaded by org-babel. It is customizable through
the customize interface.
(org-babel-do-load-languages): load those languages in
org-babel-load-languages and disable those with nil cdr's
* lisp/babel/ob.el (org-confirm-babel-evaluate): variable used to
control evaluation of code blocks, default value it t, meaning all
code block evaluation requires confirmation
(org-babel-confirm-evaluate): function used to request confirmation
of code block evaluation from the user
(org-babel-execute-src-block): this function is the single point of
entry for evaluation of code blocks (whether initiated through lob
call, through direct code block evaluation, or as part of file
exportation). Every time this function is called it will now
request confirmation from the user. The newly added
`org-confirm-babel-evaluate' variable can be used to configure this
behavior.
(org-babel-no-eval-on-ctrl-c-ctrl-c): This variable can be used to
inhibit evaluation of code blocks with C-c C-c.
* lisp/org.el (org-ctrl-c-ctrl-c): added documentation of code block
evaluation behavior
* lisp/babel/ob-keys.el (org-babel-key-bindings): adding keybindings
for executing code blocks and for opening their results
patch by Stephen Eglen.
Here is a patch for the 'capture' section of org.texi . I've added a
few lines of @comments:
+@comment SJE: Should be Org file or Org-mode file (see prev two items)?
+@comment SJE: should these sentences terminate in period?
(i.e. the following lines in the table)
+@comment SJE: org-feed is not autoloaded - should that be mentioned?
Stephen
* lisp/org-capture.el (org-capture-set-target-location): Store
exact positions for file+regexp and file+function targets.
(org-capture-place-entry, org-capture-place-item)
(org-capture-place-table-line, org-capture-place-plain-text): Respect
exact positions.
(org-capture-finalize): Make sure we are at the beginning of a line
when fixing the empty lines after the entry.
* lisp/org.el (org-entry-get-with-inheritance): New argument LITERAL-NIL.
(org-entry-get): Pass `literal-nil' into
`org-entry-get-with-inheritance'.
(org-todo): React to nil values of the LOGGING property.
Of course, an updated patch is attached.
Best -- Eric
Carsten Dominik <carsten.dominik@gmail.com> writes:
> Hi Eric,
>
> I tried to apply the patch, but it does not apply cleanly, maybe due
> to other changes. Can I ask you to update and resubmit?
>
> Thanks!
>
> - Carsten
>
> On Jun 21, 2010, at 6:37 PM, Eric Schulte wrote:
>
>> Hi Robert,
>>
>> Thanks for the thoughtful message.
>>
>> I present a couple of solutions below.
>>
>> Robert Cunningham <robut@iinet.net.au> writes:
>>
>>> G'day All,
>>>
>>> I wonder if I've missed something and there is a better way.
>>>
>>> Essentially I'm trying to use org babel with R and LaTeX to create
>>> figures
>>> with both long and short captions (for contents)
>>>
>>> I'd started with:
>>>
>>> #+CAPTION: Nice data (filled points indicate less nice data)
>>> #+LABEL: fig:nicedata
>>> #+ATTR_LaTeX: width=0.98\textwidth
>>> #+begin_src R :file ndata.pdf :width 1000 :height 617 :exports
>>> results
>>> dotchart(data$ndata)
>>> #+end_src
>>>
>>> which pointed to the need for long/short captions...
>>>
>>> feeling hopeful I tried:
>>>
>>> #+CAPTION: Nice data [Nice data (filled points indicate less nice
>>> data)]
>>> #+LABEL: fig:nicedata
>>> #+ATTR_LaTeX: width=0.98\textwidth
>>> #+begin_src R :file ndata.pdf :width 1000 :height 617 :exports
>>> results
>>> dotchart(data$ndata)
>>> #+end_src
>>>
>>
>> I'm attaching a patch [1] which adds shortname support for captions.
>> Once
>> applied, the following syntax will result in a caption with a
>> shortname
>> and a longname.
>>
>> --8<---------------cut here---------------start------------->8---
>> some pre-table text
>>
>> #+source: g-nicedata
>> #+begin_src gnuplot :file graph.png :exports results
>> plot sin(x)
>> #+end_src
>>
>> #+Caption: [nice data]{a longer description of the niceness of the
>> data}
>> #+results: g-nicedata
>> [[file:graph.png]]
>>
>> some post-table text
>> --8<---------------cut here---------------end--------------->8---
>>
>> however, while this patch is still pending there is an Org-babel
>> solution below which should work immediately.
>>
>>>
>>>
>>> but no luck there.
>>>
>>> Next effort was to try to use R and LaTex more directly with
>>> noweb. I tried
>>> this:
>>>
>>>
>>>
>>> #+srcname: r-nicedata
>>> #+begin_src R :session :file ndata.pdf :results output :exports
>>> results
>>> dotchart(data$ndata)
>>> #+end_src
>>>
>>>
>>> #+begin_src latex :noweb yes
>>> \begin{figure}[htb!]
>>> \centering
>>> \includegraphics[width=0.98\textwidth]{<<r-nicedata()>>}
>>> \caption[Nice data]{Nice data (filled points indicate less nice
>>> data)}
>>> \label{fig:nicedata}
>>> \end{figure}
>>> #+end_src
>>>
>>>
>>>
>>> This does produce the figure and long/short contents BUT ALSO
>>> produces this:
>>>
>>> #+results: r-nicedata
>>> [[file:ndata.pdf]]
>>>
>>> which upon export results in a link and consequently the plot
>>> appearing both
>>> in the figure and elsewhere. This second plot is unwelcome.
>>>
>>> I've tried assorted :results and :output options but have not found
>>> how to
>>> suppress the #+results: but still obtain the figure. I've always used
>>> the :session option.
>>>
>>> I've also tried twigging an org-export option to suppress pdf
>>> export but the
>>> link is still exported so that is not a solution.
>>>
>>> The current "working" solution is to use the noweb approach and
>>> then use sed
>>> to clean out the links to the second image-ugly to say the least!
>>>
>>
>> You were very close with the noweb approach. The following
>> combination
>> should work -- notice the ":results silent" header argument to the
>> source block.
>>
>> --8<---------------cut here---------------start------------->8---
>> some pre-table text
>>
>> #+source: g-nicedata
>> #+begin_src gnuplot :file graph.png :results silent :exports none
>> plot sin(x)
>> #+end_src
>>
>> #+begin_src latex :noweb yes
>> \begin{figure}[htb!]
>> \centering
>> \includegraphics[width=0.98\textwidth]{<<g-nicedata()>>}
>> \caption[Nice data]{some nice data -- filled points indicate less
>> nice data}
>> \label{fig:nicedata}
>> \end{figure}
>> #+end_src
>>
>> some post-table text
>> --8<---------------cut here---------------end--------------->8---
>>
>> is exported to the following latex,
>>
>> --8<---------------cut here---------------start------------->8---
>> some pre-table text
>>
>>
>>
>> \begin{figure}[htb!]
>> \centering
>> \includegraphics[width=0.98\textwidth]{graph.png}
>> \caption[Nice data]{some nice data -- filled points indicate less
>> nice data}
>> \label{fig:nicedata}
>> \end{figure}
>>
>> some post-table text
>> --8<---------------cut here---------------end--------------->8---
>>
>> Hope this helps,
>>
>> Best -- Eric
>>
>>>
>>>
>>>
>>> All this with org version 6.36c
>>>
>>>
>>> What have I missed? What is the best way to do this?
>>>
>>>
>>> Cheers,
>>>
>>> Robert Cunningham
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Emacs-orgmode mailing list
>>> Please use `Reply All' to send replies to the list.
>>> Emacs-orgmode@gnu.org
>>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>>
>> Footnotes:
>> [1] From 6a55dcab99bbd7840117b8390ab5db347d2573ef Mon Sep 17
>> 00:00:00 2001
>> From: Eric Schulte <schulte.eric@gmail.com>
>> Date: Mon, 21 Jun 2010 09:02:37 -0700
>> Subject: [PATCH] add short-names to #+captions with support for
>> latex export
>>
>> captions specified with the following syntax
>> #+CAPTION: [shortname]{longname}
>> will have their short and longnames handled appropriately.
>>
>> Thanks to Robert Cunningham for suggesting this feature.
>>
>> * lisp/org-exp.el (org-export-attach-captions-and-attributes): adding
>> a shortname attribute to caption strings under the symbol name
>> org-caption-shortn.
>>
>> * lisp/org-latex.el (org-export-latex-tables): handling caption short
>> names on table export
>>
>> (org-export-latex-convert-table.el-table): handling caption short
>> names on table.el type table export
>>
>> (org-export-latex-links): handling caption short names on link/image
>> export
>>
>> (org-export-latex-format-image): now takes an optional argument
>> specifying a caption short name
>> ---
>> lisp/org-exp.el | 14 +++++++++-----
>> lisp/org-latex.el | 21 ++++++++++++++-------
>> 2 files changed, 23 insertions(+), 12 deletions(-)
>>
>> diff --git a/lisp/org-exp.el b/lisp/org-exp.el
>> index 029e4d7..466d7da 100644
>> --- a/lisp/org-exp.el
>> +++ b/lisp/org-exp.el
>> @@ -1256,7 +1256,7 @@ the current file."
>> (goto-char (point-min))
>> (while (re-search-forward org-bracket-link-regexp nil t)
>> (org-if-unprotected-at (1+ (match-beginning 0))
>> - (let* ((md (match-data))
>> + (let* ((md (match-data))
>> (desc (match-end 2))
>> (link (org-link-unescape (match-string 1)))
>> (slink (org-solidify-link-text link))
>> @@ -1381,8 +1381,8 @@ removed as well."
>> select-tags "\\|")
>> "\\):"))
>> (re-excl (concat ":\\(" (mapconcat 'regexp-quote
>> - exclude-tags "\\|")
>> - "\\):"))
>> + exclude-tags "\\|")
>> + "\\):"))
>> beg end cont)
>> (goto-char (point-min))
>> (when (and select-tags
>> @@ -1593,11 +1593,14 @@ table line. If it is a link, add it to the
>> line containing the link."
>> "^[ \t]*\\(|[^-]\\)"
>> "\\|"
>> "^[ \t]*\\[\\[.*\\]\\][ \t]*$"))
>> - cap attr label end)
>> + cap shortn attr label end)
>> (while (re-search-forward re nil t)
>> (cond
>> ((match-end 1)
>> - (setq cap (concat cap (if cap " " "") (org-trim (match-string 1)))))
>> + (setq cap (concat cap (if cap " " "") (org-trim (match-string 1))))
>> + (when (string-match "\\[\\(.*\\)\\]{\\(.*\\)}" cap)
>> + (setq shortn (match-string 1 cap)
>> + cap (match-string 2 cap))))
>> ((match-end 2)
>> (setq attr (concat attr (if attr " " "") (org-trim
>> (match-string 2)))))
>> ((match-end 3)
>> @@ -1609,6 +1612,7 @@ table line. If it is a link, add it to the
>> line containing the link."
>> (point-at-eol)))
>> (add-text-properties (point-at-bol) end
>> (list 'org-caption cap
>> + 'org-caption-shortn shortn
>> 'org-attributes attr
>> 'org-label label))
>> (if label (push (cons label label) target-alist))
>> diff --git a/lisp/org-latex.el b/lisp/org-latex.el
>> index 01a4b05..6c2aab2 100644
>> --- a/lisp/org-latex.el
>> +++ b/lisp/org-latex.el
>> @@ -1576,7 +1576,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (org-table-last-column-widths (copy-sequence
>> org-table-last-column-
>> widths))
>> fnum fields line lines olines gr colgropen line-fmt align
>> - caption label attr floatp longtblp)
>> + caption shortn label attr floatp longtblp)
>> (if org-export-latex-tables-verbatim
>> (let* ((tbl (concat "\\begin{verbatim}\n" raw-table
>> "\\end{verbatim}\n")))
>> @@ -1585,6 +1585,8 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (progn
>> (setq caption (org-find-text-property-in-string
>> 'org-caption raw-table)
>> + shortn (org-find-text-property-in-string
>> + 'org-caption-shortn raw-table)
>> attr (org-find-text-property-in-string
>> 'org-attributes raw-table)
>> label (org-find-text-property-in-string
>> @@ -1652,7 +1654,8 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (if floatp "\\begin{table}[htb]\n"))
>> (if floatp
>> (format
>> - "\\caption{%s%s}"
>> + "\\caption%s{%s%s}"
>> + (if shortn (concat "[" shortn "]") "")
>> (if label (concat "\\\label{" label
>> "}") "")
>> (or caption "")))
>> (if (and longtblp caption) "\\\\\n" "\n")
>> @@ -1680,10 +1683,11 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>>
>> (defun org-export-latex-convert-table.el-table ()
>> "Replace table.el table at point with LaTeX code."
>> - (let (tbl caption label line floatp attr align rmlines)
>> + (let (tbl caption shortn label line floatp attr align rmlines)
>> (setq line (buffer-substring (point-at-bol) (point-at-eol))
>> label (org-get-text-property-any 0 'org-label line)
>> caption (org-get-text-property-any 0 'org-caption line)
>> + shortn (org-get-text-property-any 0 'org-caption-shortn line)
>> attr (org-get-text-property-any 0 'org-attributes line)
>> align (and attr (stringp attr)
>> (string-match "\\<align=\\([^ \t\n\r,]+\\)" attr)
>> @@ -1721,7 +1725,8 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (setq tbl (concat "\\begin{center}\n" tbl "\\end{center}")))
>> (when floatp
>> (setq tbl (concat "\\begin{table}\n"
>> - (format "\\caption{%s%s}\n"
>> + (format "\\caption%s{%s%s}\n"
>> + (if shortn (format "[%s]" shortn) "")
>> (if label (format "\\label{%s}" label) "")
>> (or caption ""))
>> tbl
>> @@ -1822,6 +1827,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> "file")))
>> (coderefp (equal type "coderef"))
>> (caption (org-find-text-property-in-string 'org-caption
>> raw-
>> path))
>> + (shortn (org-find-text-property-in-string
>> org-caption-shortn raw-path))
>> (attr (or (org-find-text-property-in-string
>> org-attributes raw-
>> path)
>> (plist-get org-export-latex-options-plist
>> :latex-image-
>> options)))
>> (label (org-find-text-property-in-string 'org-label raw-path))
>> @@ -1859,7 +1865,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (plist-get org-export-latex-options-plist :inline-images))
>> ;; OK, we need to inline an image
>> (insert
>> - (org-export-latex-format-image raw-path caption label attr)))
>> + (org-export-latex-format-image raw-path caption label
>> attr shortn)))
>> (coderefp
>> (insert (format
>> (org-export-get-coderef-format path desc)
>> @@ -1889,7 +1895,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (t (insert "\\texttt{" desc "}")))))))
>>
>>
>> -(defun org-export-latex-format-image (path caption label attr)
>> +(defun org-export-latex-format-image (path caption label attr
>> &optional shortn)
>> "Format the image element, depending on user settings."
>> (let (ind floatp wrapp multicolumnp placement figenv)
>> (setq floatp (or caption label))
>> @@ -1932,7 +1938,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (floatp "\\begin{figure}%placement
>> \\centering
>> \\includegraphics[%attr]{%path}
>> -\\caption{%labelcmd%caption}
>> +\\caption%shortn{%labelcmd%caption}
>> \\end{figure}")
>> (t "\\includegraphics[%attr]{%path}")))
>>
>> @@ -1953,6 +1959,7 @@ The conversion is made depending of STRING-
>> BEFORE and STRING-AFTER."
>> (expand-file-name path)
>> path))
>> (cons "attr" attr)
>> + (cons "shortn" (if shortn (format "[%s]" shortn) ""))
>> (cons "labelcmd" (if label (format "\\label{%s}"
>> label)""))
>> (cons "caption" (or caption ""))
>> --
>> 1.7.0.4
>>
>> _______________________________________________
>> Emacs-orgmode mailing list
>> Please use `Reply All' to send replies to the list.
>> Emacs-orgmode@gnu.org
>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>
> - Carsten
>From 5cbb38e25a2d2eae7c3c688d347f80619ecb8463 Mon Sep 17 00:00:00 2001
From: Eric Schulte <schulte.eric@gmail.com>
Date: Thu, 1 Jul 2010 08:07:17 -0700
Subject: [PATCH] add short-names to #+captions with support for latex export
captions specified with the following syntax
#+CAPTION: [shortname]{longname}
will have their short and longnames handled appropriately.
Thanks to Robert Cunningham for suggesting this feature.
* lisp/org-exp.el (org-export-attach-captions-and-attributes): adding
a shortname attribute to caption strings under the symbol name
org-caption-shortn.
* lisp/org-latex.el (org-export-latex-tables): handling caption short
names on table export
(org-export-latex-convert-table.el-table): handling caption short
names on table.el type table export
(org-export-latex-links): handling caption short names on link/image
export
(org-export-latex-format-image): now takes an optional argument
specifying a caption short name
* lisp/org.el (org-switchb): Renamed from `org-iswitchb'. Improve
docstring.
(org-iswitchb): New alias.
(org-ido-switchb): Make alias point to `org-switchb'.
* lisp/org-capture.el (org-capture-fill-template): Respect
time-of-day preference in template prompt.
In an interactive time prompt in a capture template, the users
preference of getting a stamp with time was not respected.
Reported by Markus Heller
* lisp/babel/langs/ob-python.el (org-babel-python-buffers):
technically this should be initialized as an alist, although in
practice this doesn't really make any functional difference because
whenever this variable is used it has new values properly assigned
to it, and it is supposed to start basically empty.
This patch removes an obsolete declaration and call of the function
`org-publish-initialize-files-alist' from org-protocol.el.
This function does not exist anymore. It was removed when we
implemented the new publishing cache.
Best wishes
Sebastian
* org-feed.el (org-feed-unescape): New function. Unescape
protected entities.
(org-feed-parse-atom-entry): Use function for atom:content
type text and html.
* lisp/org.el (org-time-string-to-absolute): Ignore cyclic repeater
when displaying items on todays agenda date.
Ignore the cyclic repeater when displaying items on today's agenda
date. If you have a weekly task and miss the date the agenda view
will show more than a week late now instead of resetting on the
cyclic repeating date. This makes it much more obvious when you
missed a repeating task after the repeater.
* lisp/org-agenda.el (org-agenda-get-progress): Avoid reusing previous
value of EXTRA.
Sebastien Vauban writes:
> Finally reporting the following bug. Has been there for as long as I can
> remember, but never did report it when seeing it. And kept forgetting.
>
> So, now...
>
> --8<---------------cut here---------------start------------->8---
> * 2010
>
> ** 2010-06 June
>
> *** Admin
>
> **** Organization
> :LOGBOOK:
> CLOCK: [2010-06-30 Wed 13:30]--[2010-06-30 Wed 17:50] => 4:20
> - DUPLICATED TeXt.
> :END:
>
> **** Emails and News
> :LOGBOOK:
> CLOCK: [2010-06-28 Mon 09:10]--[2010-06-28 Mon 10:40] => 1:30
> CLOCK: [2010-06-30 Wed 10:30]--[2010-06-30 Wed 12:30] => 2:00
> :END:
>
> *** ABC
> :LOGBOOK:
> CLOCK: [2010-06-30 Wed 09:30]--[2010-06-30 Wed 10:30] => 1:00
> - Transfer of files to ABC.
> :END:
> --8<---------------cut here---------------end--------------->8---
>
> generates the following timeline:
>
> --8<---------------cut here---------------start------------->8---
> Timeline of file /home/sva/Projects/ecm.org
>
> 2010-06-28 Mon _________________________________
> Clocked: (1:30) Emails and News
>
> 2010-06-29 Tue _________________________________
>
> 2010-06-30 Wed _________________________________
> Clocked: (1:00) ABC - Transfer of files to ABC.
> Clocked: (2:00) Emails and News - DUPLICATED TeXt.
> Clocked: (4:20) Organization - DUPLICATED TeXt.
> --8<---------------cut here---------------end--------------->8---
>
> As you can see, the fact that I never put a descriptive text for "reading
> emails" is wrongly reported: previous text is used in the timeline, instead.
Eric Schulte
Carsten Dominik
Stephen Eglen
Dan Davison
David Maus
Sebastian Rose
Bernt Hansen
Julien Danjou