Re: Citations merged!

[Julian M. Burgos]

Amazing!  Thank you to everyone that contributed.  I am looking forward to 
start playing with this. :)

Nicolas Goaziou writes:

> Hello,
>
> It took years, but citations are now full part of Org syntax.
>
> Thanks to everyone involved over the time!
>
> Now, it needs to be documented, but that will come a bit later.
>
> Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is

Re: [tip for EXWM users] An alternative method for isolate trees

[Julian M. Burgos]

Hi Kyle,

You are right. When running emacs without my personal config things work as 
described in the manual.  I should have verified that first.

My best,

Julian

Kyle Meyer writes:

> Julian M. Burgos writes:
>
>> I have not noticed that org-tree-to-indirect-buffer
>> reuses the indirect buffer when you call it for a second time.
>> According to the manual, "with a C-u prefix, do not remove the
>> previously used indirect buffer", but that does not seem to work.
>> When you do Cu-Cc-Cx-b from a buffer that already has an indirect
>> buffer you get a "cannot modify an area being edited in a dedicated
>> buffer".  If you try it from a different buffer, the prefix is ignored
>> and the indirect buffer is assigned to the tree from the last buffer.
>
> Hmm, could you provide a reproducer for the problem?  Here's what I
> tried with the current master (afd75d05a), Emacs 27.1, and no custom
> configuration.
>
> --8<---cut here---start->8---
> * a
> a content
> * b
> b content
> --8<---cut here---end--->8---
>
>  - on "a", C-c C-x b  ;; org-tree-to-indirect-buffer
>Displays -a-1 buffer.
>
>  - move to "b", C-u C-c C-x b
>Displays -b-1 buffer, a-1 buffer still exists.


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is

Re: [tip for EXWM users] An alternative method for isolate trees

[Julian M. Burgos]

Hi Juan,

You are right. :) I have not noticed that org-tree-to-indirect-buffer reuses 
the indirect buffer when you call it for a second time.  According to the 
manual, "with a C-u prefix, do not remove the previously used indirect buffer", 
but that does not seem to work.  When you do Cu-Cc-Cx-b from a buffer that 
already has an indirect buffer you get a "cannot modify an area being edited in 
a dedicated buffer".  If you try it from a different buffer, the prefix is 
ignored and the indirect buffer is assigned to the tree from the last buffer.

This does not seem to be a limitation from emacs, as it is possible to open 
multiple indirect buffers from a base buffer, using for example 
clone-indirect-buffer.  So it should be possible to make a function combining 
"clone-indirect-buffer" and "org-narrow-to-subtree" perhaps?  I am thinking so 
this option is available not only to EXWM users.

Ideally, there should be an option to allow org-tree-to-indirect-buffer to 
create more than one indirect buffer if desired.

My best,

Julian

Juan Manuel Macías writes:

> Hi Julian, thanks for your comment.
>
> "Julian M. Burgos"  writes:
>
>> Thank you, although I tested your functions and compared with the
>> original org-tree-to-indirect-buffer, the only difference I see is
>> that your function creates a new exwm workspace. The original function
>> already creates indirect buffers with their own names (using a slash
>> instead of the double colons). Or I am missing something?
>
> org-tree-to-indirect-buffer creates a new buffer, but (as far as I know)
> does not allow accumulating buffers. In other words, you cannot have
> several isolated trees at the time. In this method it just occurred to
> me to configure org-indirect-buffer-display as new-frame and take
> advantage of EXWM frame management.
>
> Best regards,
>
> Juan Manuel


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is

Re: [tip for EXWM users] An alternative method for isolate trees

[Julian M. Burgos]

Hi Juan Manuel,

Thank you, although I tested your functions and compared with the original 
org-tree-to-indirect-buffer, the only difference I see is that your function 
creates a new exwm workspace.  The original function already creates indirect 
buffers with their own names (using a slash instead of the double colons).  Or 
I am missing something?

My best,

Julian

Juan Manuel Macías writes:

> Hi,
>
> Since EXWM uses Emacs frames as virtual desktops, I have written this
> alternative method of `org-tree-to-indirect-buffer', which I share here.
> With this method I can have several isolated trees, with their own name,
> and access them quickly (with helm-buffer-list, for example):
>
> #+begin_src emacs-lisp
>   (defun my-goto-buffer-regexp (regexp)
> (dolist (buffer (buffer-list))
>   (let ((name (buffer-name buffer)))
>   (when (and name (not (string-equal name ""))
>  (string-match regexp name))
> (switch-to-buffer buffer)
>
>   (defun my-org-tree-to-indirect-buffer ()
> (interactive)
> (let ((buf (buffer-name))
> (ind-buf (replace-regexp-in-string "\\[.+\\]" "" (nth 4 
> (org-heading-components
> (org-indirect-buffer-display 'new-frame))
>   (org-tree-to-indirect-buffer)
>   (my-goto-buffer-regexp ind-buf)
>   (rename-buffer (concat buf "::" ind-buf
> #+end_src
>
> Best regards,
>
> Juan Manuel


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] running a source code by name

[Julian M. Burgos]

Thanks guys.  A combination of org-babel-goto-named-src-block and
org-babel-execute-src-block did the trick.

I am building an org template to create html presentations using the R
package xaringan.  In my case each slide is a markdown source block.
The elisp block tangles everything into a Rmd file, and the R block runs
rmarkdown::render and opens the resulting html file in a browser.

Thanks again. :)

Berry, Charles writes:

> OK, I have to note that this will also do the job that the OP requested:
>
> #+begin_src emacs-lisp :results silent :var result=myRcode
>
> #+end_src
>
> although it seems a little strange to write an empty src block for its side 
> effects.
>
> I suppose I should have suggested this in the first place:
>
> #+begin_src emacs-lisp :results silent :noweb yes
> <>
> #+end_src
>
> although the return value from the noweb reference could be troublesome 
> depending on what else is included in the latter src block.
>
> Chuck
>
>> On May 28, 2018, at 1:16 PM, John Kitchin  wrote:
>>
>> Here is yet another variation, that may be suitable for what you want:
>>
>>
>> #+name: myPyCode
>> #+BEGIN_SRC python
>> print('Hello')
>> #+END_SRC
>>
>>
>> #+BEGIN_SRC emacs-lisp :var results=myPyCode
>> results
>> #+END_SRC
>>
>> #+RESULTS:
>> : Hello
>>
>>
>> John
>>
>> ---
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitchingroup.cheme.cmu.edu=02%7C01%7C%7Cfdaa27b411604ed32a0108d5c4d9fa01%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636631362846470731=4K%2B96NBf5KPaoz13laaAR0%2FaqY2FlefTLy%2BPXy6YtO8%3D=0
>>
>>
>> On Mon, May 28, 2018 at 9:25 AM, Berry, Charles  wrote:
>>
>>
>> > On May 28, 2018, at 7:35 AM, Eric S Fraga  wrote:
>> >
>> > On Monday, 28 May 2018 at 11:13, Julian M. Burgos wrote:
>> >> Dear list,
>> >>
>> >> I have an org file with an R source code block.  I want to have a second
>> >> code block with an elisp call to run that first code.  Something like this
>> >>
>> >>
>> >> #+begin_src emacs-lisp :results silent :tangle no
>> >>
>> >> ... Some elisp code to run the "myRcode" block.
>> >
>> > Something along the lines of:
>> >
>> >(org-babel-goto-named-src-block "myRcode")
>> >(org-babel-execute-src-block)
>> >
>> > should do the job?
>>
>> Maybe wrap it in
>>
>> (save-excursion ... )
>>
>> or use
>>
>> (org-sbe "myRcode")
>>
>> or
>>
>> (org-babel-ref-resolve "myRcode")
>>
>> which both can also pass :var args.
>>
>> HTH,
>>
>> Chuck
>>
>>
>>
>>
>>


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] running a source code by name

[Julian M. Burgos]

Dear list,

I have an org file with an R source code block.  I want to have a second
code block with an elisp call to run that first code.  Something like this



#+begin_src emacs-lisp :results silent :tangle no

... Some elisp code to run the "myRcode" block.

#+end_src


#+NAME: myRcode
#+beg in_src R :results silent :tangle no

... My R code here

#+end_src

What would be the best way to do it?

Many thanks,

Julian


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Can export the files with bibliography only to LaTeX

[Julian M. Burgos]

I do not think there is an out-of-the-box way to export a bibliography
directly from org-mode to formats other than LaTex.  What I usually do
is export to Tex and then use Pandoc (https://pandoc.org/) to convert that 
document to other
formats, usually Word so I can share my work with my colleagues.  Pandoc
can read the bibtex file and add the right citations, doing something
like this:

pandoc --bibliography /path/to/my_bib_file.bib my_document.docx my_document.tex

There is also the ox-pandoc package, that allows you to export directly
from org using pandoc.  I have not tried yet (it is in my to-do list).

https://github.com/kawabata/ox-pandoc

Julian

Melleus writes:

> I used to think that I can export from org to bunch of different
> formats. But all of a sudden when I need this feature I see that I can
> export only to LaTeX. But when I try exporting to other format I get
>
> Wrong type argument: stringp, nil   error message.
>
> When there's no bibtex references or exporting to LaTeX everything just
> works.
>
> How can I troubleshoot the situation and possibly find the clue? I
> couldn't find any documentation on the exporting references issues on
> Worg unfortunately.
>
> My environment: Gentoo with stable keyword, Emacs 25.3.1, Org 9.1.4.
>
> Thanks ahead of time.


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] Confused about org-duration-format

[Julian M. Burgos]

Dear list,

I do not quite follow how to set up org-duration-format.  In particular,
I would like to have my clock tables represented as decimal hours (e.g.
3.50 h, rather than 3:30 h).

Any help would be welcomed.

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] org-clock-in only in current buffer

[Julian M. Burgos]

Dear org-moders,

Until a recent update (or an unintended change in my configuration), I
was able to clock in a task (org-clock-in) *without* org mode trying to
find open clocks.  I cannot figure out what changed, but now
org-clock-in opens all my agenda buffers searching for open clocks, which is 
not very convenient as I have dozens of agenda files.
What would be the best way to a) restrict the search of open clocks to
the current buffer, or b) turn off the search of open clocks?

Many thanks

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] org to static site?

[Julian M. Burgos]

Hi Matt,

Recently I started to use Hugo to maintain our project's website:

http://novasarc.hafogvatn.is/

I am liking it very much. I keep the entire site in a single file, with
each page in a single subtree. Modifications to the template are also
kept in subtrees.  I edit this page directly, rather than using the hugo
tools to create content.  Then to update the site I tangle the org file
to create all the htlm files of the site, and run hugo to create the
site files that are then copied to the server.  Pretty easy.

Julian


Matt Price writes:

> I'm trying to wean myself off of Wordpress for next year's teaching
> websites, and am wondering what solutions other people are using for
> turning a collection of org pages and/or subtrees into a static html site.
> I am leaning towards Hugo but honestly not for any sensible reason; I've
> seen other people use Jekyll, though the fact that Github doesn't support
> direct conversion from org-mode removes some of Jekyll's appeal; and I know
> there are a number of other solutions too.
>
> So, I would love to hear what you all recommend.
>
> Thanks,
> Matt


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Viewing pdf images

[Julian M. Burgos]

So if I have an org file with links to pdfs, your function will convert
those pdfs to images and also will replace the link to the pdf for the
link to the newly created png?

Kaushal Modi writes:

> On Wed, Apr 5, 2017, 5:21 AM Julian M. Burgos <julian.bur...@hafogvatn.is>
> wrote:
>
>> Can you clarify the purpose of this function?  I understand that
>> produces an image of each pdf linked to the file.
>
>
> That's correct, but the user can control when that happens by adding that
> function to the appropriate hook.
>
>  But
>
> the question in
>> emacs.stackexchange was about displaying pdf's as inline images.
>
>
> Yes, I forgot to change the hook when I updated the whole answer; I have
> fixed that now. Now the answer shows how to add this function to the
> before-save-hook.
>
>  Your
>
> function only converts the pdfs into images (and you have to do an
>> export to achieve that).
>
>
> Well, the function org-include-img-from-pdf is the workhorse here, and it
> doesn't depend on when you want the PDF to PNG conversion to happen. The
> "when" depends on the hook you add the function to.
>
>   You would still would have to add a link to
>> the image file in order to see it as an inline image.
>> add a link in order to see it, correct?
>>
>
> I didn't follow that. The user is already adding that. Example:
>
> # ()convertfrompdf:t
> # User needs to have a ./foo.pdf. That will be converted to the below
> referenced foo.png.
> [[./foo.png]]
>
> When I get to a computer, I'll confirm if the #+CAPTION: and/or #+NAME: is
> needed for the inline images to show. Above works fine for exports, so I
> assumed that the inline images should show fine too.


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Viewing pdf images

[Julian M. Burgos]

Can you clarify the purpose of this function?  I understand that
produces an image of each pdf linked to the file.  But the question in
emacs.stackexchange was about displaying pdf's as inline images.  Your
function only converts the pdfs into images (and you have to do an
export to achieve that).  You would still would have to add a link to
the image file in order to see it as an inline image.
add a link in order to see it, correct?


Kaushal Modi writes:

> In case you are interested, I have now updated the solution on
> emacs.stackexchange to not use #+HEADER for this purpose:
> http://emacs.stackexchange.com/a/401/115
>
> Earlier discussion on that:
> http://lists.gnu.org/archive/html/emacs-orgmode/2017-01/msg00260.html
>
> The solution still does the exact same thing as before.
>
> On Tue, Mar 21, 2017 at 8:37 PM Doyley, Marvin M. <m.doy...@rochester.edu>
> wrote:
>
>> Thanks,
>>
>> Much appreciated.
>>
>> Cheers,
>> M
>> > On Mar 21, 2017, at 6:34 AM, Julian M. Burgos <
>> julian.bur...@hafogvatn.is> wrote:
>> >
>> > I have the following in my .emacs file.  For this to work you need to
>> > have your emacs compiled with imagemagick support (and have imagemagick
>> > installed, of course).  It works well, although the images do not appear
>> > immediately the first time you toggle them because the conversion takes
>> > a little bit.
>> >
>> > #+BEGIN_SRC emacs-lisp
>> >
>> > (setq image-file-name-extensions
>> >   (quote
>> >("png" "jpeg" "jpg" "gif" "tiff" "tif" "xbm" "xpm" "pbm" "pgm" "ppm"
>> "pnm" "svg" "pdf" "bmp" "eps")))
>> > (add-to-list 'image-type-file-name-regexps '("\\.eps\\'" . imagemagick))
>> > (add-to-list 'image-file-name-extensions "eps")
>> > (add-to-list 'image-type-file-name-regexps '("\\.pdf\\'" . imagemagick))
>> > (add-to-list 'image-file-name-extensions "pdf")
>> > (setq imagemagick-types-inhibit (remove 'PDF imagemagick-types-inhibit))
>> >
>> > #+END_SRC
>> >
>> >
>> >
>> >
>> > Doyley, Marvin M. writes:
>> >
>> >> Doesn’t work. Emacs just Hangs :(
>> >>> On Mar 17, 2017, at 8:43 AM, Norwid Behrnd <nbeh...@yahoo.com> wrote:
>> >>>
>> >>>
>> >>> To include and display pdf files, perhaps the setup outlined here is
>> >>> still working (dates back 2014...)
>> >>>
>> >>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__emacs.stackexchange.com_questions_390_display-2Dpdf-2Dimages-2Din-2Dorg-2Dmode=DwIC-g=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=cQ2XAFEKpHWcRH33Hvyanl-V2rE3v-7glys69pwm8CY=rmvwv-l1KvLkkUN0iG1d7bT6-MNbzQOFpz5U4-fLPt0=
>> >>>
>> >>> Cheers.
>> >>>
>> >>>
>> >>>
>> >>> On 03/17/2017 01:27 PM, Doyley, Marvin M. wrote:
>> >>>> Hi there,
>> >>>>
>> >>>> For manuscripts, my research group and I typically save images in pdf
>> >>>> format, much better resolution. It would be nice to view pdf  images
>> >>>> when working in org-mode. Does anybody know how to view pdf images in
>> >>>> org-mode.
>> >>>>
>> >>>> Thanks, M
>> >>>>
>> >>>> PS We also work with svg images too, that would also love to view in
>> >>>> org-mode
>> >>>>
>> >
>> >
>> > --
>> > Julian Mariano Burgos, PhD
>> > Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
>> > Marine and Freshwater Research Institute
>> > Skúlagata 4, 121 Reykjavík, Iceland
>> > Sími/Telephone : +354-5752037 <+354%20575%202037>
>> > Bréfsími/Telefax:  +354-5752001 <+354%20575%202001>
>> > Netfang/Email: julian.bur...@hafogvatn.is
>>
>> --
>
> Kaushal Modi


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] Bug: save-some-buffers saves org-edit-special buffers to separate files

[Julian M. Burgos]

Hello all,

This has been reported before, and as I understood was fixed.

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg111340.html

But I am still having the same problem using org mode 9.0.5 in emacs
25.1.1.

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Viewing pdf images

[Julian M. Burgos]

I have the following in my .emacs file.  For this to work you need to
have your emacs compiled with imagemagick support (and have imagemagick
installed, of course).  It works well, although the images do not appear
immediately the first time you toggle them because the conversion takes
a little bit.

#+BEGIN_SRC emacs-lisp

(setq image-file-name-extensions
   (quote
("png" "jpeg" "jpg" "gif" "tiff" "tif" "xbm" "xpm" "pbm" "pgm" "ppm" "pnm" 
"svg" "pdf" "bmp" "eps")))
(add-to-list 'image-type-file-name-regexps '("\\.eps\\'" . imagemagick))
(add-to-list 'image-file-name-extensions "eps")
(add-to-list 'image-type-file-name-regexps '("\\.pdf\\'" . imagemagick))
(add-to-list 'image-file-name-extensions "pdf")
(setq imagemagick-types-inhibit (remove 'PDF imagemagick-types-inhibit))

#+END_SRC




Doyley, Marvin M. writes:

> Doesn’t work. Emacs just Hangs :(
>> On Mar 17, 2017, at 8:43 AM, Norwid Behrnd  wrote:
>>
>>
>> To include and display pdf files, perhaps the setup outlined here is
>> still working (dates back 2014...)
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__emacs.stackexchange.com_questions_390_display-2Dpdf-2Dimages-2Din-2Dorg-2Dmode=DwIC-g=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=cQ2XAFEKpHWcRH33Hvyanl-V2rE3v-7glys69pwm8CY=rmvwv-l1KvLkkUN0iG1d7bT6-MNbzQOFpz5U4-fLPt0=
>>
>> Cheers.
>>
>>
>>
>> On 03/17/2017 01:27 PM, Doyley, Marvin M. wrote:
>>> Hi there,
>>>
>>> For manuscripts, my research group and I typically save images in pdf
>>> format, much better resolution. It would be nice to view pdf  images
>>> when working in org-mode. Does anybody know how to view pdf images in
>>> org-mode.
>>>
>>> Thanks, M
>>>
>>> PS We also work with svg images too, that would also love to view in
>>> org-mode
>>>


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] org-ref and the minibuffer

[Julian M. Burgos]

Dear list,

It is possible to customize the information shown in the minibuffer when
the cursor (or the mouse pointer) is on top of an org-ref bibliography link?
The default seems to be a formatted version of the citation, which
includes authors (all of them), title, etc.  I would like just to see
the title.
Thanks!

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Problems with displaying inline images

[Julian M. Burgos]

Do'oh! It wasn't an org-mode issue.  The figures where bitmaps and I did not
have bmp in the image-file-name-extensions variables.  Sorry for the
noise!


Julian M. Burgos writes:

> Thanks Eric. I did read the description, and my link do not have any
> associated text.  It is something else. If I evaluate (print
> image-types) I get the following:
>
> (imagemagick png gif tiff jpeg xpm xbm pbm postscript).  And if I
> evaluate for example (image-type-available-p 'jpeg) I get "t".  But if I 
> evaluate (print image-library-alist), I get nil.  I think I am supposed to 
> get the
> libraries used by emacs to display the images, correct?  Do I need to
> populate this list by hand?
>
> Thanks again,
>
> Julian
>
>
> Eric S Fraga writes:
>
>> On Thursday,  9 Mar 2017 at 14:25, Julian M. Burgos wrote:
>>> Dear list,
>>>
>>> I cannot get org-mode to display inline images.  Instead, when doing M-x
>>> org-toggle-inline-images I get a "No images to display inline".  But if
>>> I click on the image link, the image appears in a new buffer with no 
>>> problems.
>>
>> Read the description of the org-display-inline-images command, which
>> org-toggle-inline-images uses.  If your link has associated text,
>> i.e. [[file:image][some text]], you will need to invoke either command
>> with C-u as, by default, only those messages with no descriptive text
>> will be displayed as they are not considered "inline".


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Problems with displaying inline images

[Julian M. Burgos]

Thanks Eric. I did read the description, and my link do not have any
associated text.  It is something else. If I evaluate (print
image-types) I get the following:

(imagemagick png gif tiff jpeg xpm xbm pbm postscript).  And if I
evaluate for example (image-type-available-p 'jpeg) I get "t".  But if I 
evaluate (print image-library-alist), I get nil.  I think I am supposed to get 
the
libraries used by emacs to display the images, correct?  Do I need to
populate this list by hand?

Thanks again,

Julian


Eric S Fraga writes:

> On Thursday,  9 Mar 2017 at 14:25, Julian M. Burgos wrote:
>> Dear list,
>>
>> I cannot get org-mode to display inline images.  Instead, when doing M-x
>> org-toggle-inline-images I get a "No images to display inline".  But if
>> I click on the image link, the image appears in a new buffer with no 
>> problems.
>
> Read the description of the org-display-inline-images command, which
> org-toggle-inline-images uses.  If your link has associated text,
> i.e. [[file:image][some text]], you will need to invoke either command
> with C-u as, by default, only those messages with no descriptive text
> will be displayed as they are not considered "inline".


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] Problems with displaying inline images

[Julian M. Burgos]

Dear list,

I cannot get org-mode to display inline images.  Instead, when doing M-x
org-toggle-inline-images I get a "No images to display inline".  But if
I click on the image link, the image appears in a new buffer with no problems.

This happens with a clean emacs instance (emacs -Q), so it is not my
configuration. I am running org mode 9.0.5 on emacs 25.1.1. with support
for ImageMagick, on CentOS 7.

Does anybody has an idea of what could be wrong?

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] HTML presentations using org-html-slideshow?

[Julian M. Burgos]

Thanks for the head up.  I will check it out.

Peter Salazar writes:

> If anyone's interested, there's a new working version of
> org-html-slideshow that's compatible with org-mode 9.x available here:
> https://github.com/aiba/org-html-slideshow.
>
> On Mon, Mar 6, 2017 at 10:04 AM, Peter Salazar 
> wrote:
>
>> Hi everyone,
>>
>> I've been using the excellent org-html-slideshow (
>> https://github.com/relevance/org-html-slideshow) to generate HTML slides
>> from org-mode, and it's been working well for me for years.
>>
>> It generates HTML slides from org-mode using the org-mode heading
>> hierarchy. Tag any heading with the org-tag :slide: and that heading and
>> its contents automatically become their own slide once you export to HTML
>> using org-export-dispatch.
>>
>> I prefer org-html-slideshow to org-reveal since it allows me the ability
>> to easily customize the look and feel of slides—by creating a custom
>> slide—simply by adding an org-tag. So if I tag an org-heading with the tag
>> :fullscreenslide: for example (so that the heading looks like * Heading
>> :slide:fullscreenslide:), it will then export that slide to HTML with
>> class="fullscreenslide" — and I can then use CSS to customize the look and
>> feel of all slides with that class.
>>
>> Org-html-slideshow also offers a great Presenter View, which opens in a
>> separate tab in your browser, and displays your speaker notes, the current
>> slide, and the next slide. Unfortunately, org-html-slideshow is no longer
>> being actively developed, and a recent update to org-mode has broken the
>> way Presenter View functions. Somehow with the new org-mode updates, the
>> "next slide" view in Presenter Notes mode no longer advances correctly. The
>> "next slide" slide gets stuck in a loop of 4-5 slides, and just repeats
>> those few slides. It does not reliably show you what the next slide is
>> going to be.
>>
>> I notice that the output from example.org when I export to HTML is fairly
>> different from the example.html that's in the repo. Something in those
>> differences is breaking the ability of Presenter Notes to advance to the
>> next slide:
>> https://gist.github.com/incandescentman/dca040c750a3e9e7e687942d69ebd53f
>>
>> Anyone else using org-html-slideshow? Does anyone have any thoughts on how
>> to get this working again? Thanks!
>>


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Using an org based init file slows down emacs startup by 50x..help needed :(

[Julian M. Burgos]

Hi Xebar,

An simple alternative is to do what I do: keep your init file in an org
mode file, and simple tangle it manually whenever you do changes.  In
this way you avoid the overload of the tangling process at startup.  My
emacs starts in about 10 seconds.

Julian

Thomas S. Dye writes:

> Aloha Xebar,
>
> Xebar Saram writes:
>
>> Ok so i think the reason really is that i have way to many lisp code blocks
>> as suggested. i found out a very interesting post that maybe of interest to
>> alot of org users
>>
>> http://www.holgerschurig.de/en/emacs-efficiently-untangling-elisp/
>>
>> this creates a new function that very efficiently tangles my org file and
>> the time goes from 6 minutes to 25 seconds!!
>>
>> this is a link to an example init file
>>
>> https://bitbucket.org/holgerschurig/emacsconf/src/416b2bba2d1d334b9c6ddbd56f8c7f8bd8bc4aab?at=master
>
> Have you seen Eric Schulte's starter-kit
> (http://eschulte.github.io/emacs24-starter-kit/)?  Using it, I keep my
> initialization functions in a few different Org mode files, which the
> starter-kit tangles to .el iff the Org mode file has been changed since
> it was last tangled.  I'm able to keep the initialization process
> reasonably organized (I'm the limiting factor), without the wait.
>
> hth,
> Tom


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Citation syntax: now supported in Pandoc

[Julian M. Burgos]

This is very interesting! I will give it a try. Thanks for the heads up.


Richard Lawrence writes:

> Hi everyone,
>
> With Org 9.0 out, I thought it might be a good time to revisit the issue
> of citation syntax.  Not much has happened with this recently, but I do
> have one bit of progress to report:
>
> About six months ago, Albert Krewinkel, who maintains the support for Org
> syntax in Pandoc [1], wrote to me about supporting the citation syntax
> we discussed previously, and that is partially implemented in
> the wip-cite branch.  You can see examples of the syntax at [2].
>
> Albert dove in, and was able to quickly add support for the syntax to
> Pandoc's Org reader.  This support has been merged into released
> versions of Pandoc.  Albert actually announced this a few months ago on
> Reddit [3], but it looks like he did not email this list.
>
> I finally got a chance to check out his work yesterday.  I converted one
> citation-heavy chapter of my dissertation to use the new syntax, and
> tested out Pandoc's support, with a couple of different CSL stylesheets,
> including a note-based style.  It works great.  Thanks, Albert, for your
> hard work!
>
> There are some minor issues that probably need more discussion after
> real-world use (like whether/when a conjunction should be inserted
> automatically before the last reference in a multi-cite citation).  But
> as far as I can tell, Albert has correctly implemented everything we
> actually discussed and agreed on.
>
> In short, Pandoc now has support for Org citation syntax, and that
> support is fully integrated with Pandoc's citation processing
> capabilities.  So there is now at least one "real" (non-prototype)
> solution for processing Org citations via CSL, with output to HTML,
> LaTeX, ODT, .docx, and the other formats that Pandoc supports.
>
> This makes it a lot easier for people to test out the syntax in the real
> world, so I encourage you to do so, and report back on what you find!
>
> Best,
> Richard
>
> [1] http://pandoc.org/
> [2] https://github.com/wyleyr/org-citeproc/blob/master/tests/testdoc.org
> [3] 
> https://www.reddit.com/r/orgmode/comments/4tes4x/ann_pandoc_v1172_has_been_released_it_now/


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

[O] project website from org

[Julian M. Burgos]

Dear list,

I have given the task to set up a website to display the research in one
of our projects.  I have little experience with html and website
maintenance, so I think this would be a good opportunity to learn.  I
would like to create the content for the website in org-mode (of
course).  Do you have any recommendations for tools to generate a static
website from org-mode?  Is a combo of Jekyll and GitHub pages a good
option?

Many thanks,

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Release 9.0

[Julian M. Burgos]

Thanks to everyone for the continuous development of org-mode!  I wish I
will learn enough emacs-lips to be able to contribute myself.  In the
mean time, kudos!
All the best,

Julian

Bastien Guerry writes:
> Hi all,
>
> Org 9.0 is out!  See the release notes here:
>
> http://orgmode.org/Changes.html
>
> Thanks to Nicolas, the non-official but real maintainer
> and to all who contributed to this long-awaited release.
>
> As usual, enjoy!


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Sharing documents with bibtex bibliography from org to non-org users

[Julian M. Burgos]

Hi Martin,

The best solution I found so far is to export to latex, and then use
pandoc to convert the tex document into word.  You can point pandoc to
your .bib file, so the bibliography gets into the word document, doing
something like this:

pandoc --bibliography /home/julian/Documents/org_files/myrefs.bib -o 
mypaper.docx mypaper.tex

This works ok.  Figures sometimes do not get inserted into the Word document,
and there are other relatively minor issues.  I have not bother looking
very deeply to figure out if they can be solved, I just pass the word
document to my collaborators for editing (so they can use the track
changes options and so for), and I also send the pdf file (from latex)
so they can see exactly how the document would look, in terms of figures
and tables.

When you get your reviews back, you need to manually insert them into
your org document, which is a pain in the back.

An alternative way is to pass the org document to your coworker, so they
can edit them in word directly.  They should ignore all the markup
language, do not use the track changes option, and save the resulting
document as a text file.  Then you can incorporate the changes directly
into your org file using ediff.  But as you said, the markup language
may turn off people that are not very friendly to some code and strange
commands.

A third way would be to export to odt.  I think you can set the exporter
so it uses libre office to convert the resulting file into .doc or
.docx.  I have not tried this very well, so I am not sure how this works
with references, figures and tables.

Hopefully somebody on the list may have a better option,

All the best,

Julian

Martin Leduc writes:

> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably 
> face problems when time comes to share a manuscript with co-authors for 
> reviewing. Unless one decides to restrict the choice of his co-authors 
> based exclusively on their knowledge of LaTeX, collaborators generally 
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply 
> copy-paste the LaTeX file into a Word document. You can then share this 
> file with other people along with a pdf-compiled version of the 
> manuscript allowing them to see all references, bibliography, equations 
> and figures. This is the most convenient approach for the first author, 
> who can simply copy-paste back the text into a tex file after the rounds 
> of review and then compile the LaTeX manuscript again following some 
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the 
> document is intended to stay into a word format for whatever reason. It 
> could be for instance because you want to be kind with some co-authors 
> that wouldn't pay much interest into a scary document filled with 
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent 
> the latter issue. To simplify, I accept that I will need to rewrite the 
> equations (and eq. numbers) in the Word document. What I really want, 
> however, is all the citations and the list of references being managed 
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf 
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word 
> document. This strategy is cumbersome because a lot of work is generally 
> needed to format the word document (page wrapping, no line breaks 
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on 
> how we could facilitate the sharing of documents containing a bibtex 
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Sharing documents with bibtex bibliography from org to non-org users

[Julian M. Burgos]

Hi Martin,

The best solution I found so far is to export to latex, and then use
pandoc to convert the tex document into word.  You can point pandoc to
your .bib file, so the bibliography gets into the word document, doing
something like this:

pandoc --bibliography /home/julian/Documents/org_files/myrefs.bib -o 
mypaper.docx mypaper.tex

This works ok.  Figures sometimes do not get inserted into the Word document,
and there are other relatively minor issues.  I have not bother looking
very deeply to figure out if they can be solved, I just pass the word
document to my collaborators for editing (so they can use the track
changes options and so for), and I also send the pdf file (from latex)
so they can see exactly how the document would look, in terms of figures
and tables.

When you get your reviews back, you need to manually insert them into
your org document, which is a pain in the back.

An alternative way is to pass the org document to your coworker, so they
can edit them in word directly.  They should ignore all the markup
language, do not use the track changes option, and save the resulting
document as a text file.  Then you can incorporate the changes directly
into your org file using ediff.  But as you said, the markup language
may turn off people that are not very friendly to some code and strange
commands.

A third way would be to export to odt.  I think you can set the exporter
so it uses libre office to convert the resulting file into .doc or
.docx.  I have not tried this very well, so I am not sure how this works
with references, figures and tables.

Hopefully somebody on the list may have a better option,

All the best,

Julian

Martin Leduc writes:

> Hi orgers,
>
> People using org-mode or LaTeX to write scientific papers inevitably 
> face problems when time comes to share a manuscript with co-authors for 
> reviewing. Unless one decides to restrict the choice of his co-authors 
> based exclusively on their knowledge of LaTeX, collaborators generally 
> use Microsoft Word to write their documents.
>
> One way to share LaTeX documents with non-LaTeX users is to simply 
> copy-paste the LaTeX file into a Word document. You can then share this 
> file with other people along with a pdf-compiled version of the 
> manuscript allowing them to see all references, bibliography, equations 
> and figures. This is the most convenient approach for the first author, 
> who can simply copy-paste back the text into a tex file after the rounds 
> of review and then compile the LaTeX manuscript again following some 
> minor debugging.
>
> However, the latter approach may not be suitable in situations where the 
> document is intended to stay into a word format for whatever reason. It 
> could be for instance because you want to be kind with some co-authors 
> that wouldn't pay much interest into a scary document filled with 
> complicated codes.
>
> So I would like to know what are the best known strategies to circumvent 
> the latter issue. To simplify, I accept that I will need to rewrite the 
> equations (and eq. numbers) in the Word document. What I really want, 
> however, is all the citations and the list of references being managed 
> automatically at the step of exporting from org to ODT or to Plain Text.
>
> The only solution I see now is to export the org document to a plain pdf 
> (e.g. with no page numbers) and then to copy-paste the pdf into a Word 
> document. This strategy is cumbersome because a lot of work is generally 
> needed to format the word document (page wrapping, no line breaks 
> between paragraphs, words hyphenation, etc).
>
> Is there any cleaner solutions to this issue ? Or more general ideas on 
> how we could facilitate the sharing of documents containing a bibtex 
> bibliography between org and non-org users ?
>
> Thanks
>
> Martin


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is

Re: [O] Org + MS DOC

[Julian M. Burgos]

The advantage of exporting via Pandoc is the possibility of including
bibliographic citations.  Do you know if it is possible to do this via
ODT?

Julian

Ken Mankoff writes:

> Hi,
>
> There is occasional discussion on the list (or SE or Reddit) about how to 
> best work with Word documents. In the past I've suggested Org -> Pandoc -> 
> DOCX because that worked best for me when producing documents with equations, 
> figures and tables. It didn't work great, but it worked best.
>
> I've recently found a new workflow that seems much better, and wanted to let 
> others know about it. It removes the need for Pandoc and only uses Org and 
> LibreOffice.
>
> 1) Export to DOC (not DOCX) via ODT. Inline \(math\) in DOCX still looks 
> pretty bad, but is fine in DOC.
>
> (require 'ox-odt)
> (setq org-odt-preferred-output-format "doc")
> (setq org-odt-convert-processes '(("LibreOffice" 
> "/Applications/LibreOffice.app/Contents/MacOS/soffice --headless --convert-to 
> %f%x %i"
>
> 2) Run the following LibreOffice Macro to clean things up. I've assigned this 
> to a toolbar button to make it easy to access. Add strings you want to 
> disappear to "mTeXStringsNO" and pairs of strings you want converted to the 
> "mTeXStringsCNV" arrays.
>
> 3) Email to Word Users. I always email the PDF copy to so they can see the 
> (psuedo)canonical version of the document.
>
> I hope this is helpful to some of you,
>
>   -k.
>
>
>
>
> Sub ReplaceTeXStrings
>   Dim mTeXStringsNO(99) As String
>   Dim mTeXStringsCNVfrom(99) As String
>   Dim mTexStringsCNVto(99) As String
>   Dim n As Long
>   Dim oDocument As Object
>   Dim oReplace As Object
>
>   mTeXStringsNO() = Array("\(", "\)", "\ref", "\mathrm", _
>   "\begin{equation}", "\end{equation}", "\left", "\right", _
>   "\singlespacing", "\doublespacing")
>   
>   mTeXStringsCNV() = Array("\sigma","σ", "\rho","ρ", "\sum","∑", _
>"\phi","ɸ", "\partial","∂", "^{th}","th", "^{{th}}","th", _
>"^{-1}","-1", "^{-2}","-2")
>   
>   oDocument = ThisComponent
>   oReplace = oDocument.createReplaceDescriptor
>   For n = lbound(mTeXStringsNO()) To ubound(mTeXStringsNO())
> oReplace.SearchString = mTexStringsNO(n)
> oReplace.ReplaceString = ""
> oDocument.replaceAll(oReplace)
>   Next n
>   For n = lbound(mTeXStringsCNV()) To ubound(mTeXStringsCNV()) Step 2
> oReplace.SearchString = mTexStringsCNV(n)
> oReplace.ReplaceString = mTexStringsCNV(n+1)
> oDocument.replaceAll(oReplace)
>   Next n
>   End Sub


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Avoiding open buffers when clocking in

[Julian M. Burgos]

Actually, the solution is obvious... I should think before posting.

(defun my-org-clock-in ()
 "Clock in and close all unmodified buffers."
  (interactive)
  (org-clock-in)
  (mapc 'kill-buffer (cdr (buffer-list (current-buffer
)



Julian M. Burgos writes:

> Thanks Kyle, I did not knew this one.  I was manually using this
> function
>
> (defun only-current-buffer () 
>   (interactive)   
> 
> (mapc 'kill-buffer (cdr (buffer-list (current-buffer)
>
> to kill all buffers after clocking in, but your solution is simpler.  
>
>
>
> Kyle Meyer writes:
>
>> "Julian M. Burgos" <jul...@hafro.is> writes:
>>
>>> When clocking in at some particular task, org-mode opens all my agenda
>>> files (I assume to check if there are dangling clocks).  I have many
>>> agenda files, and I rather avoid opening tons of new buffers.  Is there any
>>> way to make org-mode not check for dangling clocks in other agenda
>>> files?
>>
>> If you're ok with disabling automatic clock resolution entirely, setting
>> org-clock-auto-clock-resolution to nil should work.

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Avoiding open buffers when clocking in

[Julian M. Burgos]

Thanks Kyle, I did not knew this one.  I was manually using this
function

(defun only-current-buffer () 
  (interactive) 
  
(mapc 'kill-buffer (cdr (buffer-list (current-buffer)

to kill all buffers after clocking in, but your solution is simpler.  



Kyle Meyer writes:

> "Julian M. Burgos" <jul...@hafro.is> writes:
>
>> When clocking in at some particular task, org-mode opens all my agenda
>> files (I assume to check if there are dangling clocks).  I have many
>> agenda files, and I rather avoid opening tons of new buffers.  Is there any
>> way to make org-mode not check for dangling clocks in other agenda
>> files?
>
> If you're ok with disabling automatic clock resolution entirely, setting
> org-clock-auto-clock-resolution to nil should work.

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] Avoiding open buffers when clocking in

[Julian M. Burgos]

Dear list,

When clocking in at some particular task, org-mode opens all my agenda
files (I assume to check if there are dangling clocks).  I have many
agenda files, and I rather avoid opening tons of new buffers.  Is there any
way to make org-mode not check for dangling clocks in other agenda
files?  I only clock time in a single file (my journal.org file), so
I know already that there will not be dangling clocks in other files.

Or it is possible to automatically close the buffers *after* the check for 
dangling
clocks is done?

Many thanks,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] Not opening agenda files when clocking in

[Julian M. Burgos]

Dear list,

When clocking in at some particular task, org-mode opens all my agenda
files (I assume to check if there are dangling clocks).  I have many
agenda files, and I rather avoid opening tons of new buffers.  Is there any
way to make org-mode not check for dangling clocks in other agenda
files?  I only clock time in a single file (my journal.org file).

Many thanks,

Julian
-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is
n

[O] Closing buffers after clock-in

[Julian M. Burgos]

Dear list,

When clocking in at some particular task, org-mode opens all my agenda
files (I assume to check if there are dangling clocks).  I have many
agenda files, and I rather avoid opening tons of new buffers.  Is there any
way to make org-mode not check for dangling clocks in other agenda
files?  I only clock time in a single file (my journal.org file).

Many thanks,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Citations, continued

[Julian M. Burgos]

Thanks everyone for thinking about citations.  I wish I knew enough lisp
to make a contribution to this work... for now I can only sit on the
side and clap.

I am also a big fan of org-ref.  Although my needs are not complex
(basically citing from a BibLatex file and exporting to LaTex), I found
that having actionable citations is tremendously useful.  In
particular, clicking on the citation allows to open the pdf file with
the reference, the .bib file, or an org mode file with notes.  I hope
this feature is kept in whatever new org-mode reference system you guys
develop.

Keep up the good work!
All the best,

Julian

Vikas Rawal writes:

 Org-ref is very functional and has so far been able to deal with much of my 
 needs. So, I just hope we are not trying to fix something that is not broken.

 The real need in the context of citations is to somehow extend the 
 bibtex/biblatex integration to other export formats (odt/html, most 
 importantly). Will all the new stuff that is being proposed take us in that 
 direction? 

 Vikas



 On 03-Feb-2015, at 7:26 am, Richard Lawrence richard.lawre...@berkeley.edu 
 wrote:
 
 Hi Rasmus and all,
 
 Thanks for your comments!
 
 Rasmus ras...@gmx.us writes:
 
 ** Backend-agnostic formatting properties
 *** Selecting specific fields
 Selecting specific fields to display could be done by appending field
 names to cite keys after colons, much like Org tags:
 #+BEGIN_QUOTE
 [See @Doe99, pp. 34--45; also @Doe00:year, section 6] 
 
 [See their article in @Doe99:journal:year.] 
 #+END_QUOTE

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] org-ref no key found

[Julian M. Burgos]

Yes, you were right.  An update of org-mode fixed everything.  Thanks again!

John Kitchin writes:

 If you look in your messages do you see something like jit-lock errors?
 I do not recall exactly what the errors are but the ones I have seen
 that resemble what you describe have jit in them. 

 I saw this recently in an ELPA version (maybe around Sept 1), and it went 
 away when I updated
 the ELPA org version to the most recent one.


 Julian M. Burgos jul...@hafro.is writes:

 John, another issue...a really minor one, and I am not sure if it is
 org-ref related.  When I open the notes file, the org faces are not
 applied evenly.  In particular, 

 a) Text after #TITLE: or #AUTHOR appears as regular text.  If I use M-x
 describe face, I get default.  If modify in any way the face changes
 to org-document-info as it should be.

 b) Within the heading of each reference, the TODO statement appears
 with the same face as the rest of the heading (org-level-2 face).

 c) Links to pdf files appear like this, with default face:
  
 [[cite:Collie2000]] [[file:/home/julian/Documents/Refs/Collie2000.pdf][pdf]]

 And not as clickable links 
 cite:Collie2000 pdf (underlined, in blue, with org-link face)

 Again, as soon as I change anything the org-link face is applied and I
 get a clickable link.

 Of all this, the pdf links are the real issue, as they are
 non-functional until I edit them.

 Strangely, :PROPERTIES: and :END: appear in their correct face.  Also,
 if I fix the faces (editing the text or pressing enter so I get the
 right faces) and close the notes files, I get the same wriong faces when I
 reopen the file.

 Does this makes sense?  Do you know what could be the issue?
 Many thanks again,

 Julian


 Julian M. Burgos writes:

 Excellent! Many thanks... now it works like a charm.

 John Kitchin writes:

 No problem. Thanks for the tips to replicate this. It was pretty helpful
 in solving the problem (and thanks again to Nick who pointed me towards
 edebug-defun a while ago!)

 I think I have fixed this. The problem was org-ref was not finding a key
 that exists in a file. the way that is done all over org-ref is to
 insert the contents of the bibfile in temp buffer, and then use
 bibtex-search-entry on that buffer. It works like a charm usually, but
 not in the replicated steps you have below. once it works once, though,
 it seems to always work. 

 Anyway, I think it is fixed now. there is a new version at
 https://github.com/jkitchin/jmax/blob/master/org/org-ref.org

 Thanks for reporting the bug!

 Julian M. Burgos jul...@hafro.is writes:

 Hi John,

 I am resending this... I think it did not went through the previous
 time.

 I think I can replicate the org-ref bug now (if it is a bug).  This is
 the situation:

 a) If I open emacs, load a file that already has some link, and click on
 the link (or place the cursor on it and press enter) I get the no key
 found message and I cannot open the notes file (I get a Wrong type
 argument: stringp, nil), although the link to the pdf file works.  If I
 open more than one file, links do not work in any of them.  At this
 point if I check the value of the org-ref-default-bibliography
 variable, I get the correct path and filename of my .bib file.

 b) If I insert a new citation (using Ctrl-]) in any of the documents,
 links work as they should in all documents (this is, I get the title and
 I can open the notes file).

 I should say that I am not using the org-ref-insert-bibliography-link
 function, because I use biblatex and I prefer to insert the Latex
 \printbibliography command.  But if use it and insert the bibliography
 link, the behaviour does not change.

 This is what I have in my .emacs file that is related to RefTex and
 org-ref:

 --
 ;; Load RefTex
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (autoload 'reftex-mode reftex RefTeX Minor Mode t)
 (autoload 'turn-on-reftex  reftex RefTeX Minor Mode nil)
 (autoload 'reftex-citation reftex-cite Make citation nil)
 (autoload 'reftex-index-phrase-mode reftex-index Phrase mode t)
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

 ;; Make RefTeX faster
 (setq reftex-enable-partial-scans t)
 (setq reftex-save-parse-info t)
 (setq reftex-use-multiple-selection-buffers t)
 (setq reftex-plug-into-AUCTeX t)

 (setq reftex-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib))
 (setq reftex-sort-bibtex-matches author)   ; Sort entries found in 
 BibTex database 
 (setq bibtex-dialect biblatex)

 --
 (require 'org-ref)

 (setq org-ref-bibliography-notes /home/julian/Documents/org 
 files/notes.org
   org-ref-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib)
   org-ref

Re: [O] org-ref no key found

[Julian M. Burgos]

Excellent! Many thanks... now it works like a charm.

John Kitchin writes:

 No problem. Thanks for the tips to replicate this. It was pretty helpful
 in solving the problem (and thanks again to Nick who pointed me towards
 edebug-defun a while ago!)

 I think I have fixed this. The problem was org-ref was not finding a key
 that exists in a file. the way that is done all over org-ref is to
 insert the contents of the bibfile in temp buffer, and then use
 bibtex-search-entry on that buffer. It works like a charm usually, but
 not in the replicated steps you have below. once it works once, though,
 it seems to always work. 

 Anyway, I think it is fixed now. there is a new version at
 https://github.com/jkitchin/jmax/blob/master/org/org-ref.org

 Thanks for reporting the bug!

 Julian M. Burgos jul...@hafro.is writes:

 Hi John,

 I am resending this... I think it did not went through the previous
 time.

 I think I can replicate the org-ref bug now (if it is a bug).  This is
 the situation:

 a) If I open emacs, load a file that already has some link, and click on
 the link (or place the cursor on it and press enter) I get the no key
 found message and I cannot open the notes file (I get a Wrong type
 argument: stringp, nil), although the link to the pdf file works.  If I
 open more than one file, links do not work in any of them.  At this
 point if I check the value of the org-ref-default-bibliography
 variable, I get the correct path and filename of my .bib file.

 b) If I insert a new citation (using Ctrl-]) in any of the documents,
 links work as they should in all documents (this is, I get the title and
 I can open the notes file).

 I should say that I am not using the org-ref-insert-bibliography-link
 function, because I use biblatex and I prefer to insert the Latex
 \printbibliography command.  But if use it and insert the bibliography
 link, the behaviour does not change.

 This is what I have in my .emacs file that is related to RefTex and
 org-ref:

 --
 ;; Load RefTex
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (autoload 'reftex-mode reftex RefTeX Minor Mode t)
 (autoload 'turn-on-reftex  reftex RefTeX Minor Mode nil)
 (autoload 'reftex-citation reftex-cite Make citation nil)
 (autoload 'reftex-index-phrase-mode reftex-index Phrase mode t)
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

 ;; Make RefTeX faster
 (setq reftex-enable-partial-scans t)
 (setq reftex-save-parse-info t)
 (setq reftex-use-multiple-selection-buffers t)
 (setq reftex-plug-into-AUCTeX t)

 (setq reftex-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib))
 (setq reftex-sort-bibtex-matches author)   ; Sort entries found in BibTex 
 database 
 (setq bibtex-dialect biblatex)

 --
 (require 'org-ref)

 (setq org-ref-bibliography-notes /home/julian/Documents/org files/notes.org
   org-ref-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib)
   org-ref-pdf-directory /home/julian/Documents/Refs/)
  (setq org-ref-default-citation-link parencite)
  
 --

 Below I am sending you very simple .org and .bib files that (in my computer)
 reproduce this behaviour.  In this file I did use
 org-ref-insert-bibliography-link.  Let me know if I can give you any other 
 information.  

 All the best,

 Julian

 --Start trial.org file 
 

 * Trial
 Some references
 parencite:Brown2011a,Hobbs2006

 bibliography:~/Documents/trial.bib

 --End trial.org file 
 -


 --Start trial.bib file 
 

 Article{Brown2011a,
   Title= {Quantitative approaches in climate change 
 ecology},
   Author   = {Brown, C.J. and Schoeman, D.S. and Sydeman, 
 W.J. and Brander, K. and Buckley, L.B. and Burrows, M. and Duarte, C.M. and 
 Moore, P.J. and Pandolfi, J.M. and Poloczanska, E. and others},
   Journaltitle = {Global Change Biology},
   Year = {2011},

   Crossref = {burnhm},
   File = {:Brown2011a.pdf:PDF},
   Publisher= {Wiley Online Library}
 }

 @Article{Hobbs2006,
   Title= {Alternatives to statistical hypothesis testing 
 in ecology: a guide to self teaching},
   Author   = {Hobbs, N.T. and Hilborn, R.},
   Journaltitle = {Ecological Applications},
   Year = {2006},
   Number   = {1},
   Pages= {5--19},
   Volume

Re: [O] org-ref no key found

[Julian M. Burgos]

John, another issue...a really minor one, and I am not sure if it is
org-ref related.  When I open the notes file, the org faces are not
applied evenly.  In particular, 

a) Text after #TITLE: or #AUTHOR appears as regular text.  If I use M-x
describe face, I get default.  If modify in any way the face changes
to org-document-info as it should be.

b) Within the heading of each reference, the TODO statement appears
with the same face as the rest of the heading (org-level-2 face).

c) Links to pdf files appear like this, with default face:
 
[[cite:Collie2000]] [[file:/home/julian/Documents/Refs/Collie2000.pdf][pdf]]

And not as clickable links 
cite:Collie2000 pdf (underlined, in blue, with org-link face)

Again, as soon as I change anything the org-link face is applied and I
get a clickable link.

Of all this, the pdf links are the real issue, as they are
non-functional until I edit them.

Strangely, :PROPERTIES: and :END: appear in their correct face.  Also,
if I fix the faces (editing the text or pressing enter so I get the
right faces) and close the notes files, I get the same wriong faces when I
reopen the file.

Does this makes sense?  Do you know what could be the issue?
Many thanks again,

Julian


Julian M. Burgos writes:

 Excellent! Many thanks... now it works like a charm.

 John Kitchin writes:

 No problem. Thanks for the tips to replicate this. It was pretty helpful
 in solving the problem (and thanks again to Nick who pointed me towards
 edebug-defun a while ago!)

 I think I have fixed this. The problem was org-ref was not finding a key
 that exists in a file. the way that is done all over org-ref is to
 insert the contents of the bibfile in temp buffer, and then use
 bibtex-search-entry on that buffer. It works like a charm usually, but
 not in the replicated steps you have below. once it works once, though,
 it seems to always work. 

 Anyway, I think it is fixed now. there is a new version at
 https://github.com/jkitchin/jmax/blob/master/org/org-ref.org

 Thanks for reporting the bug!

 Julian M. Burgos jul...@hafro.is writes:

 Hi John,

 I am resending this... I think it did not went through the previous
 time.

 I think I can replicate the org-ref bug now (if it is a bug).  This is
 the situation:

 a) If I open emacs, load a file that already has some link, and click on
 the link (or place the cursor on it and press enter) I get the no key
 found message and I cannot open the notes file (I get a Wrong type
 argument: stringp, nil), although the link to the pdf file works.  If I
 open more than one file, links do not work in any of them.  At this
 point if I check the value of the org-ref-default-bibliography
 variable, I get the correct path and filename of my .bib file.

 b) If I insert a new citation (using Ctrl-]) in any of the documents,
 links work as they should in all documents (this is, I get the title and
 I can open the notes file).

 I should say that I am not using the org-ref-insert-bibliography-link
 function, because I use biblatex and I prefer to insert the Latex
 \printbibliography command.  But if use it and insert the bibliography
 link, the behaviour does not change.

 This is what I have in my .emacs file that is related to RefTex and
 org-ref:

 --
 ;; Load RefTex
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (autoload 'reftex-mode reftex RefTeX Minor Mode t)
 (autoload 'turn-on-reftex  reftex RefTeX Minor Mode nil)
 (autoload 'reftex-citation reftex-cite Make citation nil)
 (autoload 'reftex-index-phrase-mode reftex-index Phrase mode t)
 (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
 (add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

 ;; Make RefTeX faster
 (setq reftex-enable-partial-scans t)
 (setq reftex-save-parse-info t)
 (setq reftex-use-multiple-selection-buffers t)
 (setq reftex-plug-into-AUCTeX t)

 (setq reftex-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib))
 (setq reftex-sort-bibtex-matches author)   ; Sort entries found in BibTex 
 database 
 (setq bibtex-dialect biblatex)

 --
 (require 'org-ref)

 (setq org-ref-bibliography-notes /home/julian/Documents/org 
 files/notes.org
   org-ref-default-bibliography 
 '(/home/julian/Documents/Refs/BibTex/references.bib)
   org-ref-pdf-directory /home/julian/Documents/Refs/)
  (setq org-ref-default-citation-link parencite)
  
 --

 Below I am sending you very simple .org and .bib files that (in my computer)
 reproduce this behaviour.  In this file I did use
 org-ref-insert-bibliography-link.  Let me know if I can give you any other 
 information.  

 All the best,

 Julian

 --Start trial.org file

Re: [O] org-ref no key found

[Julian M. Burgos]

Hi John,

I am resending this... I think it did not went through the previous
time.

I think I can replicate the org-ref bug now (if it is a bug).  This is
the situation:

a) If I open emacs, load a file that already has some link, and click on
the link (or place the cursor on it and press enter) I get the no key
found message and I cannot open the notes file (I get a Wrong type
argument: stringp, nil), although the link to the pdf file works.  If I
open more than one file, links do not work in any of them.  At this
point if I check the value of the org-ref-default-bibliography
variable, I get the correct path and filename of my .bib file.

b) If I insert a new citation (using Ctrl-]) in any of the documents,
links work as they should in all documents (this is, I get the title and
I can open the notes file).

I should say that I am not using the org-ref-insert-bibliography-link
function, because I use biblatex and I prefer to insert the Latex
\printbibliography command.  But if use it and insert the bibliography
link, the behaviour does not change.

This is what I have in my .emacs file that is related to RefTex and
org-ref:

--
;; Load RefTex
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(autoload 'reftex-mode reftex RefTeX Minor Mode t)
(autoload 'turn-on-reftex  reftex RefTeX Minor Mode nil)
(autoload 'reftex-citation reftex-cite Make citation nil)
(autoload 'reftex-index-phrase-mode reftex-index Phrase mode t)
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

;; Make RefTeX faster
(setq reftex-enable-partial-scans t)
(setq reftex-save-parse-info t)
(setq reftex-use-multiple-selection-buffers t)
(setq reftex-plug-into-AUCTeX t)

(setq reftex-default-bibliography 
'(/home/julian/Documents/Refs/BibTex/references.bib))
(setq reftex-sort-bibtex-matches author)   ; Sort entries found in BibTex 
database 
(setq bibtex-dialect biblatex)

--
(require 'org-ref)

(setq org-ref-bibliography-notes /home/julian/Documents/org files/notes.org
  org-ref-default-bibliography 
'(/home/julian/Documents/Refs/BibTex/references.bib)
  org-ref-pdf-directory /home/julian/Documents/Refs/)
 (setq org-ref-default-citation-link parencite)
 
--

Below I am sending you very simple .org and .bib files that (in my computer)
reproduce this behaviour.  In this file I did use
org-ref-insert-bibliography-link.  Let me know if I can give you any other 
information.  

All the best,

Julian

--Start trial.org file 


* Trial
Some references
parencite:Brown2011a,Hobbs2006

bibliography:~/Documents/trial.bib

--End trial.org file 
-


--Start trial.bib file 


Article{Brown2011a,
  Title= {Quantitative approaches in climate change 
ecology},
  Author   = {Brown, C.J. and Schoeman, D.S. and Sydeman, W.J. 
and Brander, K. and Buckley, L.B. and Burrows, M. and Duarte, C.M. and Moore, 
P.J. and Pandolfi, J.M. and Poloczanska, E. and others},
  Journaltitle = {Global Change Biology},
  Year = {2011},

  Crossref = {burnhm},
  File = {:Brown2011a.pdf:PDF},
  Publisher= {Wiley Online Library}
}

@Article{Hobbs2006,
  Title= {Alternatives to statistical hypothesis testing in 
ecology: a guide to self teaching},
  Author   = {Hobbs, N.T. and Hilborn, R.},
  Journaltitle = {Ecological Applications},
  Year = {2006},
  Number   = {1},
  Pages= {5--19},
  Volume   = {16},

  Crossref = {Quick2010},
  File = {:Hobbs2006.pdf:PDF},
  Publisher= {Eco Soc America}
}

--End trial.bib file 
-




 Julian M. Burgos writes:

 John, for some weird reason everything seems to be working now.  Thanks
 for your help... I will let you know if I break it again.

 John Kitchin writes:

 that is odd. this means org-ref is not finding the key you clicked
 on. could you send me a small example that reproduces your problem (an
 org-file and the bib file)?

 Julian M. Burgos jul...@hafro.is writes:

 Hi John, 

 No, they still do not work even after I click on the bibliography link
 and get my .bib file opened.

 Julian

 John Kitchin writes:

 Julian M. Burgos jul...@hafro.is writes:

 If you click on the bibliography link to open the file, and then go

Re: [O] org-ref no key found

[Julian M. Burgos]

Hi John, 
I think I can replicate the org-ref bug now (if it is a bug).  This is the 
situation:

a) If I open emacs, load a file that already has some link, and click on
the link (or place the cursor on it and press enter) I get the no key
found message and I cannot open the notes file (I get a Wrong type
argument: stringp, nil), although the link to the pdf file works.  If I open 
more
than one file, links do not work in any of them.  At this point if I
check the value of the org-ref-default-bibliography variable, I get
the correct path and filename of my .bib file.

b) If I insert a new citation (using Ctrl-]) in any of the documents,
links work as they should in all documents (this is, I get the title and
I can open the notes file).  

I should say that I am not using the org-ref-insert-bibliography-link
function, because I use biblatex and I prefer to insert the Latex
\printbibliography command.  But if use it and insert the bibliography
link, the behaviour does not change.

This is what I have in my .emacs file that is related to RefTex and org-ref:

--
;; Load RefTex
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(autoload 'reftex-mode reftex RefTeX Minor Mode t)
(autoload 'turn-on-reftex  reftex RefTeX Minor Mode nil)
(autoload 'reftex-citation reftex-cite Make citation nil)
(autoload 'reftex-index-phrase-mode reftex-index Phrase mode t)
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

;; Make RefTeX faster
(setq reftex-enable-partial-scans t)
(setq reftex-save-parse-info t)
(setq reftex-use-multiple-selection-buffers t)
(setq reftex-plug-into-AUCTeX t)

(setq reftex-default-bibliography 
'(/home/julian/Documents/Refs/BibTex/references.bib))
(setq reftex-sort-bibtex-matches author)   ; Sort entries found in BibTex 
database 
(setq bibtex-dialect biblatex)

--
(require 'org-ref)

(setq org-ref-bibliography-notes /home/julian/Documents/org files/notes.org
  org-ref-default-bibliography 
'(/home/julian/Documents/Refs/BibTex/references.bib)
  org-ref-pdf-directory /home/julian/Documents/Refs/)

(setq org-ref-default-citation-link parencite)
--

I am sending you very simple .org and .bib files that (in my computer)
reproduce this behaviour.  In this file I did use
org-ref-insert-bibliography-link.  Let me know if I can give you any other 
information.  

All the best,

Julian



trial.bib
Description: Binary data


trial.org
Description: Lotus Organizer


Julian M. Burgos writes:

 John, for some weird reason everything seems to be working now.  Thanks
 for your help... I will let you know if I break it again.

 John Kitchin writes:

 that is odd. this means org-ref is not finding the key you clicked
 on. could you send me a small example that reproduces your problem (an
 org-file and the bib file)?

 Julian M. Burgos jul...@hafro.is writes:

 Hi John, 

 No, they still do not work even after I click on the bibliography link
 and get my .bib file opened.

 Julian

 John Kitchin writes:

 Julian M. Burgos jul...@hafro.is writes:

 If you click on the bibliography link to open the file, and then go back
 to your org-file, do the cite links work?

 I suspect the notes problem is related to the no key found problem.

 Hello everyone,

 I am playing around with Joh Kitchin's excellent org-ref, and I am
 having a few issues.  In my .emacs file I have set up the values for the
 org-ref-bibliography-notes, org-ref-default-bibliography, and
 org-ref-pdf-directory.

 With this I can access my .bib database and use org-ref-insert-cite link
 to add a citation link with no problems.  But when I press enter on the
 cite link, I get the following message:

 no key found
  (No key found) (p)df (u)rl (n)otes (q) quit

 If I press p I get the pdf file, but if I press n I get the
 following message: 

 Wrong type argument: stringp, nil.

 Any ideas how to solve this?

 Many thanks,

 Julian


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] org-ref no key found

[Julian M. Burgos]

John, for some weird reason everything seems to be working now.  Thanks
for your help... I will let you know if I break it again.

John Kitchin writes:

 that is odd. this means org-ref is not finding the key you clicked
 on. could you send me a small example that reproduces your problem (an
 org-file and the bib file)?

 Julian M. Burgos jul...@hafro.is writes:

 Hi John, 

 No, they still do not work even after I click on the bibliography link
 and get my .bib file opened.

 Julian

 John Kitchin writes:

 Julian M. Burgos jul...@hafro.is writes:

 If you click on the bibliography link to open the file, and then go back
 to your org-file, do the cite links work?

 I suspect the notes problem is related to the no key found problem.

 Hello everyone,

 I am playing around with Joh Kitchin's excellent org-ref, and I am
 having a few issues.  In my .emacs file I have set up the values for the
 org-ref-bibliography-notes, org-ref-default-bibliography, and
 org-ref-pdf-directory.

 With this I can access my .bib database and use org-ref-insert-cite link
 to add a citation link with no problems.  But when I press enter on the
 cite link, I get the following message:

 no key found
  (No key found) (p)df (u)rl (n)otes (q) quit

 If I press p I get the pdf file, but if I press n I get the
 following message: 

 Wrong type argument: stringp, nil.

 Any ideas how to solve this?

 Many thanks,

 Julian


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] org-ref no key found

[Julian M. Burgos]

Hello everyone,

I am playing around with Joh Kitchin's excellent org-ref, and I am
having a few issues.  In my .emacs file I have set up the values for the
org-ref-bibliography-notes, org-ref-default-bibliography, and
org-ref-pdf-directory.

With this I can access my .bib database and use org-ref-insert-cite link
to add a citation link with no problems.  But when I press enter on the
cite link, I get the following message:

no key found
 (No key found) (p)df (u)rl (n)otes (q) quit

If I press p I get the pdf file, but if I press n I get the
following message: 

Wrong type argument: stringp, nil.

Any ideas how to solve this?

Many thanks,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] org-ref no key found

[Julian M. Burgos]

Hi John, 

No, they still do not work even after I click on the bibliography link
and get my .bib file opened.

Julian

John Kitchin writes:

 Julian M. Burgos jul...@hafro.is writes:

 If you click on the bibliography link to open the file, and then go back
 to your org-file, do the cite links work?

 I suspect the notes problem is related to the no key found problem.

 Hello everyone,

 I am playing around with Joh Kitchin's excellent org-ref, and I am
 having a few issues.  In my .emacs file I have set up the values for the
 org-ref-bibliography-notes, org-ref-default-bibliography, and
 org-ref-pdf-directory.

 With this I can access my .bib database and use org-ref-insert-cite link
 to add a citation link with no problems.  But when I press enter on the
 cite link, I get the following message:

 no key found
  (No key found) (p)df (u)rl (n)otes (q) quit

 If I press p I get the pdf file, but if I press n I get the
 following message: 

 Wrong type argument: stringp, nil.

 Any ideas how to solve this?

 Many thanks,

 Julian


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] State of the art in citations

[Julian M. Burgos]

Hi Leonard,

Yes, I will be definitively interested on this!  Thanks!

Julian

Leonard Randall writes:

 Hi Julian et al.,
 I am not sure if this helps, but I am in the process of writing a new
 package for inserting citations into org buffers using RefTeX. This
 solution would make citation insertion very convenient, but it would not be
 quite as easy to read as Clément's solution, and it would only work for
 latex export. (It might work with html export if you used bibtex to html,
 but I do not have enough experience with bibtex to html to know.) On the
 other hand, it will work with multicite commands, whereas Clement's does
 not look like it will.

 I was also thinking of adding out of the box biblatex support for
 org-bibtex (see my previous post).

 Let me know if you might be interested in either of these, as I will try to
 work on them this week.

 All best,

 Leonard


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] State of the art in citations

[Julian M. Burgos]

Thanks Clément and everybody else for their comments/ideas.  I will go
through these carefully.

John Kitchin writes:

 It seems there are a lot of variants of citation handling out there! I will
 add to the list my own variants here:
 https://github.com/jkitchin/jmax/blob/master/jorg-bib.el. My citation needs
 are simple, I basically only use \cite{key1,key2} in LaTeX. And I only use
 bibtex, because I have not gotten around to anything else, bibtex works
 fine if your needs are simple (like mine).

 There is certainly duplication of some things, but the following are
 features in mine that I am not aware of anywhere else.


 1. Integration with reftex. You type C-c ] and select keys from reftex and
 insert a cite link. If you type it again on a citation, the new entries are
 appended to the end. This current conversation inspired me to implement
 this!

 2. Clickable cite links. If you have a citation link like
 cite:key1,key2,key3 you can click on key1 and open the bibliography file to
 key1, and you can click on key2 and have it open at key 2. This link would
 export in latex as \cite{key1,key2,key3}. Other cite formats, e.g. citep,
 citep*, etc... are defined too, but are relatively untested. You can also
 use completion to enter a bibtex key.

 3. citation tooltips. If clicking is too disruptive, you can run a command
 and get a tooltip of the citation under point. If clicking is too tiring,
 you can turn on an idle timer that shows a tooltip if the cursor is on a
 citation.

 4. clickable label links. clicking checks the buffer for another label by
 the same name.

 5. Clickable ref links. Clicking on the ref:label takes you to the label,
 and provides C-c  to get back to that point. You can also use completion
 to get a list of labels in the buffer to make a ref to.

 6. A bibliographystyle and bibliography link. The bibliography link opens
 the bibtex file that was clicked on.

 7. Code to make a clickable list of figures and tables.

 8. Code to extract the bibtex entries cited in an org-file to a text block
 at the end of the org-file

 9. variables to point to a notes file and pdf directory, and functions to
 jump to your notes and the pdf file from a bibtex entry.

 10. a function to build a complete pdf bibliography from your bibtex file.
 This is handy for checking the entries are spelled correctly, etc...

 11. A little function and python script to upload a bibtex entry to
 citeulike.

 I have not tried to do much with anything but LaTeX, so these links are not
 likely to be that good for html or odt I suspect.

 Anyway, there are some very interesting ideas in this code, and I am using
 it on a pretty regular basis. Maybe some of you would also find them
 interesting/helpful. I look forward to see this continue developing!

 John

 ---
 John Kitchin
 Associate Professor
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 http://kitchingroup.cheme.cmu.edu



 On Sun, Apr 27, 2014 at 12:57 PM, Clément B. clem...@inventati.org wrote:


  It appears to work for multicite for me. Or at least well enough. If I
  select multiple entries, I get this:
 
  [[ref:Author1:,Author2:,Author3:][()]]
 
  I can then easily insert the text I want into the (). It exports
  properly to LaTeX as \cite{Author1:,Author2:,Author3:}.
 
  Maybe most people multi-cite more than me, but I think it is only a bit
  of extra work to add what I want in the () and then it exports properly
  to LaTeX and, using the references-via-LaTeX, to ODT/HTML too!
 
-k.

 The problem is that you can't link to a bibtex entry,
 [[ref:Author1:,Author2:]] is not picked up by org search
 function of `org-open-file`. And even if it was, it couldn't link
 to several entries at once. So to preserve the ability to jump
 quickly to a reference, I quite like the export filter approach,
 which I was unaware of (thank you Thomas! ).


 Clément




-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] State of the art in citations

[Julian M. Burgos]

Dear list,

I use org-mode to write scientific papers, exporting mostly to LaTex/pdf
(and sometimes to Word via ODT when I have to collaborate with less
enlightened colleagues).  I keep my references in a .bib file, and so
far I have been using bibtex in a more or less standard way, using
reftex to insert citations in the documents.  

I am planning in revamping the way I deal with citations, and I was
wondering if I can get your opinions in what is the state of the art
in using citations in org-mode, in particular

- Should I use biblatex instead of bibtex?  
- Are there any contributed packages that I should consider?
- What would be the best way to get citations into html or odt?

Any comments or tips will be welcomed!
All the best,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Multiple Recursive Directories with org-agenda-files

[Julian M. Burgos]

Hi Esben,

I use find-lisp-find-files.  I have the following in my .emacs file: 

;;--
;; Load org agenda files
;;--
(load-library find-lisp)

(add-hook 'org-agenda-mode-hook (lambda () 
(setq org-agenda-files 
  (find-lisp-find-files /home/julian/Documents \.org$))
))

With this when I do C-c a, all the *.org files in my Documents directory
get added into the agenda.

According to this
http://archive.today/7McXW#selection-9101.0-9101.4

If you are on a Linux machine you can use the find utility, which can be
faster that the lisp library:

(setq org-agenda-files
  (mapcar 'abbreviate-file-name
  (split-string
   (shell-command-to-string find ~/org -name \*.org\)
  \n)))

I have not tried it though... but I may do it now.

I hope this helps.

Julian



Esben Stien writes:

 I'm trying to add a few recursive directories to org-agenda-files, but
 can't really find any examples doing this 

 I got like 250 org files spread over a few directories.

 I want to add:

 ~/foo/bar/
 ~/baz/quux/
 ~/hukarz/grault/

 ..which again includes multiple directories with .org files and a few
 other files which I don't want included.

 Anyone who does this?


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] firefox bookmarks to org-mode

[Julian M. Burgos]

Dear list,

Could anyone give me some pointers on a set-up to get links from firefox
to an org-mode file?  I would like to press a key combination in firefox
(say Ctrl-D) and have the web address of the site stored as an entry in
some org-mode file.
Many thanks,

Julian 


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] org-mode in the wild

[Julian M. Burgos]

Thank you very much John!!! Your document contains a wealth of information on 
how to
use org-mode for reproducible research!  I really like the idea of
embedding the supporting documents (bibliography, additional analysis) into the
document. Very nice.

Perhaps it would be good to have a repository of practices and examples
for reproducible research, maybe a section in Worg?

All the best,

Julian

John Kitchin writes:

 Hi everyone,

 We had another manuscript written in org-mode accepted in Topics in
 Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)!
 Check out references 14, 39 and 40 ;)

 The supporting information seems to be freely available (
 http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
 was also prepared in org-mode. It is probably best read with the Adobe PDF
 reader. This file is an interesting hybrid of data sharing methods. Some of
 the data is in the pdf, some of it is embedded in the pdf, including the
 org-mode files for the manuscript and the supporting information file
 itself. Anyone interested in seeing how we did it can check it out.

 John

 ---
 John Kitchin
 Associate Professor
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 http://kitchingroup.cheme.cmu.edu


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Other question concerning org-babel-tangle-jump-to-org

[Julian M. Burgos]

Hi Rainer,

Then sorry... this goes beyond my meager knowledge of emacs and org
mode. :)

Rainer M Krug writes:

 #secure method=pgpmime mode=sign

 Julian M. Burgos jul...@hafro.is writes:

 Hi Rainier,

 Hi Julian,

 If I understood correctly, you need to add the following to your
 .emacs file:

 (setq org-src-window-setup 'current-window)

 With this when you use C-' to switch between editing your org mode file
 and being in ESS mode you will say in the same windows.

 This is definitely true, but this is my setting, but this only effects
 C-' to start an indirect buffer - the org file is opened in a normal
 buffer, and not in an indirect buffer.

 Cheers,

 Rainer


 All the best,

 Julian


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Other question concerning org-babel-tangle-jump-to-org

[Julian M. Burgos]

Hi Rainier,
If I understood correctly, you need to add the following to your
.emacs file:

(setq org-src-window-setup 'current-window)

With this when you use C-' to switch between editing your org mode file
and being in ESS mode you will say in the same windows.

All the best,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is



Rainer M Krug writes:

 Would it be possible, that the function does not open a new window when
 executed, but uses the same window the tangled file is in? I am using
 org for literate programming in R (ESS): 
 - R console left window 
 - when there is an error, I jump to the R file in the right window and
 call there org-babel-tangle-jump-to-org and the org file is opened in
 the left window. It would be easier for debugging, if it would open in
 the right window, where the R file is already open.

 Would that be possible?

 Thanks,

 Rainer

Re: [O] Seeking advice on structuring my org-mode file

[Julian M. Burgos]

Matt, this is very useful!  I agree with you, I also tend to create
several org-mode files for a project that is becoming too large.  For
example, I keep a separate org-file for each paper or report, another
with notes, another with analysis (with R code blocks), etc.

One issue is that I use lots of TODO statemens in my files, and when
org-mode files multiply it starts to become difficult to keep the agenda
files list updated.  To do this I use this snippet that I found
somewhere (I do not remember exactly where).  This includes all
org-files in a specific directory (in my case my Documents directory)
in the agenda files list.

#+begin_src lisp
;;--
;; Load org agenda files
;;--
; Do not add agenda files by hand
(add-hook 'org-mode-hook
  (lambda ()
(org-defkey org-mode-map \C-c['undefined)
(org-defkey org-mode-map \C-c]'undefined))
  'append)

(load-library find-lisp)

(add-hook 'org-agenda-mode-hook (lambda () 
(setq org-agenda-files 
  (find-lisp-find-files /home/julian/Documents \.org$))
))
#+end_src

With this I can create org-files to my heart's content and I know that
all TODOs statements will show up in the agenda.

All the best,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Matt Lundin writes:

 Marcin Borkowski mb...@wmi.amu.edu.pl writes:

 I have an Org-mode file with notes concerning a large project connected
 with teaching at my university.  One of the headlines is dedicated to
 one particular course, where I am part of a group developing a concept
 of this course.  So, one subheadline is devoted to that.  Yet another
 (subsub)headline is a list if my proposals of things that should be
 covered during that course, and now it needs 3 more levels down.
 Summing it up: I have 5 levels of headlines and now I need a sixth
 one.  So, my question is: what are good practices of other Org-moders?
 Do you push such a monster to an external file and just include a link
 to it?  

 If a file grows to large, I simply create a new one. In this instance, I
 would recommend creating a separate file for each course.

 Below you'll find a very hackish helper function that I use to generate
 a new file from a headline. It leaves a link to the new file in the
 original location.

 Best,
 Matt

 --8---cut here---start-8---
 (defun my-org-file-from-headline (file)
   (interactive
(list
 (completing-read File: 
  (mapcar 'file-name-nondirectory
(file-expand-wildcards ~/org/*.org))
  nil nil)))
   (unless (string-match \\.org$ file)
 (error Not an org file))
   (save-excursion
 (beginning-of-line)
 (unless (org-at-heading-p)
   (error Not on a headline)))
   (let* ((exists (file-exists-p file))
  (ftags (append
  (list (file-name-sans-extension file))
  (mapcar 'substring-no-properties org-file-tags)))
  (headline (nth 4 (org-heading-components)))
  (org-archive-reversed-order t)
  (org-archive-location (concat file ::))
  (org-archive-save-context-info nil))
 (org-archive-subtree)
 (save-excursion (insert * [[file: file ][ file ]] -  headline \n))
 (find-file file)
 (goto-char (point-min))
 (save-excursion
   (if (re-search-forward #\\+FILETAGS:\\(.*\\)$ nil t)
   (progn
 (save-match-data
   (setq ftags
 (mapconcat 'identity
(org-uniquify
 (append ftags
 (split-string
  (substring-no-properties
   (match-string 1)  )))
 (replace-match (concat #+FILETAGS:  ftags)))
 (insert #+FILETAGS:  (mapconcat 'identity ftags  ) \n))
   (goto-char (point-min))
   (unless (re-search-forward #\\+CATEGORY:\\(.*\\)$ nil t)
 (insert #+CATEGORY:  (file-name-sans-extension file) \n))
   (goto-char (point-min))
   (when (re-search-forward ^Archived entries from file.+\n nil t)
 (replace-match 
   (write-file file))
 --8---cut here---end---8---

Re: [O] Export Org-mode content to Reveal.js presentations

[Julian M. Burgos]

Hi Yujie,

Thanks for the exporter!  I am still a bit confused though (seems my
natural state).  Let say I downloaded reveal.js and placed it on my home
directory (I am using Linux), so that the path to reveal.js is the
following:

/home/julian/.reveal/js/reveal.js

so then I should add to my .emacs file 

(setq org-reveal-root file:home/julian/.reveal/js/reveal.js)

and with this I should be able to do C-c C-e R R and export to reveal,
regardless of the location of the org file, right?  But it is not
working, so obviously I am doing something wrong.  I get a regular
HTML file instead.  Any ideas?

Many thanks,

Julian

Yujie Wen writes:

 Hi, Gary,

   You are right. For absolute path to reveal.js, the org-reveal-root should
 be set in URL form, file:///path_to_reveal.js.

   I will update the document to make it clear. Thanks for your suggestion.

 Regards,
 Yujie


 2013/5/15 Gary Oberbrunner ga...@oberbrunner.com

 Just want to say I just set this up, and it's great!  Easy to work with,
 and my first org-mode presentation was live in under 10 min.  One minor
 nit: on my Windows machine, I had to set org-reveal-root to a file:/// URL,
 not a filesystem path.  Otherwise the presentation wouldn't load.


 On Thu, May 9, 2013 at 4:42 PM, Simon Thum simon.t...@gmx.de wrote:

 Hi Yujie,

 thanks for your great work! I just have had my first important reveal.js
 presentation, and wished I had an org-mode exporter while I was hand-coding
 the presentation.

 Next time It'll be easier no doubt.

 Cheers,

 Simon


 On 05/03/2013 02:48 PM, Yujie Wen wrote:

 Hi,

I'd like to introduce a new Org-Mode exporter, Org-reveal, that
 exports Org-mode contents to Reveaj.js presentations.

Reveal.js is a web-based presentation framework, with beautiful 3-D
 effects and 2-D slides arrangements. The original sample illustration
 can be found at 
 http://lab.hakim.se/reveal-js/**#/http://lab.hakim.se/reveal-js/#/
 .

With Org-reveal, you can easily exports your Org documents to
 Reveal.js presentations. A sample presentation created by Org-reveal can
 be found at 
 http://naga-eda.org/home/**yujie/org-reveal/http://naga-eda.org/home/yujie/org-reveal/
 .

Org-reveal is hosted on 
 https://github.com/yjwen/org-**revealhttps://github.com/yjwen/org-reveal.
 Should
 you have any suggestion or bug-report, please contact me yjwen.ty AT
 gmail DOT com.

 Thanks and regards,
 Yujie






 --
 Gary



-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Export Org-mode content to Reveal.js presentations

[Julian M. Burgos]

Hi Yujie,

I fixed the URL, but I do not think that is the issue.  I took your
Readme.org file and exported it using the regular HTML exporter, and
then using the reveal exporter.  The HTML in both files is very
different, but when I open them in a browser both show very similar
looking pages.  The file obtained from the reveal exporter does not
generate a presentation. 

Maybe I am doing something wrong.  If I am using your Readme.org file, I
should be able to do C-c C-e R R to generate a Readme.html file with the
right HTML.  Then I should be able to copy
this file into my .reveal directory, open it with a browser and see the
presentation, right?  Or I am missing something? 

Any help will be welcomed.  I have to give a 30 minute talk on Friday
and I really like to get this working! :)

Julian

Yujie Wen writes:

 Hi, Julian,

   It seems the URL is wrong. Please see my comments below.

   Let me know if there is still problem.

 Regards,
 Yujie


 2013/5/15 Julian M. Burgos jul...@hafro.is

 Hi Yujie,

 Thanks for the exporter!  I am still a bit confused though (seems my
 natural state).  Let say I downloaded reveal.js and placed it on my home
 directory (I am using Linux), so that the path to reveal.js is the
 following:

 /home/julian/.reveal/js/reveal.js

 so then I should add to my .emacs file

 (setq org-reveal-root file:home/julian/.reveal/js/reveal.js)

 It should be three slashes ('/'), not four. Please try:
 (setq org-reveal-root file:///home/julian/.reveal/js/reveal.js)


 and with this I should be able to do C-c C-e R R and export to reveal,
 regardless of the location of the org file, right?  But it is not
 working, so obviously I am doing something wrong.  I get a regular
 HTML file instead.  Any ideas?

 Many thanks,

 Julian

 Yujie Wen writes:

  Hi, Gary,
 
You are right. For absolute path to reveal.js, the org-reveal-root
 should
  be set in URL form, file:///path_to_reveal.js.
 
I will update the document to make it clear. Thanks for your
 suggestion.
 
  Regards,
  Yujie
 
 
  2013/5/15 Gary Oberbrunner ga...@oberbrunner.com
 
  Just want to say I just set this up, and it's great!  Easy to work with,
  and my first org-mode presentation was live in under 10 min.  One minor
  nit: on my Windows machine, I had to set org-reveal-root to a file:///
 URL,
  not a filesystem path.  Otherwise the presentation wouldn't load.
 
 
  On Thu, May 9, 2013 at 4:42 PM, Simon Thum simon.t...@gmx.de wrote:
 
  Hi Yujie,
 
  thanks for your great work! I just have had my first important
 reveal.js
  presentation, and wished I had an org-mode exporter while I was
 hand-coding
  the presentation.
 
  Next time It'll be easier no doubt.
 
  Cheers,
 
  Simon
 
 
  On 05/03/2013 02:48 PM, Yujie Wen wrote:
 
  Hi,
 
 I'd like to introduce a new Org-Mode exporter, Org-reveal, that
  exports Org-mode contents to Reveaj.js presentations.
 
 Reveal.js is a web-based presentation framework, with beautiful 3-D
  effects and 2-D slides arrangements. The original sample illustration
  can be found at http://lab.hakim.se/reveal-js/**#/
 http://lab.hakim.se/reveal-js/#/
  .
 
 With Org-reveal, you can easily exports your Org documents to
  Reveal.js presentations. A sample presentation created by Org-reveal
 can
  be found at http://naga-eda.org/home/**yujie/org-reveal/
 http://naga-eda.org/home/yujie/org-reveal/
  .
 
 Org-reveal is hosted on https://github.com/yjwen/org-**reveal
 https://github.com/yjwen/org-reveal.
  Should
  you have any suggestion or bug-report, please contact me yjwen.ty AT
  gmail DOT com.
 
  Thanks and regards,
  Yujie
 
 
 
 
 
 
  --
  Gary
 


 --
 Julian Mariano Burgos, PhD
 Hafrannsóknastofnunin/Marine Research Institute
 Skúlagata 4, 121 Reykjavík, Iceland
 Sími/Telephone : +354-5752037
 Bréfsími/Telefax:  +354-5752001
 Netfang/Email: jul...@hafro.is



-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] confused about Beamer export

[Julian M. Burgos]

Dear list, 

I am a bit confused about what I have to use the new Beamer
exporter.  I have customized the org-export-backends variable to include
the Beamer exporter, and now it shows as an option when I do C-c C-e.  I
have also created a toy org file:

start org file--
#+TITLE: Example Presentation
#+AUTHOR: Julian Burgos
   
* This is a structural section
** Frame 1
This is frame 1
** Frame 2 
This is frame 2
end org file--

If I try to use any of the Beamer export commands, I get an Wrong type
argument: stringnp, nil error.

If I check the *Messages* buffer, these are the messages generated after
trying to export:

Debug (ox-odt): Searching for OpenDocument styles files...
Debug (ox-odt): Trying /usr/share/emacs/etc/org/styles/... [2 times]
Debug (ox-odt): Trying /home/julian/.emacs.d/etc/styles/...
Debug (ox-odt): Trying /home/julian/.emacs.d/elpa/org-20130514/etc/styles/...
Debug (ox-odt): Using styles under 
/home/julian/.emacs.d/elpa/org-20130514/etc/styles/
Debug (ox-odt): Searching for OpenDocument schema files...
Debug (ox-odt): Trying /usr/share/emacs/etc/org/schema/... [2 times]
Debug (ox-odt): No OpenDocument schema files installed
org-beamer--normalize-argument: Wrong type argument: stringp, nil

On the other hand, if I add 
#+LaTeX_CLASS: beamer
to the org file and use the non-beamer latex export commands, I get
the presentation in beamer with no problems, the old fashion way.  What
I am doing wrong? 

Many thanks,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Extending ODT export

[Julian M. Burgos]

Thanks Takaaki! That did the trick. Now things work as they should. :)

Takaaki ISHIKAWA writes:

 Dear Julian,

 Sorry, the code is an old setting for the previous org.
 Please try org-odt-preferred-output-format.

 #+BEGIN_SRC emacs-lisp
 (setq org-odt-preferred-output-format pdf)
  (setq org-odt-convert-processes
'((LibreOffice
   /Applications/LibreOffice.app/Contents/MacOS/soffice 
 --headless --convert-to %f%x --outdir %d %i)
  (unoconv unoconv -f %f -o %d %i)))
 #+END_SRC

 Best,
 Takaaki

 On May 8, 2013, at 12:06 AM, Takaaki ISHIKAWA tak...@ieee.org wrote:

 Dear Julian,
 
 When I use soffice with exec-path setting,
 the ODT export is failed like you.
 So currently, I use the following setting:
 
 #+BEGIN_SRC emacs-lisp
 (setq org-export-odt-preferred-output-format pdf)
 (setq org-export-odt-convert-processes
   '((LibreOffice
  /Applications/LibreOffice.app/Contents/MacOS/soffice 
 --headless --convert-to %f%x --outdir %d %i)
 (unoconv unoconv -f %f -o %d %i)))
 #+END_SRC
 
 It works fine for me.
 
 Best regards,
 Takaaki Ishikawa
 
 
 On May 7, 2013, at 10:51 PM, Julian M. Burgos jul...@hafro.is wrote:
 
 Hi Christian,
 The value
 for org-odt-convert-processes is ((LibreOffice soffice --headless 
 --convert-to %f%x --outdir %d %i)
 (unoconv unoconv -f %f -o %d %i))
 
 soffice is in my path, so I can run it from any directory.  
 
 Carsten, I have permission in /home.  That is where I had my trial org
 file. I have the same problem if I put my org file in other directory.
 
 Julian
 
 
 
 Carsten Dominik writes:
 
 On 7 mei 2013, at 14:29, Christian Moe m...@christianmoe.com wrote:
 
 
 Hi,
 
 Possible checks: What value do you have for org-odt-convert-processes?
 Does the command it provide launch LibreOffice services on your system?
 
 On my Mac, the default soffice command is not recognized out of the
 box; providing the full path to soffice
 (/Applications/LibreOffice.app/Contents/MacOS/soffice) helps. Also, it
 only seems to work when LibreOffice isn't already running, though I may
 be wrong about that (I just tried this for the first time).
 
 
 Another check:  Do you have write permissions in /home ?
 
 Why is it trying to write the file to that location?
 
 - Carsten
 
 Yours,
 Christian
 
 Julian M. Burgos writes:
 
 By the way, it also fails with the pdf and doc options...
 
 Julian M. Burgos writes:
 
 Hello everyone,
 I want to export via ODT directly into a docx format.  Following the
 instructions in the manual, I added 
 (setq org-odt-preferred-output-format docx)
 to my .emacs file.  But if I try to do an export I get the following
 error message:
 
 Export to /home/trial.docx failed
 
 I am using org-mode 8.0.2, LibreOffice 3.5.7.2, and Fedora 17.
 
 Any ideas?
 
 Julian
 
 
 
 
 -- 
 Julian Mariano Burgos, PhD
 Hafrannsóknastofnunin/Marine Research Institute
 Skúlagata 4, 121 Reykjavík, Iceland
 Sími/Telephone : +354-5752037
 Bréfsími/Telefax:  +354-5752001
 Netfang/Email: jul...@hafro.is
 
 
 --
 Takaaki ISHIKAWA tak...@ieee.org
  GITI, Waseda University
:) http://about.me/takaxp
 
 
 
 
 
 
 
 

 --
 Takaaki ISHIKAWA tak...@ieee.org
   GITI, Waseda University
 :) http://about.me/takaxp


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] odt export not working

[Julian M. Burgos]

Nick, I meant to include (setq org-export-backends '(odt)) in my .emacs
file.  I did that, and now I get the odt exporter as an option when I do
C-c C-e.  

I usually try no to use things that make changes to my .emacs file
direcly because I generate my .emacs file from an .org file (through
tangling).  Any customization would get lost next time I make a change
and tangle my .emacs file (which is quite often!).

Julian


Nick Dokos writes:

 Julian M. Burgos jul...@hafro.is writes:

 Ok, I see what you mean.  So I should do 
 (setq org-export-backends '(odt)) or something like that.  Fair enough. :)


 That's *not* what Nicolas suggested and it's *not* what you should do.

 Just do

 C-h v org-export-backends

 and click the Customize link, then mark all the (additional) backends
 you want to use. Please read the documentation of the variable: simply
 setting it in the middle of an emacs session will *not* work.

 Nick


 Nicolas Goaziou writes:

 Julian M. Burgos jul...@hafro.is writes:

 Right... I did not saw it.  And even if I did, I would not know that the
 package needed for loading the back-end for ODT is called ox-odt.

 You don't need to know that. The manual tells you to customize
 `org-export-backends' instead.


 Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

[O] Extending ODT export

[Julian M. Burgos]

Hello everyone,
I want to export via ODT directly into a docx format.  Following the
instructions in the manual, I added 
(setq org-odt-preferred-output-format docx)
to my .emacs file.  But if I try to do an export I get the following
error message:

Export to /home/trial.docx failed

I am using org-mode 8.0.2, LibreOffice 3.5.7.2, and Fedora 17.

Any ideas?

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Extending ODT export

[Julian M. Burgos]

By the way, it also fails with the pdf and doc options...

Julian M. Burgos writes:

 Hello everyone,
 I want to export via ODT directly into a docx format.  Following the
 instructions in the manual, I added 
 (setq org-odt-preferred-output-format docx)
 to my .emacs file.  But if I try to do an export I get the following
 error message:

 Export to /home/trial.docx failed

 I am using org-mode 8.0.2, LibreOffice 3.5.7.2, and Fedora 17.

 Any ideas?

 Julian


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Extending ODT export

[Julian M. Burgos]

Hi Christian,
The value
for org-odt-convert-processes is ((LibreOffice soffice --headless 
--convert-to %f%x --outdir %d %i)
 (unoconv unoconv -f %f -o %d %i))

soffice is in my path, so I can run it from any directory.  

Carsten, I have permission in /home.  That is where I had my trial org
file. I have the same problem if I put my org file in other directory.

Julian



Carsten Dominik writes:

 On 7 mei 2013, at 14:29, Christian Moe m...@christianmoe.com wrote:

 
 Hi,
 
 Possible checks: What value do you have for org-odt-convert-processes?
 Does the command it provide launch LibreOffice services on your system?
 
 On my Mac, the default soffice command is not recognized out of the
 box; providing the full path to soffice
 (/Applications/LibreOffice.app/Contents/MacOS/soffice) helps. Also, it
 only seems to work when LibreOffice isn't already running, though I may
 be wrong about that (I just tried this for the first time).
 

 Another check:  Do you have write permissions in /home ?

 Why is it trying to write the file to that location?

 - Carsten

 Yours,
 Christian
 
 Julian M. Burgos writes:
 
 By the way, it also fails with the pdf and doc options...
 
 Julian M. Burgos writes:
 
 Hello everyone,
 I want to export via ODT directly into a docx format.  Following the
 instructions in the manual, I added 
 (setq org-odt-preferred-output-format docx)
 to my .emacs file.  But if I try to do an export I get the following
 error message:
 
 Export to /home/trial.docx failed
 
 I am using org-mode 8.0.2, LibreOffice 3.5.7.2, and Fedora 17.
 
 Any ideas?
 
 Julian
 
 


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] odt export not working

[Julian M. Burgos]

Right... I did not saw it.  And even if I did, I would not know that the
package needed for loading the back-end for ODT is called ox-odt.

Nicolas Goaziou writes:

 Hello,

 Julian Burgos jul...@hafro.is writes:

 Manfred Lotz manfred.lotz at arcor.de writes:


  Are you calling (require 'ox-odt) somewhere in your config? Or
  configuring `org-export-backends'? ODT export isn't loaded by default,
  you'll have to load it explicitly by one of those two methods.


 This should be included in the manual.  From all the export options listed
 in the manual (iCalendar, HTML, LaTex, Plain Text, Publish), ODT export is
 the only (I think) that is not on by default.  The manual should explain
 clearly (perhaps in section 12.9.1) what you need to do to activate
 this option.

 This is already explained in 12.2.


 Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] odt export not working

[Julian M. Burgos]

Just thinking how to things easier for noobs like me. :)

Julian M. Burgos writes:

 Right... I did not saw it.  And even if I did, I would not know that the
 package needed for loading the back-end for ODT is called ox-odt.

 Nicolas Goaziou writes:

 Hello,

 Julian Burgos jul...@hafro.is writes:

 Manfred Lotz manfred.lotz at arcor.de writes:


  Are you calling (require 'ox-odt) somewhere in your config? Or
  configuring `org-export-backends'? ODT export isn't loaded by default,
  you'll have to load it explicitly by one of those two methods.


 This should be included in the manual.  From all the export options listed
 in the manual (iCalendar, HTML, LaTex, Plain Text, Publish), ODT export is
 the only (I think) that is not on by default.  The manual should explain
 clearly (perhaps in section 12.9.1) what you need to do to activate
 this option.

 This is already explained in 12.2.


 Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] Extending ODT export

[Julian M. Burgos]

Hi Takaaki,

Many thanks, but no luck.  I tried adding the complete path to soffice as you 
did below
(of course with the right path in my machine) and no luck.  If I do it
just like you, the export format does not change and is still ODT.  If
instead of using (setq org-export-odt-preferred-output-format pdf) I
use (setq org-odt-preferred-output-format pdf), I get the same error
message as before.

Julian

Takaaki ISHIKAWA writes:

 Dear Julian,

 When I use soffice with exec-path setting,
 the ODT export is failed like you.
 So currently, I use the following setting:

 #+BEGIN_SRC emacs-lisp
  (setq org-export-odt-preferred-output-format pdf)
  (setq org-export-odt-convert-processes
'((LibreOffice
   /Applications/LibreOffice.app/Contents/MacOS/soffice 
 --headless --convert-to %f%x --outdir %d %i)
  (unoconv unoconv -f %f -o %d %i)))
 #+END_SRC

 It works fine for me.

 Best regards,
 Takaaki Ishikawa


 On May 7, 2013, at 10:51 PM, Julian M. Burgos jul...@hafro.is wrote:

 Hi Christian,
 The value
 for org-odt-convert-processes is ((LibreOffice soffice --headless 
 --convert-to %f%x --outdir %d %i)
 (unoconv unoconv -f %f -o %d %i))
 
 soffice is in my path, so I can run it from any directory.  
 
 Carsten, I have permission in /home.  That is where I had my trial org
 file. I have the same problem if I put my org file in other directory.
 
 Julian
 
 
 
 Carsten Dominik writes:
 
 On 7 mei 2013, at 14:29, Christian Moe m...@christianmoe.com wrote:
 
 
 Hi,
 
 Possible checks: What value do you have for org-odt-convert-processes?
 Does the command it provide launch LibreOffice services on your system?
 
 On my Mac, the default soffice command is not recognized out of the
 box; providing the full path to soffice
 (/Applications/LibreOffice.app/Contents/MacOS/soffice) helps. Also, it
 only seems to work when LibreOffice isn't already running, though I may
 be wrong about that (I just tried this for the first time).
 
 
 Another check:  Do you have write permissions in /home ?
 
 Why is it trying to write the file to that location?
 
 - Carsten
 
 Yours,
 Christian
 
 Julian M. Burgos writes:
 
 By the way, it also fails with the pdf and doc options...
 
 Julian M. Burgos writes:
 
 Hello everyone,
 I want to export via ODT directly into a docx format.  Following the
 instructions in the manual, I added 
 (setq org-odt-preferred-output-format docx)
 to my .emacs file.  But if I try to do an export I get the following
 error message:
 
 Export to /home/trial.docx failed
 
 I am using org-mode 8.0.2, LibreOffice 3.5.7.2, and Fedora 17.
 
 Any ideas?
 
 Julian
 
 
 
 
 -- 
 Julian Mariano Burgos, PhD
 Hafrannsóknastofnunin/Marine Research Institute
 Skúlagata 4, 121 Reykjavík, Iceland
 Sími/Telephone : +354-5752037
 Bréfsími/Telefax:  +354-5752001
 Netfang/Email: jul...@hafro.is
 

 --
 Takaaki ISHIKAWA tak...@ieee.org
   GITI, Waseda University
 :) http://about.me/takaxp


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] odt export not working

[Julian M. Burgos]

Ok, I see what you mean.  So I should do 
(setq org-export-backends '(odt)) or something like that.  Fair enough. :)


Nicolas Goaziou writes:

 Julian M. Burgos jul...@hafro.is writes:

 Right... I did not saw it.  And even if I did, I would not know that the
 package needed for loading the back-end for ODT is called ox-odt.

 You don't need to know that. The manual tells you to customize
 `org-export-backends' instead.


 Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] window splitting and preserving folded states

[Julian M. Burgos]

 I am completely inebriated right now, so apologies for incoherence.

Isn't EUI (Emacs Under the Influence) illegal? :D

Re: [O] Saving within a source code block... a bug?

[Julian M. Burgos]

Thanks John.  I have C-s binded to the save-buffer function, while in
org-mode C-x C-s gives you the org-save-all-org-buffers function.
When running the later by hand, things work as they should.  I need to
redefine my key bindings.

All the best,

Julian


John Hendy writes:

 On Mon, Apr 22, 2013 at 10:39 AM, Julian M. Burgos jul...@hafro.is wrote:

 Hello fellow org-moders:

 I just switch to org-mode 8.0.1 and noticed a regression to a
 missbehaviour (a bug?) that happened at some point in a previous version and
 was later fixed.  This is the issue: I am working in an org-mode file
 with R code blocks, and I do C-c' to edit one of them.  I do some
 changes, and press C-s to save the changes.  At this point, I get a
 request to choose a file to save the changes into (this should not
 happen, the changes should just be saved into my org file).  Then I
 choose a file name, press RET, and the filename is not created, but
 instead the changes are saved into my org mode file.  Then, if I do more
 changes and do C-s save again, now org-mode behaves the way it should: I
 do not get asked for a filename and the changes are saved in my org mode
 file.

 Do you have any special settings regarding key bindings? I've not used
 this, but tried to reproduce with a simple example in a file I was
 already working on. Here was my block:

 #+begin_src R :session r :results output :exports results

   a - 1 + 2
   a

 #+end_src

 - Edit with =C-c '= (single quote, not backtick like I first tried as
 I edit tables this way!)
 - Code is highlighted in original buffer in yellow; new buffer opens
 with contents
 - Add line =b - 3 + 4=
 - C-x C-s to save, minibuffer reports that it's saving/wrote my file
 - The additional line above appears in file
 - =C-c '= to close minibuffer

 I can't reproduce. C-s, for me, is bound to isearch-forward.

 Org-mode version 8.0 (release_8.0-2-g77476c)

 Thought I'd see if this was release dependent, so I pulled and did
 =make clean  make  make doc= just now and I get the same
 [successful]  behavior.

 Org-mode version 8.0.1 (release_8.0.1-14-g2e6769)


 Best regards,
 John


 Hopefully this is clear.  Let me know if you have questions.
 Thanks!!

 Julian

 --
 Julian Mariano Burgos, PhD
 Hafrannsóknastofnunin/Marine Research Institute
 Skúlagata 4, 121 Reykjavík, Iceland
 Sími/Telephone : +354-5752037
 Bréfsími/Telefax:  +354-5752001
 Netfang/Email: jul...@hafro.is



-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is

Re: [O] New maintainer

[Julian M. Burgos]

I echo all the thanks that other people already gave.  My digital life
orbits around org-mode, so thanks to everyone who contributed to this
project.  Keep it up!!

Julian  

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is


Bastien writes:

 Dear all,

 I'm stepping down as the Org maintainer.

 Carsten accepted to step up, if the community agrees.
 Please raise your thumbs up or your concerns, if any.

 I'm glad I had this opportunity to work as Robin and
 I'm even more glad Batman may strike back!

 :)

[O] Saving within a source code block... a bug?

[Julian M. Burgos]

Hello fellow org-moders:

I just switch to org-mode 8.0.1 and noticed a regression to a
missbehaviour (a bug?) that happened at some point in a previous version and
was later fixed.  This is the issue: I am working in an org-mode file
with R code blocks, and I do C-c' to edit one of them.  I do some
changes, and press C-s to save the changes.  At this point, I get a
request to choose a file to save the changes into (this should not
happen, the changes should just be saved into my org file).  Then I
choose a file name, press RET, and the filename is not created, but
instead the changes are saved into my org mode file.  Then, if I do more
changes and do C-s save again, now org-mode behaves the way it should: I
do not get asked for a filename and the changes are saved in my org mode
file.
Hopefully this is clear.  Let me know if you have questions.
Thanks!!

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: jul...@hafro.is