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-
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" writes:
>
> If you click on the bibliography link to open the file, and then go back
> to your org-file, do the
em (an
> org-file and the bib file)?
>
> "Julian M. Burgos" 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:
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
Journaltitle = {Ecological Applications},
Year = {2006},
Number = {1},
Pages= {5--19},
Volume = {16},
Crossref = {Quick2010},
File = {:Hobbs2006.pdf:PDF},
Publisher
u 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" writes:
es 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 solv
t 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" writes:
>
>> John, another issue...a really minor one, and I am not sure if
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
th
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/Tele
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
s:
> On Mon, Apr 22, 2013 at 10:39 AM, Julian M. Burgos 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
>>
> I am completely inebriated right now, so apologies for incoherence.
Isn't EUI (Emacs Under the Influence) illegal? :D
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 us
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-for
ffice.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 ?
>
> W
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 writes:
>
>> Manfred Lotz arcor.de> writes:
>>
>>
>>> > Are you calling (require 'ox-odt) somewhere in yo
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,
>&g
tents/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.
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" writes:
>
>> Right... I did not saw it. And even if I did, I would not know that the
>> package ne
s/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
>&
rough
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" writes:
>
>> Ok, I see what you mean. So I should do
>> (setq org-export-backends '(odt)
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:
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 .emac
ase see my comments below.
>
> Let me know if there is still problem.
>
> Regards,
> Yujie
>
>
> 2013/5/15 Julian M. Burgos
>
>> Hi Yujie,
>>
>> Thanks for the exporter! I am still a bit confused though (seems my
>> natural state). Let say I
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
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
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" writes:
>
>> Hi Rainier,
>
> Hi Julian,
>
>> If I understood correctly, you
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 repositor
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
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
file
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
, but your solution is simpler.
Kyle Meyer writes:
> "Julian M. Burgos" 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
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 th
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
file
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
file
Hi Esben,
I use find-lisp-find-files. I have the following in my .emacs file:
;;--
;; Load org agenda files
;;--
(load-library "find-lisp")
(a
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
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 in
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
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
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
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.ht
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 y
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 re
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
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
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
t;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, Juli
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 some
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
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
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 ráðgjaf
e:
>
>> 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
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
> wrote:
>
>> Can you clarify the
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, rat
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
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 ráðgjafars
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
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
on.outlook.com/?url=http%3A%2F%2Fkitchingroup.cheme.cmu.edu&data=02%7C01%7C%7Cfdaa27b411604ed32a0108d5c4d9fa01%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636631362846470731&sdata=4K%2B96NBf5KPaoz13laaAR0%2FaqY2FlefTLy%2BPXy6YtO8%3D&reserved=0
>>
>>
>> On Mon, May 28,
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 inste
his 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"
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
>> r
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 wi
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