Re: [O] running a source code by name

2018-05-30 Thread Julian M. Burgos
ok.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: &

[O] running a source code by name

2018-05-28 Thread 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

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

2017-12-14 Thread 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

[O] Confused about org-duration-format

2017-12-04 Thread 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

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

2017-10-09 Thread 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

Re: [O] org to static site?

2017-06-01 Thread 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,

Re: [O] Viewing pdf images

2017-04-06 Thread 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:

Re: [O] Viewing pdf images

2017-04-05 Thread Julian M. Burgos
chester.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 .e

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

2017-03-27 Thread 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

Re: [O] Viewing pdf images

2017-03-21 Thread 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

[O] org-ref and the minibuffer

2017-03-14 Thread 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

Re: [O] Problems with displaying inline images

2017-03-10 Thread 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

Re: [O] Problems with displaying inline images

2017-03-10 Thread Julian M. Burgos
uot;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.

[O] Problems with displaying inline images

2017-03-09 Thread 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

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

2017-03-08 Thread 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

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

2016-12-12 Thread 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

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

2016-12-01 Thread 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

[O] project website from org

2016-11-19 Thread 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

Re: [O] Release 9.0

2016-11-04 Thread 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: > >

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

2016-08-22 Thread 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

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

2016-08-22 Thread 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

Re: [O] Org + MS DOC

2016-02-04 Thread 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

Re: [O] Avoiding open buffers when clocking in

2015-09-22 Thread 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

Re: [O] Avoiding open buffers when clocking in

2015-09-22 Thread Julian M. Burgos
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

[O] Avoiding open buffers when clocking in

2015-09-22 Thread 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

[O] Not opening agenda files when clocking in

2015-09-11 Thread 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

[O] Closing buffers after clock-in

2015-09-10 Thread 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

Re: [O] Citations, continued

2015-02-04 Thread 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

Re: [O] org-ref no key found

2014-09-16 Thread Julian M. Burgos
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

Re: [O] org-ref no key found

2014-09-15 Thread Julian M. Burgos
, 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

Re: [O] org-ref no key found

2014-09-15 Thread Julian M. Burgos
? 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

Re: [O] org-ref no key found

2014-09-12 Thread Julian M. Burgos
}, 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

Re: [O] org-ref no key found

2014-09-08 Thread Julian M. Burgos
, 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

Re: [O] org-ref no key found

2014-08-30 Thread Julian M. Burgos
-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

[O] org-ref no key found

2014-08-29 Thread 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

Re: [O] org-ref no key found

2014-08-29 Thread 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

Re: [O] State of the art in citations

2014-04-28 Thread 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

Re: [O] State of the art in citations

2014-04-28 Thread 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

[O] State of the art in citations

2014-04-25 Thread 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

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

2014-04-15 Thread 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)

[O] firefox bookmarks to org-mode

2013-11-27 Thread 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

Re: [O] org-mode in the wild

2013-11-05 Thread 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

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

2013-06-05 Thread 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

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

2013-06-04 Thread 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

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

2013-05-23 Thread 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

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

2013-05-15 Thread 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

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

2013-05-15 Thread Julian M. Burgos
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

[O] confused about Beamer export

2013-05-14 Thread 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--

Re: [O] Extending ODT export

2013-05-10 Thread Julian M. Burgos
'((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

Re: [O] odt export not working

2013-05-10 Thread Julian M. Burgos
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

[O] Extending ODT export

2013-05-07 Thread 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

Re: [O] Extending ODT export

2013-05-07 Thread 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

Re: [O] Extending ODT export

2013-05-07 Thread Julian M. Burgos
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

Re: [O] odt export not working

2013-05-07 Thread 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)

Re: [O] odt export not working

2013-05-07 Thread 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

Re: [O] Extending ODT export

2013-05-07 Thread Julian M. Burgos
))) #+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

Re: [O] odt export not working

2013-05-07 Thread 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

Re: [O] window splitting and preserving folded states

2013-04-26 Thread 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?

2013-04-23 Thread Julian M. Burgos
, 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

Re: [O] New maintainer

2013-04-22 Thread 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

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

2013-04-22 Thread 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