Would it be very hard to implement the Prefix and Suffix part of cite commands (for 'cf.' and page numers resp.): \cite[prefix][suffix]{ref}? Or would one just need to create a new custom link?

This is my first week of using org-mode and emacs all together, so there might just be a simple solution for this issue that I am not seeing. I noticed the "j" and "J" commands for agenda were not working for me when I tried integrating jmax version of org-mode with MobileOrg using this setup. My bandaid approach right now is to comment out line 283-289 of jmax-org.el to get MobileOrg to play well with my org-mode setup.

I'm getting the following error when attempting to load emacs from my linux machine:

For information about GNU Emacs and the GNU system, type C-h C-a.
(Shell command succeeded with no output) [3 times]
Importing package-keyring.gpg...done
Contacting host: jorgenschaefer.github.io:80
Loading /home-research/jboes/boes-python/jmax/elpa/helm-20150107.308/helm-autoloads.el (source)...done
ad-handle-definition: `tramp-read-passwd' got redefined
Loading /home-research/jboes/.emacs.d/recentf...done
Cleaning up the recentf list...done (0 removed)
Loading /home-research/jboes/boes-python/jmax/email.el (source)...done
Loading /home-research/jboes/boes-python/jmax/matlab/matlab-load.el (source)...done
Loading /home-research/jboes/boes-python/jmax/jmax-org.el (source)...
Loading /home-research/jboes/boes-python/jmax/org/org-show.el (source)...
Starting new Ispell process /usr/bin/aspell with default dictionary...
Loading /home-research/jboes/boes-python/jmax/org/org-show.el (source)...done
Loaded /home-research/jboes/boes-python/jmax/org/org-show.el
Loading /home-research/jboes/boes-python/jmax/org-ref/org-ref.el (source)...
eval-buffer: Cannot open load file: no such file or directory, helm-bibtex

Hi,

in my textfiles, links created with org-ref-insert-cite-link are not enclosed in brackets (textcite:sth), while those created with org-insert-link are ([[textcite:sth]]). Recently, the links without the brackets are not recognized by my emacs anymore (clicking on them results in 'no link found' and they are not exported to latex correctly).

My emacs-Version is 24.4.1, my org-mode version is 8.3.

I know that I used to be able to compile the files that contained links without brackets fine in the past. Do you have any idea what could cause this?

Thanks!

"org-ref.el" in section Scientific manuscript preparation linked to https://github.com/jkitchin/jmax/blob/master/org-ref.el, which does not exist.

When using M-x customize-group org-ref, the window that pops up will only allow me to save values to the org-ref variables if I don't load emacs with -q. To utilize the values set I need to continue loading emacs without -q.

The same is appears to be true for setting these variable manually in the users own .el file.

I don't know if not using -q will cause future problems.

I have noticed that, while it seems I can insert my cite-links just fine via org-ref-insert-cite-link, when clicking on the links to show the reference, only some references can be shown, while others will say no key found despite the fact that the key has also been inserted via org-ref.

E.g., I created the file test.bib with the following content:

% Better BibLaTeX: pinned
@thesis{bohnenberger2004decisiontheoreticplanning,
  shorttitle = {{Decision-theoretic planning for user-adaptive systems}},
  title = {{Decision-theoretic planning for user-adaptive systems: dealing with multiple goals and resource limitations}},
  url = {http://scidok.sulb.uni-saarland.de/volltexte/2005/455/},
  institution = {{Universitätsbibliothek}},
  type = {phdthesis},
  author = {Bohnenberger, Thorsten},
  urldate = {2014-06-28},
  date = {2004},
  year = {2004},
  file = {Bohnenberger - 2004 - Decision-theoretic planning for user-adaptive syst.pdf:/home/seb/.mozilla/firefox/nw2x3i1i.default/zotero/storage/XNN63PX2/Bohnenberger - 2004 - Decision-theoretic planning for user-adaptive syst.pdf:application/pdf;Snapshot:/home/seb/.mozilla/firefox/nw2x3i1i.default/zotero/storage/B5SMAVRA/455.html:text/html}
}

Now, when I set org-ref-default-bibliography to test.bib, I can insert bohnenberger2004decisiontheoreticplanning via org-ref-insert-cite-link. But when clicking on the link, org-ref says no key found. For some entries, this works fine, for others it does not, although all entries come from the same .bib.

It would be very useful if it were possible in some way to add pre- and suffixes (i.e., the «foo» and «bar» in «cite[foo][bar]{bibkey}») to reference links, to add things like page-numbers and «e.g.» keywords.

Is that feasible somehow, or does org-mode limit what kind of characters can appear in links? Otherwise, a syntax such as «cite:[e.g][p.43]bibkey» would come in handy.

Btw. thanks for taking the time working on a more canonical solution to reftex-links in org. There’s a bunch of snippets on the net, but a well-maintained and thought through solution is something sorely needed.

When citing multiple bibkeys in one command, the resulting lines are usually longer than 80 chars and visually impede the flow of the text. As a work-around, I tried wrapping my cites within org-mode link syntax. Now, if a white-space is added after the comma in a multicite, one can hard-wrap the line without breaking the link.

The problem with this is that it currently breaks org-ref. I.e., clicking on a bibkey will only work for the first line in such a multi-line link. For bibkeys on the following lines, the following error is reported: Invalid search bound (wrong side of point).

Additionally, these bibkeys are omitted when exporting to LaTeX.

A possible solution could be that when org-ref formats a link that is wrapped in the org-mode link syntax, it allows whitespace and line breaks in the list of bibkeys, and only terminates parsing the list when the final ]is hit

yasnippets can be very annoying for users who rely heavily on the TAB key for things like expanding headings or using python mode for proper indentation.

Popup agenda may be distracting to basic users.

I recommend removing both of these features for the group version.

Hello there,

I am using org-ref both on my Mac and on a Linux Desktop. While on the Mac org-ref works as expected, on the linux desktop it is not the case.

First, the key "C-c ]" is not getting defined to org-ref-insert-cite-link.

Second, if I try to do M-x org-ref-insert-cite-link, it fails with the message "concat: Wrong type argument: sequencep, 67"

I am using Emacs 24.2.1 with built-in org.

I am pretty new to emacs and org-mode, but would like to use the wonderful org-ref in my research workflow. Would be great if this is fixed and let me know if you need any more debugging output.

Loading /home/chaitanya/mytools/customizations/emacs/org-ref.el (source)...done
Loaded ~/mytools/customizations/emacs/org-ref.el
For information about GNU Emacs and the GNU system, type C-h C-a.
paper.org has auto save data; consider M-x recover-this-file
Loading reftex...done
Compiling label environment definitions...done
Scanning entire document...
Scanning file /home/chaitanya/work/mypapers/XXX/paper.org
Scanning document... done
File mode specification error: (wrong-type-argument integer-or-marker-p org-ref-insert-cite-key)
Loading vc-git...done
Using default bibliography
Scanning bibliography database mynewrefs.bib
Select: [n]ext [p]revious [r]estrict [ ]full_entry [q]uit RET [?]Help+more
concat: Wrong type argument: sequencep, 67

Error which occurs while loading into the jmax init.el file for the first time:

This is copied from the message log:
Loading /home-research/jboes/Dropbox/jmax/jmax-org.el (source)...
find-file-noselect: Wrong type argument: stringp, nil

Error was avoided by commenting out the following lines in jmax-org.el:
;; I like a random bibtex entry in my agenda.
;(defun formatted-bibtex-entry ()
; "return a bibtex entry as a formatted string. I hand-built the format.

;this treats all entries as a journal article."
; (interactive)
; (bibtex-beginning-of-entry)
; (let* ((bibtex-expand-strings t)
; (entry (bibtex-parse-entry t))
; (title (replace-regexp-in-string "\n|\t|\s+" " " (reftex-get-bib-field "title" entry)))
; (year (reftex-get-bib-field "year" entry))
; (author (replace-regexp-in-string "\n|\t|\s+" " " (reftex-get-bib-field "author" entry)))
; (key (reftex-get-bib-field "=key=" entry))
; (journal (reftex-get-bib-field "journal" entry))
; (volume (reftex-get-bib-field "volume" entry))
; (issue (reftex-get-bib-field "issue" entry))
; (pages (reftex-get-bib-field "pages" entry))
; (doi (reftex-get-bib-field "doi" entry))
; (output))
; (concat (when author author) ", "
; (when title title) ", "
; (when journal journal) ", "
; (when volume volume)
; (if issue (format "(%s), " issue) ", ")
; (when pages pages) ", "
; (when year (format "(%s)." year))
; (when doi (format " http://dx.doi.org/%s" doi)))))

;; this returns a string for my agenda.
;(defun get-random-bibtex-entry (&optional arg)
; "for printing in my agenda"
; (let ((keys) (lucky-key) (output))
; (with-current-buffer
; (find-file (car reftex-default-bibliography))
; (setq keys (bibtex-parse-keys))
; (setq lucky-key (car
; (nth
; (random (safe-length keys)) keys)))
; (goto-char (point-min))
; (re-search-forward lucky-key)
; (setq output (formatted-bibtex-entry))
; (kill-buffer)
; (format "%s\ncite:%s" output lucky-key))))

;(setq initial-scratch-message (get-random-bibtex-entry))

On several group computers, the bibliography file does not export properly using the C-c C-e j o command. The .tex file is produced in this way, but not the .bib file. Texlive has been installed on all the machines this was tested on.

upon opening a manuscript for the first time, clicking on a citation will result in the following message:

bibliography org-ref-bibliography-files = (references.bib) from references.bib
finally: org-ref-bibliography-files = (references.bib)
you selected Priyadarshini2011
looking for Priyadarshini2011 in references.bib
you found Priyadarshini2011 in nil
find-file-noselect: Wrong type argument: stringp, nil

After opening the .bib file in a separate buffer, the tools worked as expected. closing the .bib file did cause the reference tool to stop working.

Hi John,
This is not exactly an issue.

I was checking out the ms-report example pdf file. From what I remember it is "supposed" to be written in ACS format. What you have currently looks suspiciously like revtex.

Prateek

My local machine is getting the following error when selecting cite links on my linux machine:

Error running timer `org-ref-link-message': (void-function reftex-get-bib-field)

I do not get the error on Gilgamesh.

Hello John,

thank you for the impressive org-ref package!

I would love to be able to use the notes file as a quotation manager. The idea is something this:

Have a function "citeq" that parses the subheadings in the default notes.org file of a given bibtex entry's corresponding heading.
As a result we get a display in the minibuffer of every instance where a subheading has the properties :quote:, :pages: and :emphases:.

:quote: would be binary - is the following text a quotation or my personal note?
:pages: this is where the page reference information is stored. This data is added as a suffix to the LaTeX/Bibtex export of the entry.

:emphases: is binary as well: do any emphases in the text appear in the original or are they my own?

If there is a bibtex entry with a lot of quotes, the minibuffer could display the headings in a folded state.

Maybe one could also include a function for adding quotations in the notes file which asks for the user's input of these properties?

IMO this functionality would be extremely useful when combined with org's tagging feature.

I get the following error when attempting to load emacs from anywhere but Gilgamesh. Error occurs right after user files are finished loading.

Hi John.

Since I updated the org-ref.org, I can never load it normally.
Error message:Symbol's function definition is void: org-ref-define-citation-link.
Then I open the org-ref.el manually, and eval-buffer, same error.
I located the org-ref-define-citation-link definition and it seems there is no error in the definition since I can eval the function by Ctrl-x Ctrl E. After I eval the function, I tried to eval the buffer, there was another function org-ref-make-formation-function not defined. If I continues, same problem lasted.

I restarted emacs by emacs -q, and load dash by myself then i tried to eval org-ref.el, same error.

It was really strange..

org-ref-insert-ref-link does not seem to work (labels are not prompted) with figure labels.

For example, org-ref-insert-ref-link works (labels are prompted) to insert the reference for the table below, but not for any of the figures. Only the figure with the explicit \label works.

I am on Emacs 24.3.1 and Org mode 8.2.10.

A minimum example to replicate the behavior is below:

None of the references seem to work below except for the table [[ref:tab:table1]] and the figure with the explicit \label{} [[ref:fig:explicit-label]].

#+CAPTION: Table
#+NAME: tab:table1
| a | b |
| 1 | 2 |
| 3 | 4 |
| 5 | 6 |

#+CAPTION: Cap1
#+NAME: fig:org-name
\label{fig:explicit-label}
[[file:supporting_information/scripts/inkscape.png]]

#+CAPTION: Cap1
#+NAME: fig:org-name
[[file:supporting_information/scripts/inkscape.png]]

#+CAPTION: Cap1
#+ATTR_LaTeX: :width 18cm
#+NAME: fig:org-name-attr
[[file:supporting_information/scripts/inkscape.png]]

#+CAPTION: Cap1
#+ATTR_LaTeX: :width 18cm
#+LABEL: fig:org-label-attr
[[file:supporting_information/scripts/inkscape.png]]

#+CAPTION: Cap1
#+ATTR_LaTeX: :width 18cm
#+NAME: fig:org-name-label-attr
#+LABEL: fig:org-name-label-attr
[[file:supporting_information/scripts/inkscape.png]]

When attempting to check the buffer for spelling errors the following error is given in the message file:

Auto-saving...done
Starting new Ispell process [ispell::default] ...
apply: Searching for program: permission denied, ispell

This also seems to flyspell on initially starting emacs:

Starting new Ispell process [ispell::default] ...
Error enabling Flyspell mode:
(Searching for program permission denied ispell)

Hi John,

I guess pydoc might be a work in progress, but here are a couple of things that don't work for me (atleast on yosemite, emacs 24.4 and canopy).

1. I sometimes am unable to open the documentation by clicking the links, but I can open them by entering the full module path. For e.g.,
   If I open pydoc on numpy and click linalg, it says module not found, but I can open numpy.linalg without problems. However clicking random from numpy seems to work fine.
2. The back button seems to behave weirdly sometimes. If I click back on numpy.linalg, go back back to numpy, click random, and finally click back, it goes to linalg and not numpy.

Also, it might be convenient to be able to click enter on the links instead of clicking on them and have a keyboard shortcut for back. ;)

That being said, pydoc seems to be an awesome addition to jmax. Prevents me from opening the browser all the time!

Hi John,

You probably need to add git-messenger and ace-jump-zap to starter-kit-packages in packages.el or comment out their requirements in user.example to prevent error messages on jmax startup.

Prateek

Hi John,

I see this message after pulling the latest update of jmax. I was wondering if you also see it, or if it's because of something else I installed.

Warning (emacs): Possible archaic use of (hi-lock-mode).
Use (global-hi-lock-mode 1) in .emacs to enable hi-lock for all buffers,
use (hi-lock-mode 1) for individual buffers. For compatibility with Emacs
versions before 22 use the following in your init file:

    (if (functionp 'global-hi-lock-mode)
        (global-hi-lock-mode 1)
      (hi-lock-mode 1))

I had difficulty using biblatex with org-ref as it could not resolve my references when using biber as the backend which is the default. I did notice that if I run emacs default latex -> biber -> latex sequence on the tex file produced in the export stage, everything seems to work fine. It was only after noticing that your example with biblatex set the backend to bibtex8 that I could get everything to work.

I am not familiar enough with biber to prefer it as a backend, but I do like the customization I can do with biblatex. I am currently using most of your orgmode customizations for latex export, and I noticed when loading your exact configuration on github I have the same problem when trying to export using the biber backend. If you intentionally are avoiding biber, maybe you could add it into the README? Just started using org-ref, but I really like what I have found. Nice work.

Hi John,

I noticed that words not recognized by the spell checker are automatically colored red and underlined during the org-show. It would probably be a good idea to turn off flyspell in org-show mode.

Prateek

jabref has some code that downloads local pdfs (https://github.com/lehner/LocalCopy). this should be adaptable to emacs.

I discovered pydoc.el a couple of days ago, its great! No contrived setup, works out of the box, useful ... very nice idea.

I've been playing with it a bit and I've found a couple of issues, they are not specific to httplib docs but this way you can reproduce the errors.

• Executing pydoc httplib fails with:

  pydoc-make-url-links: Search failed: "http://httplib:"

  Changing the regex on line 59 to https?: seems to solve the issue.

• Python 2.x old style classes are not linkified, btw class HTTP, class HTTPConnection etc. The problem is the regex used to identify classes, it expects a list of parent classes in parentheses. This will affect python 3.x classes too.

• Executing pydoc httplib.SomeClass does not linkify the methods, in this case the problem is the number of spaces on the left side of the vertical bar.

John,

Just cloned a fresh copy of jmax and am getting the following error when I first start emacs:

(lambda (list) ...) quoted with ' rather than with #'
(lambda (dir-and-pos) ...) quoted with ' rather than with #'
(lambda (list) ...) quoted with ' rather than with #'
load-with-code-conversion: Invalid read syntax: "#"

This is stopping emacs from opening files on startup, which would be nice to have fixed.

The cloned copy is in ~jboes/Dropbox/jmax on gilgamesh if you'd like something to work with.

Currently, org-ref allows opening PDF documents for bibkeys if there exists a PDF that bears the name of the bibkey.

Some citation managers actually export a file location along with the bibtex entry. While the file key is afaik not an official bibtex key, both Zotero and Jabref seem to use a standard syntax for this key (and I once read Medeley is also using this syntax, though I cannot ascertain that). It would be useful if org-ref could check for this key and open the PDF from there.

One caveat is that the file key allows supplying multiple files, so a heuristics would have to given to select a file if more than one is found. Likely, this could mean just selecting the first PDF document in the list.

The exact syntax seems to be the following:

file = {description1:absolute-path:mime-type; description2:absolute-path:mime-type; …}

E.g.:

@article{lasersohn1999pragmatichalos,
…
file = {Lasersohn - 1999 - Pragmatic halos.pdf:/home/seb/Owncloud/zotero/storage/B5MEFRMN/Lasersohn - 1999 - Pragmatic halos.pdf:application/pdf;Snapshot:/home/seb/.mozilla/firefox/nw2x3i1i.default/zotero/storage/NNZA96NS/417059.html:text/html}
}

Dear John.

I am the guy who asked the question about interrupting the org-export process in org-mode mailing list. I spent hours for reading your ox-manuscript.el, finally I think I got something really good.

Then I use your package in my org-mode. I leave a .tex in my exporting directory and called the ox-manuscript-remove-image-extensions, it successfully removes .png. However when i call the ox-manuscript-build-submission-manuscript, the .png still exists in the intermediate .tex file. But I have seen the ox-manuscript-remove-image-extensions in the latter command. Why it does nothing?

Thank you very much for your help.

I started prototyping a document and played with inserting citation links with org-ref.
Unfortunately I ran in to some problems.

I have setup org-ref for my default bibliography in ~/research/bibliography.bib as well as for reftex.
If I only insert cite: links this works as expected and I can click the links and open pdf links etc.

If I try to export my document to a latex file with the org export command (C-c C-e) then the resulting tex file will not have any links to any bibliography files as expected.
Now if I add the bibliography key: bibliography:~/research/bibliography.bib this will exports to the tex file, however it seems tex does not support the ~ character for linking to $HOME. There are two ways to remedy this that I have found, either add "\string" in front of the link, or add/copy a link in ~/texmf/bibtex/bib/ to your bib file which makes it possible to just add "bibliography" to the tex file loosing the path from the end.

However, doing any of these two solutions breaks org-ref linking to the bibliography and org-ref can no longer find the bibliography file.

What I want to avoid is to have to copy my global bibliography to the local directory with the org file while still being able to export to latex.
Have I missed some detail of how to deal with this issue?
Is there a smart way already to avoid this and still being able to export to tex with a global bib file, and if not could this be fixed with an expand file name for "~" in the bibliography link?

Exporting on Windows does work with a defined bibliography style and bibliography inside of the document. Is there any way to make unsrt the default bibliography style and use the default bibliography defined in org-ref-default-bibliography to create the PDF?

I've also tried using org-ref-extract-bibtex-entries followed by org-babel-tangle to produce a local copy which I can use, however I can't get the text script generated to tangle out. The file i've been working with is in my dropbox user directory under ./Corelevelshift/workbook.org

Hi John,

I often get this cryptic emacs message when running code blocks,

executing Python code block...
Wrote /tmp/babel-14636JZ/ob-input-14637DW
Code block evaluation complete.
org-display-inline-images: Invalid image specification

Everything seems to work fine, and it doesn't seem to do anything as far as I can tell, but its weird that it shows up.

Prateek

Get ipython support. Open buffer in another frame.

Get autocompletion working. Rope. Ropemacs.

Pep8. Pyflakes.

When I try to use jmax, via emacs -q -l init.el, Emacs complains on the minibuffer that "Cannot open load file: ob-core" and indeed this file isn't in the repository. It appears to be something that ought to be autogenerated by running make autoloads [1] while in the org-mode directory, but nonetheless this file is never generated by make autoloads.

Running make also reports many errors with the same message.

Have you recently tried jmax on a fresh setup? Or is there just a step I'm missing?

[1] http://orgmode.org/manual/Installation.html#Installation

Hi John,

I am trying your org-ref. It is awesome.

When I use the function of label like lable:table-label, I found a problem which likes a bug.

* section 1
this is section1
* section 2
label:tab-1
#+caption: a table
| 2 | 2 | 2 | 2 | 2 |
|---+---+---+---+---|
| 2 | 2 | 2 | 2 | 2 |

table ref:tab-1

\[H=\frac{N_1I}l=\frac{N_1}l・\frac{V_1}{R_1} \eqno{(1)}
\label{eq-1}\]

As equation eqref:eq-1 shows........

It outputs:

The label of table and equation output as the label of section.

I tried to put the label:tab-1 below the +cpation: a table, but it does not output the caption of the table.

Maybe it is a unique problem in my windows, I am not very sure.

Hi John,

In latest version of jmax, I get an error during compilation.

=: Searching for program: No such file or directory, mogrify

I suspect this is coming from org-show trying to look for imagemagic or something, which I don't have installed. Anyway to get around this?

Prateek

When using C-c ] to add citations to an org document, Helm prompts the user to press C-j to insert a citation while keeping the session (I assume the Helm session).

This opens the mini-buffer with an identical Helm session, but doesn't add any citation to the org document.

Hi John,

Thanks for your org-ref.el and help before. According to your commands, I can output figure properly with the below preamble. Because there are many figures in my article, and i do not want to make them to same size (by setting (setq org-latex-image-default-width ".7\\textwidth") ), I use :width to specify the output size of figure.

#+CAPTION: caption label:fig:cutting 
#+ATTR_LaTeX: :width 0.9\textwidth

In my situation, I need to input the #+ATTR_LaTeX: :width 0.9\textwidth so many times. So a idea comes: if :width can be put in behind of label, like:

#+CAPTION: caption label:fig:cutting width:0.9

to accomplish the same function with #+ATTR_LaTeX: :width 0.9\textwidth, it will save input time and even space.

I am not sure if you are interested with this idea, if yes, any help will be appreciate!
Best regards.

More an annoyance than a real issue: in order to be able to lazzy-load pydoc it would be nice to have the pydoc function tagged with ;;;###autoload. On the opposite side, pydoc uses functions from org. If org is not already loaded emacs will complain. In order to make it more modular I think that it should requireexplicitly external dependencies.

Another minor issue.

If I do M-x org-show-mode when I am already inside a slide show, it gives me the message 'Org-show mode disabled', but does not actually exit the org show. I would have expected closing org-show-mode would automatically run org-show-stop-slideshow.

I'm really interested in org-ref, but I'd really rather not also have aspell and everything else you have in this single repo.

Would you consider splitting out org-ref and/or your other org modules, and including them as submodules or similar? That would enable me to include them in my configuration and track your work (and possibly even contribute back.)

If you are adding an «addbibresource:» link, currently, it seems as if org-ref will print the «\addbibresource» command in the exact place the link is set. However, with biblatex, both «\addbibresource» and «\bibliography» can only be used in the LaTeX preamble.

Hi John,

Can you share your tutorial to config Gnus in Windows?
I tried many instructions, but no one can make it.

Thanks in advance!