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-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 >>>>>>>>>> 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