* org-ref "no key found" @ 2014-08-29 14:54 Julian M. Burgos 2014-08-29 18:58 ` John Kitchin 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-08-29 14:54 UTC (permalink / raw) To: emacs-orgmode 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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-08-29 14:54 org-ref "no key found" Julian M. Burgos @ 2014-08-29 18:58 ` John Kitchin 2014-08-29 18:23 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: John Kitchin @ 2014-08-29 18:58 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode "Julian M. Burgos" <julian@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 -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-08-29 18:58 ` John Kitchin @ 2014-08-29 18:23 ` Julian M. Burgos 2014-08-30 12:58 ` John Kitchin 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-08-29 18:23 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode 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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-08-29 18:23 ` Julian M. Burgos @ 2014-08-30 12:58 ` John Kitchin 2014-08-30 22:18 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: John Kitchin @ 2014-08-30 12:58 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode 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" <julian@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" <julian@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 -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-08-30 12:58 ` John Kitchin @ 2014-08-30 22:18 ` Julian M. Burgos 2014-09-08 9:17 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-08-30 22:18 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode 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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-08-30 22:18 ` Julian M. Burgos @ 2014-09-08 9:17 ` Julian M. Burgos 2014-09-12 11:08 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-09-08 9:17 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode, John Kitchin [-- Attachment #1: Type: text/plain, Size: 2732 bytes --] 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 [-- Attachment #2: trial.bib --] [-- Type: application/octet-stream, Size: 1094 bytes --] @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} } [-- Attachment #3: trial.org --] [-- Type: application/vnd.lotus-organizer, Size: 91 bytes --] [-- Attachment #4: Type: text/plain, Size: 1931 bytes --] 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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-08 9:17 ` Julian M. Burgos @ 2014-09-12 11:08 ` Julian M. Burgos 2014-09-13 16:18 ` John Kitchin 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-09-12 11:08 UTC (permalink / raw) To: emacs-orgmode, John Kitchin 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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-12 11:08 ` Julian M. Burgos @ 2014-09-13 16:18 ` John Kitchin 2014-09-15 9:16 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: John Kitchin @ 2014-09-13 16:18 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode 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" <julian@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" <julian@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" <julian@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 -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-13 16:18 ` John Kitchin @ 2014-09-15 9:16 ` Julian M. Burgos 2014-09-15 10:17 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-09-15 9:16 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode 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" <julian@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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-15 9:16 ` Julian M. Burgos @ 2014-09-15 10:17 ` Julian M. Burgos 2014-09-16 2:49 ` John Kitchin 0 siblings, 1 reply; 12+ messages in thread From: Julian M. Burgos @ 2014-09-15 10:17 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode, John Kitchin 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" <julian@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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-15 10:17 ` Julian M. Burgos @ 2014-09-16 2:49 ` John Kitchin 2014-09-16 9:42 ` Julian M. Burgos 0 siblings, 1 reply; 12+ messages in thread From: John Kitchin @ 2014-09-16 2:49 UTC (permalink / raw) To: Julian M. Burgos; +Cc: emacs-orgmode 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" <julian@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" <julian@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" <julian@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" <julian@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 -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: org-ref "no key found" 2014-09-16 2:49 ` John Kitchin @ 2014-09-16 9:42 ` Julian M. Burgos 0 siblings, 0 replies; 12+ messages in thread From: Julian M. Burgos @ 2014-09-16 9:42 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode 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" <julian@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" <julian@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" <julian@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" <julian@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: julian@hafro.is ^ permalink raw reply [flat|nested] 12+ messages in thread
end of thread, other threads:[~2014-09-16 10:41 UTC | newest] Thread overview: 12+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2014-08-29 14:54 org-ref "no key found" Julian M. Burgos 2014-08-29 18:58 ` John Kitchin 2014-08-29 18:23 ` Julian M. Burgos 2014-08-30 12:58 ` John Kitchin 2014-08-30 22:18 ` Julian M. Burgos 2014-09-08 9:17 ` Julian M. Burgos 2014-09-12 11:08 ` Julian M. Burgos 2014-09-13 16:18 ` John Kitchin 2014-09-15 9:16 ` Julian M. Burgos 2014-09-15 10:17 ` Julian M. Burgos 2014-09-16 2:49 ` John Kitchin 2014-09-16 9:42 ` Julian M. Burgos
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