* Mouse-over on bibliographic citation
@ 2017-06-21 21:50 Sharon Kimble
2017-06-21 22:12 ` John Kitchin
0 siblings, 1 reply; 5+ messages in thread
From: Sharon Kimble @ 2017-06-21 21:50 UTC (permalink / raw)
To: org-mode-email
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I've got this strange problem and I'm not sure when it started, possibly
when this new computer was first put to use last Friday afternoon with a
fresh install of Debian 9, or maybe before then, I'm not sure.
Anyway, whenever I mouse-over a bibliographic citation in an org-mode
document, it used to say for (cite:0072) '\Hair loss, 2015,
http://www.regrowth.com/hair-loss-articles/ \' but now just shows
'LINK:cite:0072'.
I am using 'org-ref' which is up to date, as is org-mode, and both from
ELPA.
This is what my bibliography item actually is -
--8<---------------cut here---------------start------------->8---
@Online{0072,
Title = {Hair loss},
Author = {regrowth},
Url = {http://www.regrowth.com/hair-loss-articles/},
Year = {2015}
}
--8<---------------cut here---------------end--------------->8---
So how can I regain my previous mouse-over abilities please?
Thanks
Sharon.
--
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
DrugFacts = https://www.drugfacts.org.uk
Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7
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^ permalink raw reply [flat|nested] 5+ messages in thread* Re: Mouse-over on bibliographic citation 2017-06-21 21:50 Mouse-over on bibliographic citation Sharon Kimble @ 2017-06-21 22:12 ` John Kitchin 2017-06-22 10:13 ` Sharon Kimble 0 siblings, 1 reply; 5+ messages in thread From: John Kitchin @ 2017-06-21 22:12 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode-email [-- Attachment #1: Type: text/plain, Size: 1682 bytes --] this is a bug in the current org-mode 9.0.8. You have to revert it to org 9.0.7 for now. It has been fixed, but I am not sure when it will show up. John ----------------------------------- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu On Wed, Jun 21, 2017 at 5:50 PM, Sharon Kimble <boudiccas@skimble.plus.com> wrote: > > I've got this strange problem and I'm not sure when it started, possibly > when this new computer was first put to use last Friday afternoon with a > fresh install of Debian 9, or maybe before then, I'm not sure. > > Anyway, whenever I mouse-over a bibliographic citation in an org-mode > document, it used to say for (cite:0072) '\Hair loss, 2015, > http://www.regrowth.com/hair-loss-articles/ \' but now just shows > 'LINK:cite:0072'. > > I am using 'org-ref' which is up to date, as is org-mode, and both from > ELPA. > > This is what my bibliography item actually is - > > --8<---------------cut here---------------start------------->8--- > @Online{0072, > Title = {Hair loss}, > Author = {regrowth}, > Url = {http://www.regrowth.com/hair-loss-articles/ > }, > Year = {2015} > } > --8<---------------cut here---------------end--------------->8--- > > So how can I regain my previous mouse-over abilities please? > > Thanks > Sharon. > -- > A taste of linux = http://www.sharons.org.uk > TGmeds = http://www.tgmeds.org.uk > DrugFacts = https://www.drugfacts.org.uk > Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 > [-- Attachment #2: Type: text/html, Size: 2926 bytes --] ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: Mouse-over on bibliographic citation 2017-06-21 22:12 ` John Kitchin @ 2017-06-22 10:13 ` Sharon Kimble 2017-06-22 12:14 ` John Kitchin 0 siblings, 1 reply; 5+ messages in thread From: Sharon Kimble @ 2017-06-22 10:13 UTC (permalink / raw) To: John Kitchin; +Cc: org-mode-email [-- Attachment #1: Type: text/plain, Size: 3299 bytes --] John Kitchin <jkitchin@andrew.cmu.edu> writes: > this is a bug in the current org-mode 9.0.8. You have to revert it to org 9.0.7 for now. It has been fixed, but I am not sure when it will show up. Thanks for this John. I can confirm that with today's release of 'org-mode plus contribs' the desired over effect has returned, but with a caveat - its showing the wrong bibliographic entry! I have this in my config file - --8<---------------cut here---------------start------------->8--- #+begin_src emacs-lisp (require 'org-ref) (setq reftex-default-bibliography '("~/research/death/death.bib")) ;; see org-ref for use of these variables (setq org-ref-bibliography-notes "~/research/notes.org" org-ref-default-bibliography '("~/research/death/death.bib") org-ref-pdf-directory "~/research/death/pdfs") (setq bibtex-completion-bibliography "~/research/death/death.bib" bibtex-completion-library-path "~/research/death/pdfs" bibtex-completion-notes-path "~/research/death/helm-bibtex-notes") #+end_src [2016-09-20 Tue 04:15] [2017-01-17 Tue 11:34] --8<---------------cut here---------------end--------------->8--- Going back to '(cite:0072)' the mouse-over now shows 'NHS, , /Ovarian cancer/ (2015).', which is the reference in 'death.bib'! I'm using the exact same code-block as pre-the updated org-mode, and I've restarted emacs, so I'm not sure what ought to be changed, if anything, but I'm unhappy with what its now showing as its not correct. Do I need to revamp my code-block, and if so, how please? Thanks Sharon. > > On Wed, Jun 21, 2017 at 5:50 PM, Sharon Kimble <boudiccas@skimble.plus.com> wrote: > > I've got this strange problem and I'm not sure when it started, possibly > when this new computer was first put to use last Friday afternoon with a > fresh install of Debian 9, or maybe before then, I'm not sure. > > Anyway, whenever I mouse-over a bibliographic citation in an org-mode > document, it used to say for (cite:0072) '\Hair loss, 2015, > http://www.regrowth.com/hair-loss-articles/ \' but now just shows > 'LINK:cite:0072'. > > I am using 'org-ref' which is up to date, as is org-mode, and both from > ELPA. > > This is what my bibliography item actually is - > > --8<---------------cut here---------------start------------->8--- > @Online{0072, > Title = {Hair loss}, > Author = {regrowth}, > Url = {http://www.regrowth.com/hair-loss-articles/}, > Year = {2015} > } > --8<---------------cut here---------------end--------------->8--- > > So how can I regain my previous mouse-over abilities please? > > Thanks > Sharon. > -- > A taste of linux = http://www.sharons.org.uk > TGmeds = http://www.tgmeds.org.uk > DrugFacts = https://www.drugfacts.org.uk > Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 > -- A taste of linux = http://www.sharons.org.uk TGmeds = http://www.tgmeds.org.uk DrugFacts = https://www.drugfacts.org.uk Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 832 bytes --] ^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: Mouse-over on bibliographic citation 2017-06-22 10:13 ` Sharon Kimble @ 2017-06-22 12:14 ` John Kitchin 2017-06-22 17:17 ` [SOLVED] " Sharon Kimble 0 siblings, 1 reply; 5+ messages in thread From: John Kitchin @ 2017-06-22 12:14 UTC (permalink / raw) To: Sharon Kimble; +Cc: org-mode-email Can you add this to your org-file, run it and tell me what the output is: #+BEGIN_SRC emacs-lisp (org-ref-find-bibliography) #+END_SRC Also run M-x org-ref to see what bibliography org-ref thinks it is using in that file. There were some recent changes to (org-ref-find-bibliography) that might be causing this problem. Do you have a bibliography link in the file you are working in? Sharon Kimble writes: > John Kitchin <jkitchin@andrew.cmu.edu> writes: > >> this is a bug in the current org-mode 9.0.8. You have to revert it to org 9.0.7 for now. It has been fixed, but I am not sure when it will show up. > > Thanks for this John. > > I can confirm that with today's release of 'org-mode plus contribs' the > desired over effect has returned, but with a caveat - its showing the > wrong bibliographic entry! I have this in my config file - > > --8<---------------cut here---------------start------------->8--- > #+begin_src emacs-lisp > (require 'org-ref) > (setq reftex-default-bibliography '("~/research/death/death.bib")) > > ;; see org-ref for use of these variables > (setq org-ref-bibliography-notes "~/research/notes.org" > org-ref-default-bibliography '("~/research/death/death.bib") > org-ref-pdf-directory "~/research/death/pdfs") > > (setq bibtex-completion-bibliography "~/research/death/death.bib" > bibtex-completion-library-path "~/research/death/pdfs" > bibtex-completion-notes-path "~/research/death/helm-bibtex-notes") > #+end_src > [2016-09-20 Tue 04:15] > [2017-01-17 Tue 11:34] > --8<---------------cut here---------------end--------------->8--- > > Going back to '(cite:0072)' the mouse-over now shows 'NHS, , /Ovarian > cancer/ (2015).', which is the reference in 'death.bib'! > > I'm using the exact same code-block as pre-the updated org-mode, and > I've restarted emacs, so I'm not sure what ought to be changed, if > anything, but I'm unhappy with what its now showing as its not correct. > > Do I need to revamp my code-block, and if so, how please? > > Thanks > Sharon. > >> >> On Wed, Jun 21, 2017 at 5:50 PM, Sharon Kimble <boudiccas@skimble.plus.com> wrote: >> >> I've got this strange problem and I'm not sure when it started, possibly >> when this new computer was first put to use last Friday afternoon with a >> fresh install of Debian 9, or maybe before then, I'm not sure. >> >> Anyway, whenever I mouse-over a bibliographic citation in an org-mode >> document, it used to say for (cite:0072) '\Hair loss, 2015, >> http://www.regrowth.com/hair-loss-articles/ \' but now just shows >> 'LINK:cite:0072'. >> >> I am using 'org-ref' which is up to date, as is org-mode, and both from >> ELPA. >> >> This is what my bibliography item actually is - >> >> --8<---------------cut here---------------start------------->8--- >> @Online{0072, >> Title = {Hair loss}, >> Author = {regrowth}, >> Url = {http://www.regrowth.com/hair-loss-articles/}, >> Year = {2015} >> } >> --8<---------------cut here---------------end--------------->8--- >> >> So how can I regain my previous mouse-over abilities please? >> >> Thanks >> Sharon. >> -- >> A taste of linux = http://www.sharons.org.uk >> TGmeds = http://www.tgmeds.org.uk >> DrugFacts = https://www.drugfacts.org.uk >> Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 >> -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 5+ messages in thread
* [SOLVED] Re: Mouse-over on bibliographic citation 2017-06-22 12:14 ` John Kitchin @ 2017-06-22 17:17 ` Sharon Kimble 0 siblings, 0 replies; 5+ messages in thread From: Sharon Kimble @ 2017-06-22 17:17 UTC (permalink / raw) To: John Kitchin; +Cc: org-mode-email [-- Attachment #1: Type: text/plain, Size: 5503 bytes --] John Kitchin <jkitchin@andrew.cmu.edu> writes: > Can you add this to your org-file, run it and tell me what the output is: > > #+BEGIN_SRC emacs-lisp > (org-ref-find-bibliography) > #+END_SRC > > Also run M-x org-ref to see what bibliography org-ref thinks it is > using in that file. There were some recent changes to > (org-ref-find-bibliography) that might be causing this problem. --8<---------------cut here---------------start------------->8--- Bibliography No bibliographystyle found. Using these bibtex files: (/home/boudiccas/research/hair17/hair17.bib /home/boudiccas/research/age-and-trans/cancer/cancer.bib) --8<---------------cut here---------------end--------------->8--- > > Do you have a bibliography link in the file you are working in? > This is in a file called hair17.org and this is its bibliography install - --8<---------------cut here---------------start------------->8--- #+latex_header: \usepackage[backend=biber,style=authoryear,doi=true,hyperref=true,backref=true,backrefstyle=two,date=year,maxcitenames=3]{biblatex} #+LATEX_HEADER: \addbibresource{/home/boudiccas/research/hair17/hair17.bib} --8<---------------cut here---------------end--------------->8--- Right, I've sorted the problem out. Somehow I had various things that I was building the pdf with, meaning #+latex_header:, which included a reference to 'cancer.bib'. I thought that it was commented out, but when I deleted all comments out latex_headers I've found that it is only referencing hair17.bib as shown in this output. --8<---------------cut here---------------start------------->8--- Bibliography No bibliographystyle found. Using these bibtex files: (/home/boudiccas/research/hair17/hair17.bib) --8<---------------cut here---------------end--------------->8--- Sorry for all the hassle and noise that I've caused. Sorry Sharon. > > Sharon Kimble writes: > >> John Kitchin <jkitchin@andrew.cmu.edu> writes: >> >>> this is a bug in the current org-mode 9.0.8. You have to revert it to org 9.0.7 for now. It has been fixed, but I am not sure when it will show up. >> >> Thanks for this John. >> >> I can confirm that with today's release of 'org-mode plus contribs' the >> desired over effect has returned, but with a caveat - its showing the >> wrong bibliographic entry! I have this in my config file - >> >> --8<---------------cut here---------------start------------->8--- >> #+begin_src emacs-lisp >> (require 'org-ref) >> (setq reftex-default-bibliography '("~/research/death/death.bib")) >> >> ;; see org-ref for use of these variables >> (setq org-ref-bibliography-notes "~/research/notes.org" >> org-ref-default-bibliography '("~/research/death/death.bib") >> org-ref-pdf-directory "~/research/death/pdfs") >> >> (setq bibtex-completion-bibliography "~/research/death/death.bib" >> bibtex-completion-library-path "~/research/death/pdfs" >> bibtex-completion-notes-path "~/research/death/helm-bibtex-notes") >> #+end_src >> [2016-09-20 Tue 04:15] >> [2017-01-17 Tue 11:34] >> --8<---------------cut here---------------end--------------->8--- >> >> Going back to '(cite:0072)' the mouse-over now shows 'NHS, , /Ovarian >> cancer/ (2015).', which is the reference in 'death.bib'! >> >> I'm using the exact same code-block as pre-the updated org-mode, and >> I've restarted emacs, so I'm not sure what ought to be changed, if >> anything, but I'm unhappy with what its now showing as its not correct. >> >> Do I need to revamp my code-block, and if so, how please? >> >> Thanks >> Sharon. >> >>> >>> On Wed, Jun 21, 2017 at 5:50 PM, Sharon Kimble <boudiccas@skimble.plus.com> wrote: >>> >>> I've got this strange problem and I'm not sure when it started, possibly >>> when this new computer was first put to use last Friday afternoon with a >>> fresh install of Debian 9, or maybe before then, I'm not sure. >>> >>> Anyway, whenever I mouse-over a bibliographic citation in an org-mode >>> document, it used to say for (cite:0072) '\Hair loss, 2015, >>> http://www.regrowth.com/hair-loss-articles/ \' but now just shows >>> 'LINK:cite:0072'. >>> >>> I am using 'org-ref' which is up to date, as is org-mode, and both from >>> ELPA. >>> >>> This is what my bibliography item actually is - >>> >>> --8<---------------cut here---------------start------------->8--- >>> @Online{0072, >>> Title = {Hair loss}, >>> Author = {regrowth}, >>> Url = {http://www.regrowth.com/hair-loss-articles/}, >>> Year = {2015} >>> } >>> --8<---------------cut here---------------end--------------->8--- >>> >>> So how can I regain my previous mouse-over abilities please? >>> >>> Thanks >>> Sharon. >>> -- >>> A taste of linux = http://www.sharons.org.uk >>> TGmeds = http://www.tgmeds.org.uk >>> DrugFacts = https://www.drugfacts.org.uk >>> Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 >>> > > > -- > Professor John Kitchin > Doherty Hall A207F > Department of Chemical Engineering > Carnegie Mellon University > Pittsburgh, PA 15213 > 412-268-7803 > @johnkitchin > http://kitchingroup.cheme.cmu.edu > -- A taste of linux = http://www.sharons.org.uk TGmeds = http://www.tgmeds.org.uk DrugFacts = https://www.drugfacts.org.uk Debian 9.0, fluxbox 1.3.5-2, emacs 25.1.1, org-mode 9.0.7 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 832 bytes --] ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2017-06-22 17:17 UTC | newest] Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2017-06-21 21:50 Mouse-over on bibliographic citation Sharon Kimble 2017-06-21 22:12 ` John Kitchin 2017-06-22 10:13 ` Sharon Kimble 2017-06-22 12:14 ` John Kitchin 2017-06-22 17:17 ` [SOLVED] " Sharon Kimble
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