* 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
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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
>
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^ 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
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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 --]
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^ 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
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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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