emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
* 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

[-- Attachment #1: Type: text/plain, Size: 1192 bytes --]


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: signature.asc --]
[-- Type: application/pgp-signature, Size: 832 bytes --]

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: Mouse-over on bibliographic citation
  2017-06-21 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

Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).