* org-ref no bibliography generated in pdf
@ 2016-02-06 13:42 Nikolai Stenfors
2016-02-06 14:07 ` Eric S Fraga
0 siblings, 1 reply; 11+ messages in thread
From: Nikolai Stenfors @ 2016-02-06 13:42 UTC (permalink / raw)
To: emacs-orgmode
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Hi,
Org-ref appears to be an excellent reference handling tool for org-mode. I
have followed the installation according to org-ref homepage.
However, I have problems exporting the org-file to pdf. The generated
intermediate latex-file appears visually OK. In the pdf, references are
shown as [?] and no bibliography is generated.
Exporting to html works. Thus, i suppose the problem is converting the file
from .tex to .pdf.
I have search and browsed the internet on everything related to reftex,
org-latex-pdf, org-ref and bib-tex similar to Rainer Krug(
http://thread.gmane.org/gmane.emacs.orgmode/102603/focus=102637)
Please find my struggles attached as files.
Any suggestions/directions?
Yours sincerely,
Nikolai Stenfors
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[-- Attachment #3: manuskript.pdf --]
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* Introduction
An article cite:Stenfors2010
*
bibliographystyle:unsrt
bibliography:reference.bib
[-- Attachment #6: reference.bib --]
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 13:42 org-ref no bibliography generated in pdf Nikolai Stenfors
@ 2016-02-06 14:07 ` Eric S Fraga
2016-02-06 18:04 ` Nikolai
0 siblings, 1 reply; 11+ messages in thread
From: Eric S Fraga @ 2016-02-06 14:07 UTC (permalink / raw)
To: Nikolai Stenfors; +Cc: emacs-orgmode
On Saturday, 6 Feb 2016 at 14:42, Nikolai Stenfors wrote:
> Hi,
> Org-ref appears to be an excellent reference handling tool for org-mode. I
> have followed the installation according to org-ref homepage.
> However, I have problems exporting the org-file to pdf. The generated
> intermediate latex-file appears visually OK. In the pdf, references are
> shown as [?] and no bibliography is generated.
What is the setting of org-latex-to-pdf-process? It looks like bibtex
was not run, having looked at the LaTeX code that was generated, which
looks perfectly fine. Have you looked at the LaTeX log output when
exporting to PDF? There will be a buffer with this log.
--
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3.3-548-g99697a
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
@ 2016-02-06 15:19 John Kitchin
2016-02-06 17:16 ` Nikolai
0 siblings, 1 reply; 11+ messages in thread
From: John Kitchin @ 2016-02-06 15:19 UTC (permalink / raw)
To: Nikolai Stenfors, emacs-orgmode@gnu org
It could also be you didn't specify a bibliographystyle.
Try running M-x org-ref on the file. It checks that some things like that are correct. Sometimes it is helpful to manually build the puff at the command line. Org hides a lot of errors sometimes.
On February 6, 2016, at 9:23 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
On Saturday, 6 Feb 2016 at 14:42, Nikolai Stenfors wrote:
> Hi,
> Org-ref appears to be an excellent reference handling tool for org-mode. I
> have followed the installation according to org-ref homepage.
> However, I have problems exporting the org-file to pdf. The generated
> intermediate latex-file appears visually OK. In the pdf, references are
> shown as [?] and no bibliography is generated.
What is the setting of org-latex-to-pdf-process? It looks like bibtex
was not run, having looked at the LaTeX code that was generated, which
looks perfectly fine. Have you looked at the LaTeX log output when
exporting to PDF? There will be a buffer with this log.
--
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3.3-548-g99697a
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 15:19 John Kitchin
@ 2016-02-06 17:16 ` Nikolai
2016-02-06 17:46 ` John Kitchin
0 siblings, 1 reply; 11+ messages in thread
From: Nikolai @ 2016-02-06 17:16 UTC (permalink / raw)
To: emacs-orgmode
John Kitchin <johnrkitchin <at> gmail.com> writes:
>
> It could also be you didn't specify a bibliographystyle.
>
> Try running M-x org-ref on the file. It checks that some things like that
are correct. Sometimes it is
> helpful to manually build the puff at the command line. Org hides a lot of
errors sometimes.
>
Thank you Prof. Kitchen,
Tried your suggestions with same result: references marked as [?] and no
bibliography generated.
/Nikolai
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 17:16 ` Nikolai
@ 2016-02-06 17:46 ` John Kitchin
0 siblings, 0 replies; 11+ messages in thread
From: John Kitchin @ 2016-02-06 17:46 UTC (permalink / raw)
To: Nikolai; +Cc: emacs-orgmode@gnu.org
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Then Eric is probably right:what is org-latex-to-pdf-process set to?
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 Sat, Feb 6, 2016 at 12:16 PM, Nikolai <nikolai.stenfors@gapps.umu.se>
wrote:
> John Kitchin <johnrkitchin <at> gmail.com> writes:
>
> >
> > It could also be you didn't specify a bibliographystyle.
> >
> > Try running M-x org-ref on the file. It checks that some things like that
> are correct. Sometimes it is
> > helpful to manually build the puff at the command line. Org hides a lot
> of
> errors sometimes.
> >
>
> Thank you Prof. Kitchen,
>
> Tried your suggestions with same result: references marked as [?] and no
> bibliography generated.
>
> /Nikolai
>
>
>
>
>
>
>
>
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 14:07 ` Eric S Fraga
@ 2016-02-06 18:04 ` Nikolai
2016-02-06 18:08 ` John Kitchin
0 siblings, 1 reply; 11+ messages in thread
From: Nikolai @ 2016-02-06 18:04 UTC (permalink / raw)
To: emacs-orgmode
Eric S Fraga <e.fraga <at> ucl.ac.uk> writes:
>
> On Saturday, 6 Feb 2016 at 14:42, Nikolai Stenfors wrote:
> > Hi,
> > Org-ref appears to be an excellent reference handling tool for org-mode. I
> > have followed the installation according to org-ref homepage.
> > However, I have problems exporting the org-file to pdf. The generated
> > intermediate latex-file appears visually OK. In the pdf, references are
> > shown as [?] and no bibliography is generated.
>
> What is the setting of org-latex-to-pdf-process? It looks like bibtex
> was not run, having looked at the LaTeX code that was generated, which
> looks perfectly fine. Have you looked at the LaTeX log output when
> exporting to PDF? There will be a buffer with this log.
OK,
pdflatex -interaction nonstopmode -output-directory %o %f
pdflatex -interaction nonstopmode -output-directory %o %f
pdflatex -interaction nonstopmode -output-directory %o %f
tried to add "bibtex %b" or "bibtex %o %f" without luck
Nikolai
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 18:04 ` Nikolai
@ 2016-02-06 18:08 ` John Kitchin
2016-02-06 18:49 ` Nikolai Stenfors
2016-02-07 23:21 ` Andreas Kiermeier
0 siblings, 2 replies; 11+ messages in thread
From: John Kitchin @ 2016-02-06 18:08 UTC (permalink / raw)
To: Nikolai; +Cc: emacs-orgmode@gnu.org
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that is why you don't get bibtex run then ;) try this
(setq org-latex-pdf-process
'("pdflatex -shell-escape -interaction nonstopmode -output-directory
%o %b"
"bibtex %b"
"pdflatex -shell-escape -interaction nonstopmode -output-directory
%o %b"
"pdflatex -shell-escape -interaction nonstopmode -output-directory
%o %b"))
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 Sat, Feb 6, 2016 at 1:04 PM, Nikolai <nikolai.stenfors@gapps.umu.se>
wrote:
> Eric S Fraga <e.fraga <at> ucl.ac.uk> writes:
>
> >
> > On Saturday, 6 Feb 2016 at 14:42, Nikolai Stenfors wrote:
> > > Hi,
> > > Org-ref appears to be an excellent reference handling tool for
> org-mode. I
> > > have followed the installation according to org-ref homepage.
> > > However, I have problems exporting the org-file to pdf. The generated
> > > intermediate latex-file appears visually OK. In the pdf, references are
> > > shown as [?] and no bibliography is generated.
> >
> > What is the setting of org-latex-to-pdf-process? It looks like bibtex
> > was not run, having looked at the LaTeX code that was generated, which
> > looks perfectly fine. Have you looked at the LaTeX log output when
> > exporting to PDF? There will be a buffer with this log.
>
>
> OK,
>
> pdflatex -interaction nonstopmode -output-directory %o %f
> pdflatex -interaction nonstopmode -output-directory %o %f
> pdflatex -interaction nonstopmode -output-directory %o %f
>
> tried to add "bibtex %b" or "bibtex %o %f" without luck
>
> Nikolai
>
>
>
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 18:08 ` John Kitchin
@ 2016-02-06 18:49 ` Nikolai Stenfors
2016-02-07 23:21 ` Andreas Kiermeier
1 sibling, 0 replies; 11+ messages in thread
From: Nikolai Stenfors @ 2016-02-06 18:49 UTC (permalink / raw)
To: John Kitchin; +Cc: emacs-orgmode
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YES, IT WORKS!
Thank you, Eric and John!
2016-02-06 19:08 GMT+01:00 John Kitchin <jkitchin@andrew.cmu.edu>:
> that is why you don't get bibtex run then ;) try this
> (setq org-latex-pdf-process
> '("pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"
> "bibtex %b"
> "pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"
> "pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"))
>
> 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 Sat, Feb 6, 2016 at 1:04 PM, Nikolai <nikolai.stenfors@gapps.umu.se>
> wrote:
>
>> Eric S Fraga <e.fraga <at> ucl.ac.uk> writes:
>>
>> >
>> > On Saturday, 6 Feb 2016 at 14:42, Nikolai Stenfors wrote:
>> > > Hi,
>> > > Org-ref appears to be an excellent reference handling tool for
>> org-mode. I
>> > > have followed the installation according to org-ref homepage.
>> > > However, I have problems exporting the org-file to pdf. The generated
>> > > intermediate latex-file appears visually OK. In the pdf, references
>> are
>> > > shown as [?] and no bibliography is generated.
>> >
>> > What is the setting of org-latex-to-pdf-process? It looks like bibtex
>> > was not run, having looked at the LaTeX code that was generated, which
>> > looks perfectly fine. Have you looked at the LaTeX log output when
>> > exporting to PDF? There will be a buffer with this log.
>>
>>
>> OK,
>>
>> pdflatex -interaction nonstopmode -output-directory %o %f
>> pdflatex -interaction nonstopmode -output-directory %o %f
>> pdflatex -interaction nonstopmode -output-directory %o %f
>>
>> tried to add "bibtex %b" or "bibtex %o %f" without luck
>>
>> Nikolai
>>
>>
>>
>
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-06 18:08 ` John Kitchin
2016-02-06 18:49 ` Nikolai Stenfors
@ 2016-02-07 23:21 ` Andreas Kiermeier
2016-02-08 0:03 ` John Kitchin
2016-02-08 2:57 ` Nick Dokos
1 sibling, 2 replies; 11+ messages in thread
From: Andreas Kiermeier @ 2016-02-07 23:21 UTC (permalink / raw)
To: John Kitchin; +Cc: Nikolai, emacs-orgmode@gnu.org
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On 7 February 2016 at 04:38, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> that is why you don't get bibtex run then ;) try this
> (setq org-latex-pdf-process
> '("pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"
> "bibtex %b"
> "pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"
> "pdflatex -shell-escape -interaction nonstopmode
> -output-directory %o %b"))
>
Hi John & list,
is there any reason why we should be hardcoding multiple runs of pdflatex
(& bibtex) instead of using texify?
I have my org-latex-to-pdf set to
"texify -p -b --tex-option=-shell-escape %f"
(I'm on Windows 10, running MikTex 2.9), which hasn't given my any
problems to date and seem to be a little more efficient.
I'm just curious.
Cheers,
AK
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-07 23:21 ` Andreas Kiermeier
@ 2016-02-08 0:03 ` John Kitchin
2016-02-08 2:57 ` Nick Dokos
1 sibling, 0 replies; 11+ messages in thread
From: John Kitchin @ 2016-02-08 0:03 UTC (permalink / raw)
To: Andreas Kiermeier; +Cc: Nikolai, emacs-orgmode@gnu.org
no reason. I do not actually use this code below. I have another
function that probably does want texify does ;) maybe some extra stuff
like running makeindex, etc....
Andreas Kiermeier writes:
> On 7 February 2016 at 04:38, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
>> that is why you don't get bibtex run then ;) try this
>> (setq org-latex-pdf-process
>> '("pdflatex -shell-escape -interaction nonstopmode
>> -output-directory %o %b"
>> "bibtex %b"
>> "pdflatex -shell-escape -interaction nonstopmode
>> -output-directory %o %b"
>> "pdflatex -shell-escape -interaction nonstopmode
>> -output-directory %o %b"))
>>
>
> Hi John & list,
>
> is there any reason why we should be hardcoding multiple runs of pdflatex
>
> (& bibtex) instead of using texify?
>
> I have my org-latex-to-pdf set to
> "texify -p -b --tex-option=-shell-escape %f"
> (I'm on Windows 10, running MikTex 2.9), which hasn't given my any
> problems to date and seem to be a little more efficient.
>
> I'm just curious.
>
> Cheers,
>
> AK
--
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] 11+ messages in thread
* Re: org-ref no bibliography generated in pdf
2016-02-07 23:21 ` Andreas Kiermeier
2016-02-08 0:03 ` John Kitchin
@ 2016-02-08 2:57 ` Nick Dokos
1 sibling, 0 replies; 11+ messages in thread
From: Nick Dokos @ 2016-02-08 2:57 UTC (permalink / raw)
To: emacs-orgmode
Andreas Kiermeier <andreas.kiermeier@gmail.com> writes:
> On 7 February 2016 at 04:38, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
> that is why you don't get bibtex run then ;) try this
> (setq org-latex-pdf-process
> '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %b"
> "bibtex %b"
> "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %b"
> "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %b"))
>
> Hi John & list,
>
> is there any reason why we should be hardcoding multiple runs of pdflatex
>
> (& bibtex) instead of using texify?
>
> I have my org-latex-to-pdf set to
> "texify -p -b --tex-option=-shell-escape %f"
> (I'm on Windows 10, running MikTex 2.9), which hasn't given my any problems to date and
> seem to be a little more efficient.
>
They are not hardcoded: that's just the default value of
org-latex-pdf-process which can be customized.
The three pdflatex runs are a "safe" default which avoids
incompatibilities between systems.
The customization options for org-latex-pdf-process list some other
possibilities which one might choose in preference to the default. If
texify can do the job (even if it does not exist on all systems of
interest), I would suggest adding it to the customizations menu of the
variable, so it can be chosen by a user as his/her personal default.
--
Nick
^ permalink raw reply [flat|nested] 11+ messages in thread
end of thread, other threads:[~2016-02-08 2:57 UTC | newest]
Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-02-06 13:42 org-ref no bibliography generated in pdf Nikolai Stenfors
2016-02-06 14:07 ` Eric S Fraga
2016-02-06 18:04 ` Nikolai
2016-02-06 18:08 ` John Kitchin
2016-02-06 18:49 ` Nikolai Stenfors
2016-02-07 23:21 ` Andreas Kiermeier
2016-02-08 0:03 ` John Kitchin
2016-02-08 2:57 ` Nick Dokos
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2016-02-06 15:19 John Kitchin
2016-02-06 17:16 ` Nikolai
2016-02-06 17:46 ` John Kitchin
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