org-ref no bibliography generated in pdf

org-ref no bibliography generated in pdf

[Nikolai Stenfors]

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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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* Introduction
An article cite:Stenfors2010
* 
bibliographystyle:unsrt
bibliography:reference.bib


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Re: org-ref no bibliography generated in pdf

[Eric S Fraga]

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

Re: org-ref no bibliography generated in pdf

[John Kitchin]

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

Re: org-ref no bibliography generated in pdf

[Nikolai]

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

Re: org-ref no bibliography generated in pdf

[John Kitchin]

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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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Re: org-ref no bibliography generated in pdf

[Nikolai]

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 

Re: org-ref no bibliography generated in pdf

[John Kitchin]

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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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Re: org-ref no bibliography generated in pdf

[Nikolai Stenfors]

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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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Re: org-ref no bibliography generated in pdf

[Andreas Kiermeier]

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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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Re: org-ref no bibliography generated in pdf

[John Kitchin]

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

Re: org-ref no bibliography generated in pdf

[Nick Dokos]

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