[Bioc-devel] Using LaTeX packages in vignettes

[Janssen-10, R.R.E.]

Obenchain, Valerie writes:
> Hi,
> 
> On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote:
>> Hello all,
>>
>> We wrote our vignette in Sweave/LaTeX, and I am running into a problem with citing to other papers.
>> I would like to use the APA style of citing which looks like: "Determine the optimal factorization rank using the
>> NMF package (Gaujoux and Seoighe, 2010). ..."
>>
>> Now, to achieve that, I could use the package "apacite", but I wonder whether it's available on the build nodes of
>> Bioconductor, and whether it's desired to choose our own citation style.  Can we choose our own citation style in
>> vignettes? And if so, is "apacite" available on the build infrastructure of Bioconductor?
>
> apacite is included in TeXLive which is on the build machines.
>
> Valerie

Thanks!  There's one problem left now.  I think the Bioconductor theme sets the \bibliographystyle to "unsrt".  I would like to add the following to my vignette:
> \usepackage[natbibapa]{apacite}
> \bibliographystyle{apacite}

The problem is that there can only be a single \bibliographystyle definition in the TeX file:
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
>   Running 'texi2dvi' on 'Introduction_to_MutationalPatterns.tex' failed.
> BibTeX errors:
> The top-level auxiliary file: Introduction_to_MutationalPatterns.aux
> The style file: apacite.bst
> Illegal, another \bibstyle command---line 20 of file Introduction_to_MutationalPatterns.aux
>  : \bibstyle
>  :          {/gnu/store/87z400wdxx9ii0h2nfi8864wl0c3vsaq-r-biocstyle-2.2.1/site-library/BiocStyle/resources/tex/unsrturl}

Do you know how I can get around this?

Thanks for your time.

Kind regards,
Roel Janssen

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