[Bioc-devel] Using LaTeX packages in vignettes

[Andrzej Oleś]

Dear Roel,

to override the default \bibliographystyle{unsrt} use
`BiocStyle::latex(use.unsrturl=FALSE)` as documented in ?BiocStyle::latex

Best, Andrzej

On Mon, Apr 3, 2017 at 2:29 PM, Janssen-10, R.R.E. <
R.R.E.Janssen-10 at umcutrecht.nl> wrote:

> 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/87z400wdxx9ii0h2nfi8864wl0c3vs
> aq-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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