[Bioc-devel] Vignette Latex error

[Karl Stamm]

Thank you so much. That fixed the issue. My package is now building
correctly on all services.  We switched from biblatex to natbib. I did have
to update the citation commands in the text to go with the natbib standard,
and meanwhile did some reformatting of the vignette overall.

On Thu, Apr 4, 2019 at 7:47 PM Pages, Herve <hpages using fredhutch.org> wrote:

> Hi Karl,
>
> On 4/2/19 15:03, Karl Stamm wrote:
> > I'm having a build error on only the OSX servers.
> >
> > * creating vignettes ... ERROR
> > --- re-building ‘rgsepd.Rnw’ using knitr
> > Error: processing vignette 'rgsepd.Rnw' failed with diagnostics:
> > Running 'texi2dvi' on 'rgsepd.tex' failed.
> > LaTeX errors:
> > ! Use of \blx using bbl@verbadd using i doesn't match its definition.
> > l.142     \verb
> >
> >
> > The tex file is written by the Rnw with knitr, so maybe it's a knitr
> > problem, or an incompatibility to the OSX side??   I tried removing
> > all references to \verb and that doesnt seem to have done anything.
>
> A little bit of detective work indicates that the vignette was building
> fine on all platforms until commit 7ed2a00e This commit added 2 things
> to the rgsepd.Rnw vignette: (1) a new biblio entry and (2) a \verb
> paragraph with reference to the new biblio entry.
>
> Apparently, the new biblio entry is causing problems. It seems to
> trigger some bad interaction between knitr and biblatex that seems to be
> specific to the MacTeX version (mactex-20161009) that we use on our Mac
> builders. Remember that we're stuck with El Capitan on these builders so
> updating things there can be tricky.
>
> Anyway, the problem goes away if you use natbib (used by hundreds of
> Bioconductor packages) instead of biblatex (only used by a handful of
> Bioconductor packages). That is, if you replace:
>
>    \usepackage[backend=bibtex]{biblatex}
>
> with
>
>    \usepackage{natbib}
>
> and move
>
>    \bibliography{references}
>
> to the line where you currently have
>
>    \printbibliography
>
> (get rid of the \printbibliography directive)
>
> With this change, I can successfully 'R CMD build rgsepd' on merida2
> (didn't try on celaya2 though).
>
> Hope this helps,
>
> H.
>
>
> >
> >
> > I want to get the package building without errors before the brach
> > lockdown in a few weeks.
> >
> > Since it builds on my end just fine, and also on the Windows and Linux
> > servers, surely it's a build server platform specific problem.   Maybe
> > Knitr is not supported anyone and I need to change everything over to
> > another RMD format ?
> >
> >       [[alternative HTML version deleted]]
> >
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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