[Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

[Shepherd, Lori]

The cslreferences problem seems to be caused by some recent changes to Pandoc/rmarkdown.  We downgraded pandoc on tokay2 to 2.7.3  which has remedied the error.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Tuesday, May 19, 2020 2:19 PM
To: Mike Smith <grimbough using gmail.com>; bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

Pandoc 2.9.2  appears to be installed on tokay2




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Mike Smith <grimbough using gmail.com>
Sent: Monday, May 18, 2020 11:49 AM
To: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

Reading around, it looks more likely this is an issue with pandoc than
LaTeX directly.  I guess it'd help to know what version of pandoc is
running on the build machine, I'm unable to recreate either using the
pandoc supplied with RStudio.

Mike

On Fri, 15 May 2020 at 21:09, Sergio Picart Armada <sergi.picart using upc.edu>
wrote:

> Dear bioc devel,
>
> We are having the same problem with our package FELLA.
> Any help is appreciated!
>
> Best,
> Sergi
>
> Missatge de petr smirnov <psmirnov2000 using gmail.com> del dia dv., 15 de maig
> 2020 a les 19:42:
>
> > I am having trouble reproducing some vignette build errors for our
> > PharmacoGx package on Windows (tokay2).
> >
> > The error is a Latex error:
> > LaTeX Error: Environment cslreferences undefined.
> >
> > It seems likely to be due to a missing dependency for the style file
> > we are using, however, I do not understand why it works on all other
> > build machines. tokay1 does not have the same error, and is building
> > the same vignette. Likewise, none of the other OS machines are missing
> > this dependency.
> >
> > I also tried to reproduce in a newly reinstalled Windows environment.
> > After installing R 4.0, Rtools, all the package dependencies, and:
> > knitr, knitcitations, rmarkdown, pander, and tinytex, the package
> > builds on the machine. As far as I can tell, all these packages are
> > also installed on tokay2.
> >
> > Does tokay2 use a different Latex distribution from what is installed
> > by tinytex ?
> >
> > --
> > Petr Smirnov
> >
> > psmirnov2000 using gmail.com
> >
> > _______________________________________________
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