[Bioc-devel] [devteam-bioc] BiocStyle and knitr: option clash for package color

[Martin Morgan]

On 07/22/2013 01:56 PM, Maintainer wrote:
> Dear BiocStyle-Maintainer,
>
> I try to use BiocStyle (0.0.13) in a knitr vignette. It seems both knitr and
> BiocStyle include the color package with different options (knitr: without any
> option; BiocStyle with usenames,dvipsnames). That's why "R CMD build" fails:
> ...
> * installing the package to re-build vignettes
> * creating vignettes ... ERROR
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>    Running ‘texi2dvi’ on ‘cleaver.tex’ failed.
> LaTeX errors:
> ! LaTeX Error: Option clash for package color.
> ...
>
> Please find some minimal working examples on:
> https://gist.github.com/sgibb/6057514
>
> The following small patch should fix this problem (at least my knitr vignette
> is build correctly):

Thanks this has been incorporated into 0.0.14. Martin

>
> --- Bioconductor.sty    2013-07-22 22:17:27.154142990 +0200
> +++ Bioconductor-patched.sty    2013-07-22 22:17:22.466143142 +0200
> @@ -7,7 +7,8 @@
>   %% \ExecuteOptions{pdftitle,pdfauthor}
>   %% \ProcessOptions
>
> -\RequirePackage[usenames,dvipsnames]{color}
> +\PassOptionsToPackage{usenames,dvipsnames}{color}
> +\RequirePackage{color}
>   \definecolor{BiocBlue}{RGB}{24,129,194}
>   \definecolor{BiocGreen}{RGB}{135,177,63}
>   \RequirePackage[%
>
>
> Kind regards,
>
> Sebastian
>
>
> ________________________________________________________________________
> devteam-bioc mailing list
> To unsubscribe from this mailing list send a blank email to
> devteam-bioc-leave at lists.fhcrc.org
> You can also unsubscribe or change your personal options at
> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793