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

[Sebastian Gibb]

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):

--- 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