[Bioc-devel] "R CMD check" and par(mfrow=…) in vignettes

Wolfgang Huber whuber at embl.de
Tue Aug 6 14:25:35 CEST 2013


one of my packages [1] has several places in its vignette where multi-panel figures are generated via the likes of "par(mfrow=c(4,2))" within <<fig=TRUE>> code chunks. The package builds fine with 'R CMD build', and the vignette builds fine when calling Sweave manually. However, 'R CMD check' fails with
* checking running R code from vignettes ...
   ‘Hiiragi2013.Rnw’ ... failed
Errors in running code in vignettes:
  When sourcing ‘Hiiragi2013.R’:
Error: figure margins too large

I believe this is because R CMD check calls Stangle on the .Rnw and then sources the .R file disregarding any device size settings. I can think of several ways to work around this, but this seems like a rather basic deficiency of the current system that asks for a more generic answer. Does anybody have any insight here?

	Best wishes

PS I am sorry if this has been discussed elsewhere, but digging in the R-exts manual and in Google did not turn up a solution for me.  

[1] https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkg/Hiiragi2013

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