[Bioc-devel] odd vignette dependency issue

[Dan Tenenbaum]

----- Original Message -----
> From: "Daniel Schmolze" <saps at schmolze.com>
> To: bioc-devel at r-project.org
> Sent: Monday, October 6, 2014 7:52:49 AM
> Subject: [Bioc-devel] odd vignette dependency issue
> 
> I'm getting a vignette error from the BioC build servers that I can't
> reproduce locally:


What's the name of your package?

Dan


> 
> * creating vignettes ... ERROR
> Quitting from lines 116-119 (saps.Rmd)
> Error: processing vignette 'saps.Rmd' failed with diagnostics:
> could not find function "survfit"
> 
> The offending lines in saps.Rmd call a function in my package,
> plotKM(), which in turn calls makes the following call:
> 
> survcomp::km.coxph.plot(
>  formula.s = survival::Surv(survivalTimes, followup) ~ cluster,
>  data.s = dd, main.title=title, y.label=y.label, x.label=x.label,
>  o.text=text, ...)
> 
> survfit() is part of the "survival" package, and nowhere is it
> explicitly called, but I suppose it's being called from within
> km.coxph.plot()? My package imports both the "survival" and
> "survcomp"
> packages in the DESCRIPTION file.
> 
> R CMD check, R CMD check --as-cran, and R CMD BiocCheck all work fine
> on several different computers for me. Any ideas?
> 
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