[Bioc-devel] odd vignette dependency issue

Daniel Schmolze saps at schmolze.com
Mon Oct 6 16:52:49 CEST 2014

I'm getting a vignette error from the BioC build servers that I can't
reproduce locally:

* 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:

 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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