[Bioc-devel] odd vignette dependency issue
On 10/06/2014 07:52 AM, Daniel Schmolze wrote:
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: 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.
Hi Daniel --
if it's being called by km.coxph.plot, then the problem is with survcomp, which
from this line
> getNamespaceImports("survcomp")$survival
survivalROC survivalROC.C
"survivalROC" "survivalROC.C"
is failing to import(survival, survfit). The survcomp author needs to update
their package; you could add survival to your Depends: field, but there are then
circumstances when your package would not work (e.g., when the next guy down
Imports: or Depends: on your package).
Martin
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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