[Bioc-devel] odd vignette dependency issue

[Martin Morgan]

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?
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793