[Bioc-devel] odd vignette dependency issue

[Martin Morgan]

On 10/06/2014 10:29 AM, Daniel Schmolze wrote:
> Thanks Martin, that makes sense. I think your suggestion may be my only option.

I hope by 'my suggestion' you mean contacting the survcomp maintainer(s) (I have 
bcc'd them on this email) and letting them know!

Martin

>
> On Mon, Oct 6, 2014 at 1:19 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> 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


-- 
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