[Bioc-devel] warnings in biodonductor package "SPIA"

Hervé Pagès hpages at fhcrc.org
Thu Oct 14 19:36:28 CEST 2010

Hi Adi,

On 10/14/2010 10:04 AM, Tarca, Adi wrote:
> Hi all,
> Anyone has an idea how to find out wich dataset in my package is the one about which the RCMD check is complaining:?
> Undocumented data sets:
>    .required
> All user-level objects in a package should have documentation entries.
> See the chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
> I do not see any names and this same package did not give warnings with the previous version of R.

You need to use 'all.names=TRUE' to see objects with a name which
begins with a ‘.’:

 > load("SPIA/data/colorectalcancer.RData")
 > ls(all.names=TRUE)
[1] "ALL_Colorectal" "DE_Colorectal"  ".required"      "top"


> Thanks,
> Adi
> ________________________________
> From: Dan Tenenbaum [dtenenba at fhcrc.org]
> Sent: Wednesday, October 13, 2010 6:22 PM
> To: Tarca, Adi
> Subject: warnings in biodonductor package "SPIA"
> Hello,
> The Bioconductor package mentioned in the subject line has you listed as maintainer.
> This package is generating warnings for one or more platforms. We need all warnings to be resolved before we release Bioconductor 2.7 in a few days.
> Can you please fix the package so the warnings no longer appear? Thank you!
> You can see the warnings here:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/
> (search for the name of your package, then click on the "WARNINGS" text in orange).
> Thanks,
> Dan Tenenbaum
> Bioconductor Team / Fred Hutchinson Cancer Research Center
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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