[BioC] Problem with hgu133plus2.db package

[Morten Hansen]

Hi Martin

Yes - my package is using a namespace.

Everything worked fine after adding your suggestions to the DESCRIPTION and NAMESPACE files.

I need all the info in the hgu133plus2GO2PROBE - I think...

Which function from AnnotationDbi can you suggest to extract information with?

Br - Morten

________________________________________
Fra: Martin Morgan [mtmorgan at fhcrc.org]
Sendt: 16. juni 2009 13:41
Til: Morten Hansen
Cc: bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] Problem with hgu133plus2.db package

Hi Morten --

Does your package have a namespace? Maybe you need to have

Imports: AnnotationDbi

in the DESCRIPTION file and

importMethodsFrom(AnnotationDbi, as.list)

in the NAMESPACE file. But is this really what you want to do? Maybe
it's better to use the standard AnnotationDbi interface to extract just
the information you're interested in, instead of making everything into
a list?

Martin

Morten Hansen wrote:
> I have a problem with the hgu133plus2.db package.
>
> Usually when I want to use the data from hgu133plus2GO2PROBE , I do the following:
>
>> a <- as.list( hgu133plus2GO2PROBE )
>
> Works fine.
>
> Now I am making a package and need to do the same. When running a function inside the package that does the same as above I get the following error:
>
> Error in as.list.default(hgu133plus2GO2PROBE) :
>   no method for coercing this S4 class to a vector
>
> I also tried using mappedkeys() as explained in the example in help, but I get the same error.
>
> I have tested it on a clean R and Bioconductor installation.
>
> Any suggestions?
>
> My sessionInfo():
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_DK.UTF-8;LC_NUMERIC=C;LC_TIME=en_DK.UTF-8;LC_COLLATE=en_DK.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_DK.UTF-8;LC_PAPER=en_DK.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_DK.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] icmmUtils_1.0.0       biomaRt_2.0.0         hgu133plus2.db_2.2.11 annotate_1.22.0       annaffy_1.16.0        KEGG.db_2.2.11
>  [7] GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4             AnnotationDbi_1.6.0   Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.98-1 XML_2.5-1    xtable_1.5-5
>
> Br - Morten Hansen
>
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