[BioC] Missing as.list generic from AnnotationDbi?

[Ryan C. Thompson]

Never mind, reinstalling the AnnotationDbi package seems to have solved 
the problem. No idea what was wrong.

On Mon 17 Jun 2013 03:23:54 PM PDT, Ryan C. Thompson wrote:
> According to here:
> https://stat.ethz.ch/pipermail/bioc-devel/2009-December/002061.html
>
> the AnnotationDbi pacakge promotes as.list to an S4 generic that knows
> about Bimap objects and such. However, after loading AnnotationDbi in
> my R, I get:
>
> > showMethods("as.list")
>
> Function "as.list":
> <not an S4 generic function>
>
> Furthermore, when loading the annotate package, I get:
>
> > library(annotate)
> Warning message:
> In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
> No generic function found corresponding to requested imported methods
> for "as.list" from package "AnnotationDbi" (malformed exports?)
>
> And now all the functions from annotate, such as getSYMBOL, lookUp,
> etc., fail with an error, exemplified by the following snippet from
> the help text of lookUp:
>
> > library("hgu95av2.db")
> > library("GO.db")
> >
> > data(sample.ExpressionSet)
> > gN <- featureNames(sample.ExpressionSet)[100:105]
> > lookUp(gN, "hgu95av2", "SYMBOL")
> Error in as.list.default(envir) :
> no method for coercing this S4 class to a vector
>
> Can anyone help me find my missing S4 as.list generic?
>
> -Ryan Thompson
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] annotate_1.39.0 AnnotationDbi_1.23.15 Biobase_2.21.4
> [4] BiocGenerics_0.7.2
>
> loaded via a namespace (and not attached):
> [1] colorspace_1.2-2 DBI_0.2-7 IRanges_1.19.12 RSQLite_0.11.4
> [5] stats4_3.0.1 XML_3.96-1.1 xtable_1.7-1
> > biocVersion()
> [1] ‘2.13’
>