[BioC] Missing as.list generic from AnnotationDbi?
Ryan C. Thompson
rct at thompsonclan.org
Tue Jun 18 00:23:54 CEST 2013
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’
More information about the Bioconductor
mailing list