[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’



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