[Bioc-devel] mget and AnnDbBimap problem
beniltoncarvalho at gmail.com
Tue Oct 4 21:32:27 CEST 2011
import AnnotationDbi to your RCytoscape package (on both DESCRIPTION
and NAMESPACE files)
On 4 October 2011 20:21, Paul Shannon <pshannon at systemsbiology.org> wrote:
> There is a function in my RCytoscape package which fails on a call to mget when passed an AnnDbBimap ('org.Hs.egSYMBOL2EG'). The same mget call works fine in client code. I figure this is caused by package structure, NAMESPACE, or something related. But I cannot figure it out.
> client code: tbls.trompeter <- read.interactions ('trompeter.tsv', org.Hs.egSYMBOL2EG)
> error from package: Error in mget(toupper(node.names), name.map, ifnotfound = NA): second argument must be an environment
> executing this: name.lookup.tbl <- mget (toupper (node.names), name.map, ifnotfound=NA)
> from function defined: read.interactions <- function (filename, name.map)
> However, if I call mget (toupper (node.names), org.Hs.egSYMBOL2EG) directly in the client code, it works fine.
> Confused by this, and not sure whether AnnDbBimap can be construed as an environment, I tried showMethods, to no avail:
> > showMethods("mget")
> Function: mget (package base)
> x="ANY", envir="AnnDbBimap"
> x="ANY", envir="ANY"
> So I guessed that RCytoscape does not know about the AnnotationDbi class, so when it executes in its namespace, it does not know that org.Hs.egSYMBOL2EG can be construed as an environment; it is therefore not a legal second argument to mget.
> So I tried adding AnnotationDbi to the Depends line of DESCRIPTION, but that did not help.
> There is something basic I am missing here.
> Can anyone help?
> - Paul
>> sessionInfo ()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>  en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  yeastMetabolism_1.0.41 RCurl_1.6-7 bitops_1.0-4.1 genefilter_1.34.0 org.Hs.eg.db_2.5.0
>  RSQLite_0.9-4 DBI_0.2-5 KEGGgraph_1.9.2 XML_3.4-0 RCytoscape_1.3.22
>  AnnotationDbi_1.14.1 Biobase_2.12.1 XMLRPC_0.2-4 graph_1.30.0 RUnit_0.4.26
> loaded via a namespace (and not attached):
>  annotate_1.30.0 splines_2.13.0 survival_2.36-5 tools_2.13.0 xtable_1.5-6
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