[Bioc-devel] mget and AnnDbBimap problem

[Benilton Carvalho]

import AnnotationDbi to your RCytoscape package (on both DESCRIPTION
and NAMESPACE files)

b

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)
>
> locale:
> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] yeastMetabolism_1.0.41 RCurl_1.6-7            bitops_1.0-4.1         genefilter_1.34.0      org.Hs.eg.db_2.5.0
>  [6] RSQLite_0.9-4          DBI_0.2-5              KEGGgraph_1.9.2        XML_3.4-0              RCytoscape_1.3.22
> [11] 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):
> [1] annotate_1.30.0 splines_2.13.0  survival_2.36-5 tools_2.13.0    xtable_1.5-6
>
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