[Bioc-devel] mget and AnnDbBimap problem

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Oct 4 21:30:59 CEST 2011

Hi Paul,

Two guesses/comments:

On Tue, Oct 4, 2011 at 3:21 PM, 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)

Are you sure `name.map` is what you think it is in your method? Maybe
you can drop a call to `browser()` in your code to make sure name.map
is a bimap thing?

If `name.map` is what you expect it to be, maybe doing something like
`AnnotationDbi::mget(toupper(..), name.map, ...)` would work?


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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