[Bioc-devel] mget and AnnDbBimap problem

[Paul Shannon]

Thanks to both of you!

This from Steve worked:

    name.lookup = AnnotationDbi::mget (toupper (node.names), name.map, ifnotfound=NA)

and this from Benilton:

   importClassesFrom(AnnotationDbi)
   importMethodsFrom(AnnotationDbi, mget)

I assume the latter is recommended?  

 - Paul


On Oct 4, 2011, at 12:32 PM, Benilton Carvalho wrote:

> 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
>> 
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>> 
> 
> 
> 
> -- 
> Successful people ask better questions, and as a result, they get
> better answers. (Tony Robbins)