[Bioc-devel] mget and AnnDbBimap problem

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)

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

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

-- 
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)

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

--
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)