[BioC] namespace error with goProfiles package

[Martin Morgan]

Juerg --

Thanks for the report.

Most packages use 'GO.db', but 'safe' Depends on 'GO'. The first time 
you run your code, the search path looks something like

 > search()
  [1] ".GlobalEnv"            "package:goProfiles"    "package:GO.db" 

  [4] "package:AnnotationDbi" "package:RSQLite"       "package:DBI" 

  [7] "package:Biobase"       "package:tools"         "package:stats" 

[10] "package:graphics"      "package:utils"         "package:datasets"
[13] "package:grDevices"     "package:methods"       "Autoloads"
[16] "package:base"

whereas after loading 'safe' you get

 > search()
  [1] ".GlobalEnv"            "package:safe"          "package:GO" 

  [4] "package:SparseM"       "package:annotate"      "package:xtable" 

  [7] "package:goProfiles"    "package:GO.db"     "package:AnnotationDbi"
[10] "package:RSQLite"       "package:DBI"           "package:Biobase"
[13] "package:tools"         "package:stats"         "package:graphics"
[16] "package:utils"         "package:datasets"      "package:grDevices"
[19] "package:methods"       "Autoloads"             "package:base"

Note 'package:GO' in position 3. goProfiles tries to perform an 
operation (toTable) that works with objects from GO.db but not from GO. 
Unfortunately, goProfiles looks on the search path (implicitly) instead 
of asking for GO.db in particular. This means that after loading safe it 
finds the mapping in GO, and the error occurs.

There are three different solutions.

1. You can work around this by issuing

 > detach('package:GO')

after library(safe). This might cause problems if 'safe' really only 
works with GO, and not with GO.db

2. the 'safe' maintainer (cc'd) can update their package to use 'GO.db' 
instead of GO. This will have to be done before the next release anyway.

3. The 'goProfiiles' maintainer (also cc'd) can modify their package 
code to explicitly request the appropriate version of GO, e.g.,

library(annotate)
getAnnMap("TERM", "GO.db")

Thanks again for the report.

Martin

Straubhaar, Juerg wrote:
> The following code is from the goProfiles package and works fine:
> 
> require(goProfiles)
> data(prostateIds)
> welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db")
> singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db")
> welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh"))
> printProfiles(welsh.singh.MF, percentage = TRUE)
> 
> But if I load the libraries:
> 
> library(mouse4302.db)
> library(annaffy)
> library(annotate)
> library(GSEAlm)
> library(safe)
> 
> and run the above code an error is produced:
> 
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "toTable", for signature "environment"
> 
>> sessionInfo()
> R version 2.7.0 (2008-04-22) 
> x86_64-pc-linux-gnu 
> 
> locale:
> C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
>  [1] org.Hs.eg.db_2.2.0  goProfiles_1.2.0    safe_2.2.0         
>  [4] GO_2.2.0            SparseM_0.78        GSEAlm_1.0.0       
>  [7] annotate_1.18.0     xtable_1.5-2        annaffy_1.12.1     
> [10] KEGG.db_2.2.0       GO.db_2.2.0         mouse4302.db_2.2.0 
> [13] AnnotationDbi_1.2.1 RSQLite_0.6-8       DBI_0.2-4          
> [16] Biobase_2.0.1
> 
> If I load only the libraries:
> 
> library(mouse4302.db)
> library(annaffy)
> library(annotate)
> library(GSEAlm)
> 
> or only the library
> 
> library(safe)
> 
> the above code works.
> 
> Kind regards,
> Juerg
> UMASS Med School
> 
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> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793