[Bioc-devel] NAMESPACE and GOstats summary

[rcaloger]

Hi,
I am the mantainer of oneChannelGUI package, which is a graphical 
interface to some Bioconductor packages.
I am working on the implementation of NAMESPACE for my package.
I am actually having problems in using the summary for object 
GOHyperGResult from the GOstats package.
If I call the summary for an object generated by the function hyperGTest 
without using the NAMESPACE
hgOver <- hyperGTest(params)
summary(hgOver)
I get as output a data frame as expected.
However, if I add the namespace to my package:
import(GOstats)
exportPattern("^[^\\.]")

When I execute:
hgOver <- hyperGTest(params)
summary(hgOver)
I get as output
Length          Class           Mode
             1 GOHyperGResult             S4

It seems that I did not load the summary method.

I also tried to import the summary method modifying the NAMESPACE in the 
following way:
import(GOstats)
importMethodsFrom(GOstats, summary)
exportPattern("^[^\\.]")

But I get the following warning during compilation:
Warning message:
In namespaceImportFrom(self, asNamespace(ns), allVars, allFuns,  :
  Found methods to import for function "condGeneIdUniverse" but not the 
generic itself

and I do not get the data frame ether.

Any suggestions how to handle this problem?
Cheers
Raffaele

 > sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=Italian_Italy.1252;LC_CTYPE=Italian_Italy.1252;LC_MONETARY=Italian_Italy.1252;LC_NUMERIC=C;LC_TIME=Italian_Italy.1252

attached base packages:
 [1] grid      splines   tcltk     tools     stats     graphics  
grDevices utils     datasets
[10] methods   base    

other attached packages:
 [1] hgu133a.db_2.2.5    Rgraphviz_1.20.2    GOstats_2.8.0       
Category_2.8.0    
 [5] genefilter_1.22.0   survival_2.34-1     RBGL_1.18.0         
annotate_1.20.0   
 [9] xtable_1.5-4        GO.db_2.2.5         RSQLite_0.7-0       
DBI_0.2-4         
[13] AnnotationDbi_1.4.0 graph_1.20.0        oneChannelGUI_1.8.6 
tkWidgets_1.20.0  
[17] DynDoc_1.20.0       widgetTools_1.18.0  affylmGUI_1.16.0    
affyio_1.10.0     
[21] affy_1.20.0         limma_2.16.2        Biobase_2.2.0     

loaded via a namespace (and not attached):
[1] cluster_1.11.11      GSEABase_1.4.0       preprocessCore_1.4.0 
XML_1.94-0.1       
 >








-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero