[Bioc-devel] NAMESPACE and GOstats summary

[rcaloger]

Thanks to the suggestions of Martin Morgan, I managed to solve the 
problem of NAMESPACE in the following way:
importFrom(AnnotationDbi, summary)
import(GOstats)
export(summary)

Now when I load the package I get:
The following object(s) are masked from package:base :

         summary

and when I execute:

> hgOver <- hyperGTest(params)
> summary(hgOver)

I get a table as expected.

Thanks again for the help.

Raffaele

rcaloger <raffaele.calogero at gmail.com> writes:


> > 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