[Bioc-devel] class union with AffyBatch
mtmorgan at fhcrc.org
Thu Oct 9 19:40:47 CEST 2008
Hi Audrey --
audrey <audrey at ebi.ac.uk> writes:
> Hi all,
> In my package, I am trying to set a class union the following way:
> setClassUnion("OneColour", c("ExpressionSet", "AffyBatch"))
> In the NAMESPACE if I write the following:
> importClassesFrom("Biobase", "ExpressionSet")
> importClassesFrom("Biobase", "AffyBatch")
definitely the last line is not correct.
> When I build the package I have this error message
> Error: package 'affy' does not have a name space
> Execution halted
> If I remove the importClassesFrom("Biobase", "AffyBatch") from my
> NAMESPACE, I have this warning:
> Warning in .findOrCopyClass(class1, classDef, where, "superClass") :
> Class "AffyBatch" is defined (with package slot "affy") but no
> metadata object found to revise superClass information---not exported?
> Making a copy in package "arrayQualityMetrics"
> In the dependencies in the DESCRIPTION, I do depend on the package
> "affy". This is using R2.8 and affy_1.19.0.
> Any idea on how I could solve that? Is it possible to import a class
> from a package that does not have a namespace?
I think there's something else going on. If I create a package with
Imports: Biobase, methods
setClassUnion("OneColour", c("ExpressionSet", "AffyBatch"))
I can build and check without error with
> R --version
R version 2.8.0 beta (2008-10-09 r46680)
In arrayQualityMetrics, if I add a file like tmp.R, move methods to
Imports: (thinking that the end user doesn't need access to the
functionality of the methods package to use my package), add
imports(methods) and exportClasses("OneColour") then again I can build
and check without errors / warnings.
My only real suggestion is to update R.
Sorry to be less than helpful
> Audrey Kauffmann
> EMBL - EBI
> Cambridge UK
> Bioc-devel at stat.math.ethz.ch mailing list
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