Hi
I have been using a bit of namespaces in the past, but the following
alludes me.
I am dealing with the Bioconductor packages Biobase and affy. Biobase
has a namespace and affy does not. affy contains the S4 class
"AffyBatch" which extends the "eSet" class in Biobase.
I am extending the AffyBatch class myself. My code works fine as long
as I do not have any NAMESPACE file.
Now I am trying to add one. I am importing Biobase, but I cannot
import affy since it does not have a NAMESPACE. However, when I try R
CMD INSTALL it complains that it cannot find AffyBatch :
Error in setIs(Class, class2, classDef = classDef, where = where) :
Unable to find package environment for class "AffyBatch" to revise
subclass information
So how do I make the classes in affy available for my package when
affy does not have a NAMESPACE?
The relevant lines from my DESCRIPTION file is
Depends: R (>= 2.6), affy (>= 1.16), affxparser (>= 1.10),
Biobase, methods
LazyLoad: yes
and from my NAMESPACE file I have
exportPattern("^[^\\.]")
import(Biobase)
I have also tried (in desperation) to add a "require(affy)" in
both .onLoad and .onAttach, but to no help.
While I am at this: as I remember it, in the old days we needed
"require(methods)" in .onLoad to work with S4, is that still
necessary?
I am using R-2.6.0 on OS X (PPC)
Thanks, Kasper