Thanks Martin.  I was probably making it more complicated than it needed to
be.  I just want to load bigmemory package (if it is installed) and redefine
the classes. I followed your advice and now AllClasses.R is

setClassUnion("mymatrix", c("mymatrix"))
setClass("mydata", representation(x="numeric", y="cnmatrix"))

and zzz.R is

.onLoad <- function(libname, pkgname) {
  bigmem <-
suppressWarnings(suppressPackageStartupMessages(require(bigmemory)))
  if (bigmem) {
    setClassUnion("cnmatrix", c("matrix", "big.matrix"))
    setClass("mydata", representation(x="numeric", y="cnmatrix"))
  }}

Now it seems to work but I get the following warning message both on R CMD
check and loading the package within R

Class "big.matrix" is defined (with package slot bigmemory) but no metadata
object found to revise superClass information---not exported?  Making a copy
in package foo

I assume it is because NAMESPACE doesn't have importClasseFrom(bigmemory,
big.matrix)

Is there a way I can change the NAMESPACE (in .onLoad or elsewhere)?

Thanks again,
Venkat


On Thu, Aug 26, 2010 at 7:58 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 08/26/2010 12:58 PM, Venkatraman Seshan wrote:
> > In AllClasses.R I used
> >
> > setClassUnion("cnmatrix", c("matrix"))
> >
> > Sorry for the typo.
> >
> > Venkat
> >
> > On Thu, Aug 26, 2010 at 3:31 PM, Venkatraman Seshan <veseshan@gmail.com
> >wrote:
> >
> >> Can the class definition in package "foo" be changed after the package
> is
> >> attached?  I am trying to do the following.
> >>
> >> The AllClasses.R file has the following class definitions.
> >>
> >> setClassUnion("mymatrix", c("mymatrix"))
> >> setClass("mydata", representation(x="numeric", y="cnmatrix"))
> >>
> >> In zzz.R the .onLoad has the following:
> >>
> >>   setHook(packageEvent("bigmemory", "attach"),
> >>           function(...){
> >>             setIs("big.matrix", "cnmatrix")
> >>             setClass("mydata", representation(x="numeric", y="cnmatrix")
> >>           })
> >>
> >> When I now do R CMD check pkg it is completed but I get a note
> >>
> >> * checking R code for possible problems ... NOTE
> >> Error in setIs("big.matrix", "cnmatrix") :
> >>   cannot create a 'setIs' relation when neither of the classes
> >> ("big.matrix" and "cnmatrix") is local and modifiable in this package
> >>
> >> How do I modify the definition of a class in a package?
>
> Hi Venkat -- not really answering your question, but I don't really
> think you want to do either setClassUnion or setIs -- inheritance is
> difficult enough to understand without adding novel relationships
> between classes. And I don't think you really want to conditionally
> define class relationships on package load either (which I is guess what
> setHook(packageEvent()) accomplishes; I've never seen that before);
> these all sound like you're making trouble for yourself (and users of
> your package) in the future.
>
> But...
>
> .onLoad is run after Import: and Depend: packages have been loaded, and
> before the name space of the package in which .onLoad is defined is
> 'sealed'. I think this means that if you had Import'ed or Depend'ed on
> bigmemory, then a setIs and setClass in .onLoad (not setHook(...)) would
> be successful, just as
>
> > library(bigmemory)
> > setClassUnion("cnmatrix", "matrix")
> [1] "cnmatrix"
> > setIs("big.matrix", "cnmatrix")
> > setClass("mydata", representation(x="numeric", y="cnmatrix"))
> [1] "mydata"
>
> are successful when run in an R session.
>
> So I guess what happens is the 'packageEvent' isn't actually evaluated
> in .onLoad, but afterward, when bigmemory is loaded (by some other code
> in your package? I'm not understanding how R CMD check is detecting the
> error) and your name space has already been sealed (which occurs after
> the .onLoad hook runs) and is therefore not modifiable. Maybe you could
> create an environment in your package
>
>  .secrets <- new.env(parent=emptyenv())
>  setPackageName("MyPackage", .secrets)
>
> and place your class definition there
>
>  setClass("cnmatrix", where=.secrets)
>
> .secrets isn't sealed, so the class definition might still be
> modifiable. I really don't know how this would work, e.g., exporting
> cnmatrix from your package name space, invoking methods, etc., or
> whether it would provide a way to modify the class definition once the
> name space is sealed. My little experiments suggest that you can create
> an instance with
>
>  new(getClassDef("cnmatrix", where=MyPackage:::.secrets))
>
> or by
>
>  attach(MyPackage:::.secrets, name="search")
>  new("MyClass")
>
> and create a setIs relationship, without generating errors or warnings,
> with
>
>  attach(MyPackage:::.secrets, name="secrets")
>  setIs("big.matrix", "cnmatrix", where="secrets")
>  detach("secrets")
>
> but all of this seems like a big hack.
>
> Martin
>
> >>
> >> Thanks,
> >> Venkat
> >>
> >> My R.Version()
> >> $platform
> >> [1] "x86_64-pc-linux-gnu"
> >>
> >> $arch
> >> [1] "x86_64"
> >>
> >> $os
> >> [1] "linux-gnu"
> >>
> >> $system
> >> [1] "x86_64, linux-gnu"
> >>
> >> $status
> >> [1] ""
> >>
> >> $major
> >> [1] "2"
> >>
> >> $minor
> >> [1] "11.1"
> >>
> >> $year
> >> [1] "2010"
> >>
> >> $month
> >> [1] "05"
> >>
> >> $day
> >> [1] "31"
> >>
> >> $`svn rev`
> >> [1] "52157"
> >>
> >> $language
> >> [1] "R"
> >>
> >> $version.string
> >> [1] "R version 2.11.1 (2010-05-31)"
> >>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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