OK.  Can you help me with the following then?

I want to create a class with two slots, "x" a numeric vector and "y" a
rectangular array of numeric data which can be a matrix, big.matrix,
ff_matrix etc.  I want to be agnostic to any of the large data package.  So
I don't want my package to depend on any of them (since matrix is always
available). The only methods for the slot y I want are the ability to access
and replace rows, columns and sub arrays (i.e the usual [ and [<-
operators).  Can this be done or is it a fools errand?

Venkat


On Fri, Aug 27, 2010 at 12:22 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 08/26/2010 05:58 PM, Venkatraman Seshan wrote:
> > 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)?
>
> I guess you're trying to develop a package that has functionality that
> has code that is conditional on the bigmemory package -- if bigmemory is
> available then do one thing, otherwise do another. But this is not, in
> my opinion, a good idea -- your user gets different behavior on Monday
> versus Wednesday (because they installed bigmemory on Tuesday) and you
> have two code branches to maintain (which leads to headaches, as
> evidenced by this thread!). So I think you really just want to
>
>  Imports: bigmemmory
>
> in your DESCRIPTION file,
>
> importClassesFrom(bigmemory, big.matrix)
>
> in NAMESPACE
>
> and
>
> setClassUnion("cnmatrix", c("matrix", "big.matrix"))
> setClass("mydata",
>          representation=representation(x="numeric", y="cnmatrix"))
>
> in the 'top level' (i.e., not in .onLoad or other function call) of some
> R/*R file.
>
> Actually my stronger advice is that you avoid the setClassUnion --
> you're really saying that your 'cnmatrix' walks and talks exactly like a
> matrix and a big.matrix, and vice versa, when really you have no control
> over what methods are defined for matrix or big.matrix (any package can
> define methods for these classes) so you have no idea whether the
> methods are appropriate for cnmatrix. Better in my opinion to implement
> the interface that is directly relevant to cnmatrix, even if it is often
> simple delegation to a 'matrix' slot of cnmatrix.
>
> Martin
>
>
> >
> > 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
> >>
> >
>
>
> --
> 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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