[Rd] Recursion error after upgrade to R_2.11.1 [Sec=Unclassified] [Sec=Unclassified]
Troy Robertson
Troy.Robertson at aad.gov.au
Fri Oct 8 08:25:04 CEST 2010
Thanks Kasper,
I have been meaning to have a good look at some of the Bioconductor source for a while now. So will check it out.
But I am also quite enthusiastic about what is happening with referenced classes and will be having a good play around with that in the coming weeks.
Troy
> -----Original Message-----
> From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com]
> Sent: Friday, 8 October 2010 3:13 PM
> To: Troy Robertson
> Cc: Martin Maechler; r-devel at R-project.org; John Chambers
> Subject: Re: [Rd] Recursion error after upgrade to R_2.11.1
> [Sec=Unclassified] [Sec=Unclassified]
>
>
> Troy
>
> For what it's worth, the ExpressionSet / eSet class in
> Biobase from Bioconductor has for a long time implemented a
> pass-by-reference system, using amongst other stuff locked
> environments to make sure things are read only. You might
> find this useful to look at.
>
> In general it is hard to complement on your use case without
> knowing the details. I often find that careful programming
> and profiling can make R code much faster than initially
> hypotised. Having said that, sometimes (esp. for very big,
> read-only objects) environments make sense.
>
> Kasper
>
> On Thu, Oct 7, 2010 at 6:52 PM, Troy Robertson
> <Troy.Robertson at aad.gov.au> wrote:
> >> -----Original Message-----
> >> From: Martin Maechler [mailto:maechler at stat.math.ethz.ch]
> >> Sent: Thursday, 7 October 2010 9:50 PM
> >> To: Troy Robertson
> >> Cc: 'Martin Morgan'; 'r-devel at R-project.org'; 'John Chambers'
> >> Subject: Re: [Rd] Recursion error after upgrade to R_2.11.1
> >> [Sec=Unclassified] [Sec=Unclassified]
> >>
> >>
> >> >>>>> "TR" == Troy Robertson <Troy.Robertson at aad.gov.au>
> >> >>>>> on Thu, 7 Oct 2010 13:50:49 +1100 writes:
> >>
> >> >>
> >> >> On 10/06/2010 06:12 PM, Troy Robertson wrote:
> >> >> > Hi all,
> >> >> >
> >> >> > After no replies to my previous message I thought I might
> >> show some
> >> >> > code to demonstrate the change and again seek any
> >> >> explanation for the
> >> >> > error now thrown by my code after upgrading from
> 2.10.1 to
> >> 2.11.1.
> >> >> >
> >> >> > Thanks
> >> >> > Troy
> >> >> > --------------------------------------------------------
> >> >> > setClass("PortableObject",
> >> >> > representation(test1 = "character"),
> >> >> >
> >> >> > prototype( test1 = ""),
> >> >> > contains = ".environment"
> >> >> > )
> >> >> >
> >> >> > setMethod("initialize", "PortableObject",
> >> >> > function(.Object, ...,
> >> .xData=new.env(parent=emptyenv())) {
> >> >> > .Object <- callNextMethod(.Object, ...,
> >> >> .xData=.xData)
> >> >> >
> >> >> > .Object at test1 <- "Foo"
> >> >> > # Following line works under 2.10.1
> >> but now throws
> >> >> > # Error: evaluation nested too deeply:
> >> >> infinite recursion / options(expressions=)?
> >> >> > #####.Object[["test2"]] <- "Bar"
> >> >> > # The following does what I want though
> >> >> > .Object$test3 <- "Baa"
> >> >> >
> >> >> > return(.Object)
> >> >> > }
> >> >> > )
> >> >> >
> >> >> > e <- new("PortableObject")
> >> >>
> >> >> The explicit example does help -- it's clear what
> bug you are
> >> >> encountering. Here's the code in R-2.10
> >> >>
> >> >> > selectMethod("[[<-", ".environment")
> >> >> Method Definition:
> >> >>
> >> >> function (x, i, j, ..., value)
> >> >> {
> >> >> call <- sys.call()
> >> >> call[[2]] <- x at .Data
> >> >> eval.parent(call)
> >> >> x
> >> >> }
> >> >>
> >> >>
> >> >> and 2.11.1
> >> >>
> >> >> > selectMethod("[[<-", ".environment")
> >> >> Method Definition:
> >> >>
> >> >> function (x, i, j, ..., value)
> >> >> {
> >> >> .local <- function (x, i, j, ..., exact = TRUE, value)
> >> >> {
> >> >> call <- sys.call()
> >> >> call[[2]] <- x at .Data
> >> >> eval.parent(call)
> >> >> x
> >> >> }
> >> >> .local(x, i, j, ..., value = value)
> >> >> }
> >> >>
> >> >> Apparently the 'exact' argument has been added, and because
> >> >> the method signature differs from the generic, a .local
> >> >> function is created. That 'sys.call()' originally returned
> >> >> the environment in which the generic was called, but now it
> >> >> returns the environment in which .local is defined. And so
> >> >> eval() keeps evaluating .local(). This I think is a bug.
> >>
> >> TR> Yes, afer the email from William Dunlop, I found this
> >> difference in the methods between 2.10.1 and 2.11.1
> >> TR> I had a play and by adding my own method to
> overload "[[<-"
> >> for my PortableObject was able to reinstate the original
> >> functionality without the recursive error.
> >>
> >> TR> setMethod("[[<-", "PortableObject",
> >> TR> function (x, i, j, ..., value)
> >> TR> {
> >> TR> call <- sys.call()
> >> TR> call[[2]] <- x at .Data
> >> TR> eval.parent(call)
> >> TR> x
> >> TR> }
> >> TR> )
> >>
> >> >>
> >> >> For what it's worth, if I were interested in minimizing
> >> >> copying I would set up initialize so that it ended with
> >> >> callNextMethod(<...>), on the hopes that the method
> >> >> eventually called would take care not to make too
> many copies
> >> >> on slot assignment.
> >> >>
> >> >> Martin
> >> >>
> >>
> >> TR> Hmmm, not sure what you mean here? My code passes objects
> >> such as these as parameters to other S4 classes which alter their
> >> data. If the .xData slot is used then I have no need to
> return the
> >> object. No copy-on-change is performed but data held by the
> >> PortableObject is modified. This speeds up my execution time by a
> >> LARGE amount.
> >>
> >> TR> I could very well have things all arse-about, having come
> >> from a Java OO background, but this is the only way I have
> been able
> >> to create a pass-by-reference paradigm using S4 classes. Any
> >> suggestions for alternative solutions would be greatfully received.
> >>
> >> TR> Troy
> >>
> >> R 2.12.2 (currently beta) has in its NEWS :
> >>
> >> o A facility for defining reference-based S4 classes
> (in the OOP
> >> style of Java, C++, etc.) has been added experimentally to
> >> package methods; see ?ReferenceClasses.
> >>
> >> ---> Please get R-2.12.2 beta and tell here about your
> >> experiences. John Chambers (you have in CC) will be particularly
> >> interested in your feedback.
> >>
> >> Martin Maechler, ETH Zurich
> >>
> >>
> >
> > Well...
> >
> > Just been having a read of the doco for the new reference classes.
> > This opens up a whole new world in R doesn't it. Very exciting.
> > Except for the fact that it negates a lot of what I have
> been doing on
> > top of S4 objects. I will probably now be rewritting a lot
> of code.
> > Ouch!
> >
> > I'll start having a bit of a play and exploring this new
> way of doing
> > things and let you know how I go. Will probably have
> questions along
> > the way too.
> >
> > Thank you to everyone involved for their hard work.
> >
> > Troy
> >
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