Re: [Rd] Inspecting promises
Please keep in mind that while lazy evaluation and delayedAssign are
documented parts of the language, promises are an internal
implementation mechanism that is subject to change. In particular the
fact that substitute behaves the way it does is a coincidence of the
current implementation that may very well change. Currently, for
example, the use of promises to make substitute work means promises
need to be kept around once thei are forced. This is inefficient in
several ways and may need to be fixed at some point.
It may well be useful to provide some reflection mechanisms for
examining environments, but there are more issues to consider than
pending evaluations (active bindings for example). I'm not sure when
this will rise to the top of anyone's priority list for
implementation.
luke
On Sun, 23 Sep 2007, Gabor Grothendieck wrote:
> Is there some way of displaying the expression and evaluation environment
> associated with a promise? I have found the following:
>
>> # first run these two commands to set up example
>> e <- new.env()
>> delayedAssign("y", x*x, assign.env = e)
>
>> # method 1. shows expression but not evaluation environment
>> str(as.list(e))
> List of 1
> $ y: promise to language x * x
>
>> # method 2. shows expression but not evaluation environment
>> substitute(y, e)
> x * x
>
> which shows two different ways of displaying the expression
> associated with a promise but neither shows the evaluation
> environment. The first technique may actually be a bug in
> R based on previous discussion on r-devel.
>
> Is there a way to display both the expression and the evaluation
> environment associated with a promise. Its a bit difficult to debug
> code involving promises if you can't inspect the objects you are
> working with.
>
>> R.version.string # Vista
> [1] "R version 2.6.0 beta (2007-09-19 r42914)"
>
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>
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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[Rd] 'load' does not properly add 'show' methods for classes extending 'list'
The GeneSetCollection class in the Bioconductor package GSEABase
extends 'list'
> library(GSEABase)
> showClass("GeneSetCollection")
Slots:
Name: .Data
Class: list
Extends:
Class "list", from data part
Class "vector", by class "list", distance 2
Class "AssayData", by class "list", distance 2
If I create an instance of this class and serialize it
> x <- GeneSetCollection(GeneSet("X"))
> x
GeneSetCollection
names: NA (1 total)
> save(x, file="/tmp/x.rda")
and then start a new R session and load the data object (without first
library(GSEABase)), the 'show' method is not added to the appropriate
method table.
> load("/tmp/x.Rda")
> x
Loading required package: GSEABase
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
An object of class "GeneSetCollection"
[[1]]
setName: NA
geneIds: X (total: 1)
geneIdType: Null
collectionType: Null
details: use 'details(object)'
Actually, the behavior is more complicate than appears; in a new R
session after loading /tmp/x.Rda, if I immediately do x[[1]] I get the
show,GeneSetCollection-method but not show,GeneSet-method.
Sorry for the somewhat obscure example.
Martin
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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