Message-ID: <4D669699.8080304@gmail.com>
Date: 2011-02-24T17:34:17Z
From: Duncan Murdoch
Subject: Objects must be passed as an argument or generated in the function, right?
In-Reply-To: <AANLkTikyWij_1jirT-g5VspAw8D9mg+=8TmyiH65dvqX@mail.gmail.com>
On 24/02/2011 9:59 AM, Jk Zheng wrote:
> Hi,
>
> I'm new to R, and found this code confusing. It is from the bioconductor
> package "RpsiXML".
>
> entryCount<- length(nodes)
>
> The "nodes" object is either the argument nor generated in the function.
> How can R find the "nodes" object? What am I missing here?
Functions in R are more properly called "closures". They are made up of
code *and an associated environment*. Normally the environment is the
one in which the function is created, e.g. the global environment for
functions entered at the command line, the namespace of a package for
functions there, or an evaluation frame for a function created within
another one.
When evaluating a closure, R sets up an evaluation frame with the
closure's environment as its parent, so any variables defined in the
environment are also visible. Presumably "nodes" was defined in the
namespace of RpsiXML, but it's possible that parseXmlEntryNodeSet has a
different environment, depending on how it has been created. (Or maybe
it's a typo.)
Duncan Murdoch
> Thanks
>
> Zheng Jk
>
>
> parseXmlEntryNodeSet<- function(psimi25file, psimi25source, verbose=TRUE) {
>
> psimi25Doc<- xmlTreeParse(psimi25file, useInternalNodes = TRUE)
>
> psimi25NS<- getDefaultNamespace(psimi25Doc)
> namespaces<- c(ns = psimi25NS)
> entry<- getNodeSet(psimi25Doc, "/ns:entrySet/ns:entry", namespaces)
>
> if(verbose)
> statusDisplay(paste(length(entry),"Entries found\n",sep=" "))
>
> entryCount<- length(nodes)
> entryList<- list()
> for(i in 1:entryCount) {
> entryList[[i]]<- parseXmlEntryNode(doc=psimi25Doc, index=i,
> namespaces=namespaces,
> psimi25source=psimi25source,
> verbose=verbose)
> }
>
> [[alternative HTML version deleted]]
>
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