[Bioc-devel] Versioned (Biobase) "initialize" method

[Morgan, Martin]

Hi Michael -- sorry not to respond sooner.

The lessons in the StackOverflow post were learned by the mistakes in Biobase; many of the classes there fail to follow its advice. Also, there are a number of packages in Bioconductor that depend on the existing Biobase formulation. Unfortunately, the inertia here is strong.

A work-around might be to write an initialize method for "A" that uses callNextMethod() with an argument versions=, thereby freeing up ... for copy construction.

The S4Vectors infrastructure is in many ways a better starting point for new class development.

Martin 
________________________________________
From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Stravs, Michael [Michael.Stravs at eawag.ch]
Sent: Thursday, January 07, 2016 10:41 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Versioned (Biobase) "initialize" method

Hi,

The "initialize" method of the Versioned class in Biobase is defined in a way that breaks when inheriting classes want to define a copy constructor.

Code to reproduce:

library(Biobase)
setClass("A",
         representation = representation(var1="integer"),
         prototype=prototype(var1=integer(),
                             new("Versioned", versions=c(A = "0.1.0"))),
         contains="Versioned")

ia <- new("A")
ia2 <- new("A", ia)
# "ia" is mapped to the argument "versions" of the Versioned "initialize" method!

Full gist snippet including bugfix:
https://gist.github.com/meowcat/c51a4260fb710e2fa51a

For explanation, see:
http://stackoverflow.com/questions/16247583/inheritance-in-r/16248773#16248773

The Versioned class in Biobase has the following "initialize" method:

function (.Object, ...)
{
    .local <- function (.Object, versions = list(), ...)
    {
        .Object <- callNextMethod(.Object, ...)
        classVersion(.Object)[names(versions)] <- versions
        .Object
    }
    .local(.Object, ...)
}

Can you change it as follows:


function (.Object, ...)

{

    .local <- function (.Object, ..., versions = list())

    {

        .Object <- callNextMethod(.Object, ...)

        classVersion(.Object)[names(versions)] <- versions

        .Object

    }

    .local(.Object, ...)

}

This will fix the problem.


Michael Stravs
Eawag
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+41 58 765 6742


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