similar to: removing union class

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

'?removeClass' shows that 'removeClass' is from package 'package:methods'. Is there a command which can show me all the functions and the classed defined in a package such as 'package:methods'?

Dear colleagues, there is a behaviour with S4 (virtual) classes that I find very hard to understand: Depending on the position of setAs(), the tree of inheritance changes. This is my baseline example that defines the classes "grandma", "mother", "daughter" and a virtual class "mr_x". For a new instance if "daughter", "mr_x" is betweeen

Dear list: I am looking for a good way to create an S4 class that would extend numeric, but would allow NULL instead of data as well. As far as I can see there is no way at the moment to do that, but please correct me if I am wrong. The best solution I came up with so far was the following (it also indicates a problem of using setClassUnion with numeric as one of the classes): I define a class

As far as I can tell, there's no trivial way to set arbitrary S4 slots to NULL. Most of the online examples I can find, use setClassUnion and are about 10 years old. Which, in my opinion, is defective. There's nothing "robust" about making something that should be trivially simple, really complicated. Maybe there is a simpler way, and I just haven't worked it out, yet. But

Hi all, I came across an issue in using the Matrix package which made it that I could only subset Matrices using the numeric class, but could not using integers. Steps to reproduce the problem: library(Matrix) # this class has *nothing* to do with Matrix setClass("MyClass", representation(myvalue = "numeric"), prototype(myvalue = NA_real_)) # this class also has

Hi, Short story ----------- setClassUnion("ArrayLike", "array") showClass("ArrayLike") # no slot setClass("MyArrayLikeConcreteSubclass", contains="ArrayLike", representation(stuff="ANY") ) showClass("MyArrayLikeConcreteSubclass") # 2 slots!! That doesn't seem right. Long story ----------

On 03/18/2016 03:28 PM, Michael Lawrence wrote: > > On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s <hpages at fredhutch.org > <mailto:hpages at fredhutch.org>> wrote: > > Hi, > > Short story > ----------- > > setClassUnion("ArrayLike", "array") > > showClass("ArrayLike") # no slot > >

On 03/19/2016 01:22 AM, Michael Lawrence wrote: > > > On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s <hpages at fredhutch.org > <mailto:hpages at fredhutch.org>> wrote: > > On 03/18/2016 03:28 PM, Michael Lawrence wrote: > > > On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s > <hpages at fredhutch.org <mailto:hpages at

the code below has me confused: setClassUnion("index", c("numeric", "character", "logical")) extends("numeric") # i don't see the class union library(Matrix) extends("numeric") # now i see the class union i am aware that the "Matrix" package separately defines the "index" class union. is it the case that

Hi all, The function call series genericForPrimitive -> .findBasicFuns -> .findAll happens 4400 times while the GenomicRanges package is loading. Each time .findAll follows a chain of environments to determine that the methods namespace is the only one that holds a variable called .BasicFunsList. This accounts for ~10% of package loading time. I'm sure there is some history to that

dear all, I try to update my Rversion fro 1.7.1 to 1.8.1 on linux. I have a problem when I try to install pacakges from Bioconductors with : source("http://www.bioconductor.org/getBioC.R") and getBioC(relLevel="release") somme errors append and when I make a library(affy) for example I obtain : > library(affy) Error in setIs("character",

Doing it like this: genericForPrimitive <- function(f, where = topenv(parent.frame()), mustFind = TRUE) { ans = .BasicFunsList[[f]] ## this element may not exist (yet, during loading), dom't test null if(mustFind && identical(ans, FALSE)) stop(gettextf("methods may not be defined for primitive function %s in this version of R",

Hello, I apologize that I am cross posting here after getting no answer from my initial question on stack overflow <http://stackoverflow.com/questions/33492601/r-setoldclass-only-if-needed>. I should certainly have posted it first here.. I am using 3 packages: - xts - quantmod - 'myPackage' quantmod is creating a union class by doing: setOldClass("xts");

Hi all. I'm reading in a flat, comma-delimited flat file using read.csv. It works marvelously for the most part. I am using the colClasses argument to, basically, create numeric, factor and character classes for the columns I'm reading in. However, a couple of the fields in the file are date fields. I'm fully aware that POSIXct can be used as a class, however the field must obey,

I am trying to create a class union of class unions to facilitate method dispatch. When I execute code in the global environment, everything acts as expected, however when I put the same code in the context of a package, selectMethod can no longer find the correct method. This first block below puts the code in the context of a package: fn <- "codefile.R" writeLines( c(

Hello, I have a question concerning "setClassUnion". I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. I tried to use "setClassUnion" in a package I am currently working on. The situation is similar to the following example: The DESCRIPTION file has entries: Depends: R (>= 2.0.0), methods Imports: methods LazyLoad: yes The NAMESPACE file has

Hello, I have a question concerning "setClassUnion". I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. I tried to use "setClassUnion" in a package I am currently working on. The situation is similar to the following example: The DESCRIPTION file has entries: Depends: R (>= 2.0.0), methods Imports: methods LazyLoad: yes The NAMESPACE file has

Thanks, I'll look into it. On Tue, Feb 18, 2020 at 8:32 AM Ezra Tucker <ezztucker at gmail.com> wrote: > > Hi Robert, > > This looks like a bug to me (tested in R 3.6.2 on Windows), f(new("a")) > should return "hi!". I'll add that this DOES work properly in 3.6.1 > which leads me to suspect this could be due to the subtle change in the > way

Dear John and Seth, dear R-devels, once again the question of method dispatch in S4 -- this time with setClassUnion(); taking up your advice in https://stat.ethz.ch/pipermail/r-devel/2006-April/037200.html https://stat.ethz.ch/pipermail/r-devel/2006-April/037201.html I have been too quick in stating that >setClassUnion()---at least in my case---solves the problem; > The problem arises