similar to: using initialize or using a constructor function

as.factor / as.ordered is not written as a generic. This differs from as.numeric, as.matrix, and other as.*. The following seems to address this and does not break make check-all. FWIW, the patch is against r55563, because with r55564 I see /home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15: error: storage size of ?dt? isn?t known /home/mtmorgan/src/R-devel/src/main/dounzip.c:88:5: warning:

Hello list, I'm having troubles setting up a basic calss hierarchy with S4. Here is a simplified schema of what I'd like to do: - Two classes: A and B that extends A - Ensure that the slots added by B are consistent with the slots of A - Let A initialize itself (I'm not supposed to know the internal cooking of A) - By default set the slots of B based on the slots that A initialized

Hi, I recently ran into this problem. I couldn't find any mention of it in the setClass documentation. setClass("Foo", representation(file = "character")) setMethod("initialize", "Foo", function(.Object, file) { print(file) }) setClass("Bar", contains = "Foo") And the error: Error in print(file) : argument "file" is

Hello, I've got a DESCRIPTION file with a the first line: Package: Repitools But, when I run R CMD INSTALL Repitools I get: * installing *source* package Repitools ... ** R ** data ** inst ** preparing package for lazy loading Warning in FUN(X[[1L]], ...) : Created a package name, "2011-04-20 09:05:40", when none found ** help *** installing help indices ** building package

Hello, I am trying to improve my skill on S4 classes. But there's something strange (to me) happening with "initialize" methods. This is probably a normal behaviour... but... something is unclear in my mind I declare two classes, namely "A", and "B", which has a slot of type A. The class "A" has an initialize method. What I do not understand is that

Folks, My object oriented background is in Java and C++. I am a novice to using S4/object-oriented coding in R but not to R. Below is an example that I found that I have expanded on. I am not getting how "prototype" and "initialize" work together, if at all. Here is output from a short "session" > setClass("xx", +

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

>>>>> Martin Morgan <mtmorgan at fredhutch.org> >>>>> on Mon, 11 May 2015 10:18:07 -0700 writes: > On 05/10/2015 08:19 AM, Martin Morgan wrote: >> Loading an S4 object from a file without first loading the library sometimes (?, >> the example below and actual example involves a virtual base class and the show >> generic)

Hi Martin, Indeed it does (and I should have confirmed myself with R-patched and R-devel before posting...) Thanks, and sorry for the noise. Kevin On Tue, Aug 25, 2015, 13:11 Martin Morgan <mtmorgan at fredhutch.org> wrote: > On 08/25/2015 12:54 PM, Kevin Ushey wrote: > > Hi all, > > > > The following fails for me (on OS X, although I imagine it's the same >

To test two environments for object equality (Lisp EQ), I can use 'identity': > e1 <- environment(local(function()x)) > e2 <- environment(local(function()x)) > identical(e1,e2) # compares object identity [1] FALSE > identical(as.list(e1),as.list(e2)) # compares values as name->value mapping [1] TRUE # (is there a

Dears, I have a question about copying reference objects using the initialize method. 1) If the latter has no arguments, there is no problem to copy an object. myClass = setRefClass("myClass", fields = list(value = "numeric") ) myClass$methods(initialize = function(...){ ? value <<- 1 ? callSuper(...) }) newObject = myClass$new() newObject$value = 2 copyObject =

Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54

Dear list I am running some simulations in R involving reading in several hundred datasets, performing some statistics and outputting those statistics to file. I have noticed that it seems that the time it takes to process of a dataset (or, say, a set of 100 datasets) seems to take longer as the simulation progresses. Has anyone else noticed this? I am curious to know if this has to do with how R

Hi, from the man page ?methods, I expected to be able to build pairs (class,package) for a given S3 method, e.g., print, using attr(methods(print), 'info'). However all the methods, except the ones defined in base or S4 methods, get the 'from' value "registered S3method for print", instead of the actual package name (see below for the first rows). Is this normal

Hi! In a function, I may have an instance in which all elements are equal. > x <- rep(1,5) > > x [1] 1 1 1 1 1 > identical(x) Error in .Internal(identical(x, y, num.eq, single.NA, attrib.as.set)) : 'y' is missing > all.equal(x) Error in is.expression(x) : 'x' is missing > I don't care what particular value it is, I just want to know if they are all

Hi everybody! I'm creating an object of a S4 class that has two slots: ListExamples, which is a list, and idx, which is an integer (as the code below). Then, I read a data.frame file with 10000 (ten thousands) of lines and 10 columns, do some pre-processing and, basically, I store each line as an element of a list in the slot ListExamples of the S4 object. However, many operations after this

invoking parLapply without a cluster fails to find a previously registered cluster > library(parallel) > setDefaultCluster(makePSOCKcluster(2)) > parLapply(X=1:2, fun=function(...) {}) Error in cut.default(i, breaks) : invalid number of intervals This is because in parLapply length(cl) is determined before defaultCluster(cl) is called. By inspection, this appears to be true of

If I try to build a package with a vignette R CMD build Biobase I see * checking for file 'Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src Error in setwd(pkgname) : cannot change working directory Execution halted This is

With C:\Users\User>R --version R version 2.14.0 RC (2011-10-23 r57410) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-mingw32/x64 (64-bit) running download.file('http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip', tempfile()) sometimes gets 52% (according to the dialog box) of the way through, and then

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" PkgA promotes 'unique' to a generic and exports that DESCRIPTION: Imports: methods R/f.R: setGeneric("unique") NAMESPACE: export(unique) and PkgB creates and exports a method on unique DESCRIPTION Imports: methods, PkgA R/f.R: setClass("B",