similar to: infinite recursion when printing former S4 objects

R-Devel: When I get the data part of an S4 class that contains="data.frame", it gives me a list, even when the "data.frame" is the S4 version: > d<-data.frame(x=1:3) > isS4(d) [1] FALSE # of course > dS4<-new("data.frame",d) > isS4(dS4) [1] TRUE # ok > class(dS4) [1] "data.frame"

2017-09-22 19:04 GMT+02:00 Michael Lawrence <lawrence.michael at gene.com>: > The %*% function is a primitive. As it says in the documentation under > ?Methods_Details > > Methods may be defined for most primitives, and corresponding > metadata objects will be created to store them. Calls to the > primitive still go directly to the C code, which will

> setClass("A", "integer") > isS4(new("A")) [1] TRUE > identical(isS4(new("A")), TRUE) [1] FALSE > sessionInfo() R Under development (unstable) (2012-10-04 r60876) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5]

Hi, Given a simple three class hierarchy: A <-- B <-- C I want to define an initialize method for each class such that when I call new("C", x=5), the initialize methods for A and B are used to incrementally build the object. When I do what seems obvious to me using callNextMethod, I get an infinite recursion. An example follows... setClass("A",

If one accidentally calls match(x, obj), where obj is any S4 instance, the result is NA. I was expecting an error because, in general, if a match method is not defined for a particular S4 class, I don't know what a reasonable default could be. Specifically, here's what I see setClass("FOO", representation(a="numeric")) foo <- new("FOO", a=10)

The default initialization for slots of class "factor" and "data.frame" gives NULL. This seems odd, since those slots can't ever be set to NULL by the user. I would expect zero-length instances of factor and data.frame. Here is an example: setClass("FOO", representation(a="factor", b="data.frame", c="numeric")) [1] "FOO"

Should functions or the user be responsible for coercing an S4 object argument containing the proper object (and thus should below be considered a bug in the packages or not)? The example is with RSQLite but the same thing happens with RMySQL, and other DBI packages. > library("RSQLite") Loading required package: DBI > m <- dbDriver("SQLite") > con <-

Sorry, I can't reproduce the example below even on the same machine. However, the following example produces the same error as NULL values in prior examples: > setClass("FOOCLASS", +????????? representation("list") + ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > isS4(ma) [1] TRUE > data.frame(a=1:3) == ma Error in

Hi, after updating R 2.5.0 devel yesterday we today observed many new unexpected failures in our daily package build and test system runs, which can be traced to recent changes in the implementation in try() (as noted in NEWS). Investigating this new implementation I come across an issue in conjuntion with using S4 classes and methods. try(expr) does not return an object with attribute

Hi, I have a S3 package with namespace called "myS3Pkg". Inside my package I would like to create a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"),

Hi all, I'm trying to implement the matrix multiplication operator, which is S4 generic, for an old-style S3 class. The following works as expected: x <- 1:10 class(x) <- "myClass" setOldClass("myClass") setGeneric("myMethod", function(x, y) standardGeneric("myMethod")) setMethod("myMethod", c("myClass", "myClass"),

A recent revision (svn version 39077) has introduced an internal flag (a bit in the C structure) that is turned on by the code that generates objects from an S4 class. There are corresponding tests for an S4 object, isS4() in R and IS_S4_OBJECT() in C. These are fast and reliable, and should replace any heuristic tests previously used. The tests are not currently used widely, but in the

Hi, Using latest R 2.5.0 Patched, I'm unable to install the Matrix package from cran.fhcrc.org. I get: Creating a new generic function for "isSymmetric" in "Matrix" Creating a new generic function for "unname" in "Matrix" Error in conformMethod(signature, mnames, fnames, f) : In method for function "!": formal arguments omitted in

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

Dear all, I have a question regarding setIs and method dispatch in S4 classes: Consider the following example: ##################################################### ## A02 "contains" A01 by setIs: setClass("A01", representation(a="numeric",b="numeric")) setClass("A02", representation(a="numeric",d="numeric"))

Hello, I wonder if this will make it through the spam filters given the subject line. I'm seeing the following when trying to call a dollar method inside of a dollar method. setClass("Foo", representation(d="list")) [1] "Foo" f <- new("Foo", d=list(bob=1, alice=2)) ## We can call dollar at this level and it works as expected

I'm using an S4 object with a slot of type 'call': I would like to be able to initialize it with something like NULL or NA (indicating that there is no information in the slot) but the value should comply with the fact that it must be of type call. Is there any simple way to obtain this? Thanks for any hint, Roberto -- <r/> | Roberto Brunelli - [scientist at Fondazione

Hi Mehmet, On 11/29/2017 11:22 AM, Suzen, Mehmet wrote: > Hi Herve, > > I think you are confusing subclasses and classes. There is no > contradiction. `is` documentation > is very clear: > > `With one argument, returns all the super-classes of this object's class.` Yes that's indeed very clear. So if "list" is a super-class of "data.frame" (as

I ran into a problem recently trying to update a package which uses S4 methods using a recent beta of R. I think I can reproduce it with a simple example. I have package called `testpkg' in directory testpkg/. In the R/ subdirectory of testpkg/ I have a file called testpkg.R which contains the following two lines: setClass("testpkg", representation(pts = "list"))

(I am not sure if this is a bug or a request for a more understandable warning, or possible something obvious I should be posting on r-help.) I am trying to coerce an new class object to be a DBIConnection and it does not work the way I think it should: R version 2.5.1 (2007-06-27) ... > require("RMySQL") # or require("RSQLite") Loading required package: RMySQL Loading