similar to: Infinite recursion in getGeneric (PR#4561)

Hi, I found the following on Windows 2000/NT R Version 1.9.1 (2004-06-21) (also Version 1.9.0): The S4 group "Math" doesn't work as documented; i.e., "log", "log10", "gamma" and "lgamma" are included in the documentation but don't work. See example code below. Moreover, what about 'genericForPrimitive' which is used in

I have some questions about S4 style methods and generics. First of all, is there any way of using default values for arguments in the generics/methods? My own experiments show that such arguments are always ignored. The green book seems to be silent on this matter. The second question is about using a non-trivial function body for generics. Page 351 of the green book gives an example of this

Hi! Trying to reproduce some examples from "Programming with Data" page 341. Can not reproduce it neither on R1.8.1. nor R1.9.0devel? library(methods) setClass("track",representation(x="numeric",y="numeric")) setMethod("[" ,"track" ,function(x,...,drop=T){ track(x at x[...],y at y[...]) }

Hi, I'm trying to write a method such that my own classes can be used with the groups like "Summary" and "Math", but when I tried to look for examples or just wanted to get an idea of which functions are the members of a group, I found out that the function "getGroupMembers" is not present... I couldn't find an alternative function, if there is one. Does

i think these two code snippets exhibit a bug. they are identical but for the inclusion of an initial line in snippet [2] [1] setMethod("Math", signature(x = "numeric"), function(x) "Works") getGeneric("sqrt")(4) [2] getGeneric("sqrt")(4) setMethod("Math", signature(x = "numeric"), function(x) "Works")

On Jan 28, 2015, at 6:37 PM, Michael Lawrence <lawrence.michael at gene.com> wrote: > At this point I would just due: > > formals(body(method)[[2L]]) > > At some point we need to figure out what to do with this .local() confusion. Agreed, definitely. The current hack is to avoid re-matching arguments on method dispatch, so a fix would need to be fairly deep in the

I wish it didn't have to depend on the name '.local'. Back when I wrote a lot of S4 methods I avoided the auto-generated .local and named the local function something that made sense so that is was easier for a user to track down the source of an error. E.g., define the generic QQQ with numeric and integer methods: setGeneric("QQQ", function(x, ...)NULL)

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

Hello, ?as.character says that the as.character function is a generic with usage: as.character(x, ...). So, I want to create an S4 object with an as.character method following the above usage, but I get the below error telling me that ... isn't in the generic for as.character. > setClass("tmp", "numeric") > setMethod("as.character", "tmp",

Hello, ?as.character says that the as.character function is a generic with usage: as.character(x, ...). So, I want to create an S4 object with an as.character method following the above usage, but I get the below error telling me that ... isn't in the generic for as.character. > setClass("tmp", "numeric") > setMethod("as.character", "tmp",

I noticed this oddity about [ and setMethod. First, I define testFunc, which sorts a data frame by the first column and returns the entries that aren't NAs, and testIt, which runs testFunc repeatedly on a random large data frame, each time saving the return into a dummy placeholder (for demonstration's sake). > require(methods) Loading required package: methods [1] TRUE > testFunc

I noticed this oddity about [ and setMethod. First, I define testFunc, which sorts a data frame by the first column and returns the entries that aren't NAs, and testIt, which runs testFunc repeatedly on a random large data frame, each time saving the return into a dummy placeholder (for demonstration's sake). > require(methods) Loading required package: methods [1] TRUE > testFunc

Would we really need the special class or would simply checking the formals of the method against those of the generic be simple and fast enough? On Thu, Jan 29, 2015 at 9:41 AM, John Chambers <jmc at r-project.org> wrote: > I wouldn't want to add more to the current approach; if someone would like > to devote some time, the much preferable idea IMO would be to replace the >

Hello, Thomas Stabla (statho3@web.de) has already sent this question to R-help, Wed, 12 Nov 2003 21:21:31 +0100, but we are not sure whether we should better post this mail to this audience than to R-help: --------------------------------------------------------------------- We are using S4-classes and want to force a validity check when an object is created. How can this be done, when an

Hi! Consider this code. setClass("Ctest" ,representation( test="character" ,bla="character" ,mod="lm" ) ) new("Ctest",test="bla") #This produces an error. #Error in validObject(.Object) : Invalid "Ctest" object: Invalid object for slot "mod" in class "Ctest": got class

I am another person who has had trouble documenting S4 classes and (particularly) methods. The methods package itself is pretty cool by the way, but it is a pity that there are as yet no guidelines on S4 in the "Writing R Extensions" document. I have actually put together a guide on S4 documentation myself for the use of my own lab which is at

Dear List, I am trying to override the replace method "[<-" for objects of class "matrix"... with little success... Would anyone know where I am wrong ? > library(methods) > setReplaceMethod("[", "matrix", function(x, i, j, ..., value) {cat("I'm here.\n")}) [1] "[<-" > m <- new("matrix", 0, 5, 2) >

# Your mailer is set to "none" (default on Windows), # hence we cannot send the bug report directly from R. # Please copy the bug report (after finishing it) to # your favorite email program and send it to # # r-bugs@r-project.org # ###################################################### > x <- rnorm(10) > y <- 1:10 > xyplot(y ~ x) >

Hi, I don't understand why this code doesn't work (f(b2)): ///////////////// setClass("B0", representation(b0 = "numeric")) setClass("B1", representation("B0", b1 = "character")) setClass("B2", representation("B1", b2 = "logical")) f <- function(x) class(x) setMethod("f", "B0",

How would you implement attach()ing to a user-defined class with multiple slots in R? A primary goal of my software is to hide the data representation from the user, allowing them to attach() to my program's complex classes and refer to their contents by name - THEREBY avoiding having to pass the classes to every function call. Also, is it true that attaching to a to a sub-classed list