similar to: setGeneric(); R CMD check

Dear all, I can't see how setGeneric() works. I know perfectly well how to define library(methods); setClass("Square", representation(side="numeric")); # Will become the default method. getArea <- function(object) { stop(paste("Method getArea() is not defined for this class:", data.class(object))); } setMethod("getArea",

In the last few days I've received couple of messages pointing out that our SparseM package fails to install on the patched version of 1.7.0. Laurent Gaultier kindly suggested that replacing: setGeneric("as.matrix.csr") by setGeneric("as.matrix.csr", function(x, nrow, ncol, eps) standardGeneric("as.matrix.csr")) was sufficient to fix the problem.

I'm still having difficulties with methods...is the following behavior expected? (This is without loading any libraries) R : Copyright 2003, The R Development Core Team Version 1.7.0 Under development (unstable) (2003-03-31) > ls() character(0) > > diag(2) [,1] [,2] [1,] 1 0 [2,] 0 1 > setGeneric("diag") [1] "diag" > diag(2) Error in

Hi, while playing with the `methods' package I was not able to find what the recommended way of dealing with the following problem is. Suppose there is a generic function `foo' and two functions `foo.default' and `foo.formula', in the classical way: foo <- function(y, ...) UseMethod("foo") foo.default <- function(y, ...) {} foo.formula <- function(formula,

I am trying to use R interfaced with MySQL. Present goal is that R should calculate the 85% quantile of AvgSpeed for each LinieID. Looking through documentation of the RMySQL Package, I guessed that dbApply would do the trick due to this example ## compute quanitiles for each network agent con <- dbConnect(MySQL(), group="vitalAnalysis") res <- dbSendQuery(con,

My question has two parts. The first is with regard to the frame or environment in which generic functions are defined in packages. It seems as though they are defined (i.e. exist as objects) in frame 1, even when defined in a package. The following is a short example: setClass("track",representation(x="numeric",y="numeric")) plotTrack <- function(x,y,...)

Full_Name: Henrik Bengtsson Version: R v1.4.1 OS: WinMe Submission from: (NULL) (217.208.14.137) Doing the following library(methods) setGeneric("foo", function(x) standardGeneric("foo")) setMethod("foo", "ANY", function(x) cat(x)) fails with Error in while (value[n] == "ANY") n <- n - 1 : missing value where logical needed It

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

Hello, I have defined a new class > setClass("myclass", representation(min = "numeric", max = "numeric")) and want to write accessor functions, so that for > foo = new("myclass", min = 0, max = 1) > min(foo) # prints 0 > max(foo) # prints 1 At first i created a generic function for "min" > setGeneric("min",

I'm trying to write a package which uses classes/methods as defined in the `methods' package. I have a single .R file which defines the class and various methods for that class. At the top of the file I have require(methods) and then setClass("myclass", ...) setGeneric("intersect") setMethod("intersect", "myclass", function(x,y) ...) I noticed

I do lots of analyses on large microarray data sets so memory use and speed and both important issues for me. I have been trying to estimate the overheads associated with using formal S4 data objects instead of ordinary lists for large data objects. In some simple experiments (using R 1.7.1 in Windows 2000) with large but simple objects it seems that giving a data object a formal class

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

Hi, Please consider the following trivial example. In the sample code I first define a class MVCa using composition. This class contains a slot of type list. Next I define an inheritance relation using the function setIs -> MVCa "is a" list. Then I define a function printlength which prints the list-length which is defined for the type "list". If I call this function

Hi, The following question might come from my (deep) misunderstanding of the concepts in the package 'methods'. I have a class 'A', and a class 'B' inheriting 'A' (so defined with 'setClass' and the parameter 'contains="A"'. The class A has a method 'mymethod'. A call to 'showMethods("mymethod")' return the

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

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: >

Full_Name: Fernando Henrique Ferraz Pereira da Rosa Version: 1.8.0 OS: Linux 2.4.21 Submission from: (NULL) (200.206.211.169) After installing R 1.8.0, the R DBI interface stopped working. I tracked it down as a problem in the 'methods' package, that comes in the default installation. Somehow the function '.valueClassTest' which is defined on package 'methods',

Hi, In section 4.6.7 of "Writing R Extensions" (Version 1.2.1, 2001-01-15) the C function defineVar() is described as "... the equivalent of assign(symbol, value, envir = rho, inherits = FALSE) ..." I interpreted the above (wrongly) as meaning that defineVar() makes a copy of its "value" argument into the object whose name is specified in "symbol" in

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