similar to: user interface and documentation of setIs and setAs, some suggestions (S4).

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

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (128.102.184.81) annaffy 1.0.1 (in BioC CVS) fails to load. annaffy 1.0 (on the BioC web site) has the same problem. It looks like the load is failing because of a bug in completeSubclasses() in r-devel. It calls setIs() and doesn't specify an environment via the "where" argument. setIs()

Hi the list I am fighting with the twins setAs and setIs... Here are some questions and comments (comments to myself but that migth be wrong, it is why I am posting them) 1. Very surprising : using setIs define 'is', 'as<-' but not 'as' ??? 2. Using setAs define 'as', 'as<-' but not 'is'... What surprise me is that as<- can be define by

Hello, am I using 'setIs' in the correct way in the subsequent (artifical) example? Do I have to specify explicit 'setAs' for 'list' and 'vector' or should this work automatically, since "getClass("List1")" states an explicit coerce also for these classes. I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. Thanks for your

Andreas, As far as I can tell (/conjecture), this is because the list of classes a particular class inherits from directly is appended to as needed, and so the order that a class extends others isd refined by the order that those connections are defined. We can see this with two setClassUnion calls, rather than required setAs: > setClass("grandma", slots = c(a =

(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

Hi list, I've got a class B that contains a slot obj of class A. I'd like to be able to call all the methods of class A directly on objects of class B as if I had called the method on slot obj. This without overloading all methods of class A to work on class B. I don't define B as an extension of A, because I want class B to also work with objects of classes that inherit from

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 R core team Please apologize for posting the same question twice on R-help and R-devel. Since I was not sure which list is appropriate I tried R-help (Tue Mar 22), but got no answer. Now I do not know if the formulation of my question was unclear or the question is not so easy to answer or to easy (what I do not hope). My problem: I create a new S4 class, containing one slot, data (of

Dear R gurus I've a question concerning the transformation of a new S4 class (that I defined) and the existing class "POSIXlt". I did the following: ## Definition of the new class: setClass("dtime", representation(data = "POSIXlt"), prototype(data = as.POSIXlt("2004/06/01"))) ## Transformation between the new class "dtime"

I'm trying to resolve a small problem that has arisen from introducing a NAMESPACE for the package SparseM. Prior to the namespace I had a class "matrix.diag.csr" that consisted of diagonal sparse matrices. It was defined to have the same attributes as the matrix.csr class and setAs was used to define how to coerce integers and vectors into this form:

Dear list, I'd like to write coercion methods for some of my Reference Classes. However, using 'setAs()' is not a real option as its argument 'def' only allows for functions depending on one single argument. In some cases, that is simply too much of a limitation for me. And I don't really see why it needs to be this way, so I guess this question is also some sort of a

An example sent by Ross Ihaka points out a non-obvious step needed to export the results of setAs(). The as() mechanism can't use ordinary method dispatch because the second argument is the name of a class, not an object from the class. So it uses a "helper" function, coerce(), and sets methods for that function. Therefore, if you want to export the results of setAs(), at the

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"))

Consider this: $ cat test.dat 1 a 2 b Now, we want to read the 2nd column as a factor and ignore the first (since it's just a sequential ID). We can't just put "factor" among the colClasses (would have been nice), so let's try this instead > setAs("character","factor",as.factor) Arguments in definition changed from (x) to (from) >

This seemed too advanced for r-help and is related to the recent discussion of character vectors in dataframes. Following Brian Ripley's most excellent advice, we are moving to a world in which character vectors in dataframes are always of class AsIs. The cool way of doing this seemed to be the following: > cat(c("x", "y", "z"), file = "test.txt",

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"))

On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s <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 fredhutch.org>> wrote: >> >> Hi, >> >> Short story >> ----------- >> >>

I've recently updated from an early February version of 1.7.0 to Version 1.7.0 Under development (unstable) (2003-03-25) and am now having problems with errors giving the message: ' getExtends(ClassDef) : @ must be used on an object with a formal class' which seems to be caused by 'setIs("character","character or NULL")' which attempts to define

Hi, While checking the package I am getting all the time the following complain about the function: Undocumented S4 methods: generic coerce and siglist matrix,Massvector I have not defined the function nowhere in the R files. My gues is that this has something to do with the following definition of the setAs function. setAs("matrix","Massvector" ,def=