similar to: function showMethods and inheritance

Hi, Strange things happen. Here is a simple example: > setClass("A", contains="integer") > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod())) Creating a generic function for ?as.matrix? from package ?base? in the global environment [1] "as.matrix" > a <- new("A", 1:3) > as.matrix(a)

showMethods isn't reporting inherited methods when it is first called. The methods are there and after calling them, showMethods gives the right output. Here is an example (using R-devel r39647): setClass("A", representation(x="numeric"), prototype=list(x=1)) setClass("B", contains="A", prototype=list(x=2))

Hi, In the situation below the note issued by the dispatch algo doesn't seem right: setClass("A", representation(stuff="complex")) setAs("ANY", "A", function(from) new("A", stuff=as.complex(from))) > as(6, "A") An object of class "A" Slot "stuff": [1] 6+0i > as(6L, "A")

Hi, I'm developing in S4 and I wanted to see the methods for a specific class using showMethods but I didn't succed. Can someone help ? See the example below. setClass("myclass", representation( name ="character" ) ) setGeneric("mymeth", function(obj, ...){ standardGeneric("mymeth") } ) setMethod("mymeth",

Hi, perhaps a little bit unusual: is it possible to use "<- " as generic function with a new signature? The following example doesn't work: > isGeneric("<-") [1] FALSE > setClass("A",representation(x = "numeric")) [1] "A" > setClass("B",representation(x = "numeric")) [1] "B" > myAssign.A <-

(a new thread, on purpose) >>>>> "RobG" == Robert Gentleman <rgentlem at fhcrc.org> >>>>> on Mon, 27 Jul 2009 16:55:50 -0700 writes: RobG> Hi, I just committed a change to R-devel so that if RobG> debug is called on an S3 generic function, all methods RobG> will also automatically have debug turned on for them RobG>

Hi r-devels, I am stuck in some S4 inheritance problem: setClass("A",representation(a="numeric")) setClass("A1",representation(b="numeric"),contains="A") setClass("A2",representation(c="numeric"),contains="A1") if(!isGeneric("foo")){ setGeneric("foo", function(x,y,z, ...)

hello, if i load the RSQLite package in addition to the RPostgreSQL package, i get various errors when trying to use RPostgreSQL functions. here is an example transcript showing one such error: ========================================================== R version 2.15.0 (2012-03-30) [...] > packageVersion('RPostgreSQL') [1] 0.3.2 > packageVersion('RSQLite') [1] 0.11.1

Hi, It doesn't seem that the dispatching algo is finding my coerce method under some circumstances. Let's say I have 2 classes, A and AA and that AA is just a direct extension of A with no additional slots: setClass("A", representation(ii="integer")) setClass("AA", contains="A") I can define a method for coercing my objects to an integer

Apologies for asking something that is probably super obvious, i just started with S4 classes and i guess i am not finding documentation that layout the grammar rules and give enough examples. Some questions i am having are these 1. I understand that main method of writing a member function is to write a generic function and setMethod for this particular object. This, however, presumes that there

As I tried to say on Dec. 11, there are two levels of "fix": 1. The fix to the complaint in the OP's subject heading is to conform to the default third argument, strict=TRUE: as(1L, "numeric") == 1.0 This generates some incompatibilities, as for classes that extend "numeric". But still leaves class(1.0) "numeric" and typeof(1.0) "double".

Dear all, I am experiencing some problems with S4 method overloading. I have defined a generic for graphics:plot, using setGeneric("plot", useAsDefault = plot) and with importFrom('graphics', 'plot') and exportMethods('plot') in the NAMESPACE file of pkg A. I then proceed to define a method for signature c('myS4class', 'missing'). This works

(I think this is being caused by the new methods package in RC.) In the RC (March 24) some of my packages are generating a Note Note: Method with signature "MySQLConnection#integer" chosen for function "coerce", target signature "TSMySQLConnection#integer". "dbObjectId#integer" would also be valid This is coming from a call to dbGetQuery() in package

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

Hi, S4 method dispatch can be very slow. Would it be reasonable to cache the most recent dispatch, anticipating the next invocation will be on the same type? This would be very helpful in loops. fun0 <- function(x) sapply(x, paste, collapse="+") fun1 <- function(x) { paste <- selectMethod(paste, class(x[[1]])) sapply(x, paste,

Hi, I ran into the following peculiarity involving S4 method dispatch and namespaces. I develop a package which have a namespace and which depends on 'pixmap' package, which itself does not have a namespace. Now, in my package I have a class which has a slot for objects from class "pixmap" and I want to have a "plot" method for this new class. Not to clutter the

Dear all, Assume that I have an S4 class "MyClass" with a slot "myname", which is initialized to: myname="" in method("initialize"): myclass <- new("MyClass", myname="") Assume that class "MyClass" has a method "mymethod": "mymethod.MyClass" <- function(object, myname=character(0), ...) {

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: >

after this setClass("A") setGeneric("bar", function(x, y) standardGeneric("bar")) setMethod(bar, signature(x="A", y="A"), function(x, y) {}) setMethod(bar, signature(x="A", y="ANY"), function(x, y) {}) the method for signature c("A", "A") contains package information > str(getMethod(bar,

Might it be an idea to make "?" a special operator akin to "+" or "[", R users could then write their own help functions - may be even making "?" generic? With the proposed xml help system one could imagine quite sophisticated context sensitive help systems. Regards, John Marsland PS this has been a very useful debate for those of us enthusiastically