search for: deriveddefaultmethod

...e(): - bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !identical(sys.function(-1L), as.data.frame))) + bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !( + identical(sys.function(-1L), as.data.frame) || ( + .isMethodsDispatchOn() && + methods::is(sys.function(-1L), 'derivedDefaultMethod') && + identical( + sys.function(-1L)@generic, + structure('as.data.frame', package = 'base') + ))))) .Deprecated( msg = gettextf( "Direct call of '%s()' is deprecated. Use '%s()' or '%s()' instead", The patch p...

...r.org/packages/release/bioc/html/IRanges.html) removeGeneric("paste") library(IRanges) showMethods(paste) ## Function: paste (package BiocGenerics) ## ...="ANY" ## ...="Rle" selectMethod(paste, "ANY") ## Method Definition (Class "derivedDefaultMethod"): ## ## function (..., sep = " ", collapse = NULL) ## .Internal(paste(list(...), sep, collapse)) ## <environment: namespace:base> ## ## Signatures: ## ... ## target "ANY" ## defined "ANY" microbenchmark(fun0(lst), fun...

...: Error in .cellValues(x, y, ...) : unused arguments (fun = new("standardGeneric", .Data = function (x, ...) standardGeneric("mean"), generic = "mean", package = "base", group = list(), valueClass = character(0), signature = "x", default = new("derivedDefaultMethod", .Data = function (x, ...) UseMethod("mean"), target = new("signature", .Data = "ANY", names = "x", package = "methods"), defined = new("signature", .Data = "ANY", names = "x", package = "methods"), gene...

...<- quote(if((sys.nframe() <= 1L || !identical(sys.function(-1L), as.data.frame))) > + bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !( > + identical(sys.function(-1L), as.data.frame) || ( > + .isMethodsDispatchOn() && > + methods::is(sys.function(-1L), 'derivedDefaultMethod') && > + identical( > + sys.function(-1L)@generic, > + structure('as.data.frame', package = 'base') > + ))))) > .Deprecated( > msg = gettextf( > "Direct call of '%s()' is deprecated. Use '%s()' or > ...

...r other people wanting to add a regression test to their patch. I see that tests/reg-tests-1e.R is already running under options(warn = 2), so if I add the following near line 750 ("Deprecation of *direct* calls to as.data.frame.<someVector>")... # Should not warn for a call from a derivedDefaultMethod to the raw # S3 method -- implementation detail of S4 dispatch setGeneric('as.data.frame') as.data.frame(factor(1)) ...then as.data.frame will remain an S4 generic. Should the test then rm(as.data.frame) and keep going? (Or even keep the S4 generic?) Is there any hidden state I may be brea...

...Slots, prototype of class "function" Extends: "OptionalFunction", "PossibleMethod" Known Subclasses: Class "MethodDefinition", from data part Class "genericFunction", from data part Class "functionWithTrace", from data part Class "derivedDefaultMethod", by class "MethodDefinition" Class "MethodWithNext", by class "MethodDefinition" Class "SealedMethodDefinition", by class "MethodDefinition" Class "standardGeneric", by class "genericFunction" Class "nonstandardGeneric...

...ession > test to their patch. I see that tests/reg-tests-1e.R is already running > under options(warn = 2), so if I add the following near line 750 > ("Deprecation of *direct* calls to as.data.frame.<someVector>")... > # Should not warn for a call from a derivedDefaultMethod to the raw > # S3 method -- implementation detail of S4 dispatch > setGeneric('as.data.frame') > as.data.frame(factor(1)) > ...then as.data.frame will remain an S4 generic. Should the test then > rm(as.data.frame) and keep going? (Or even keep the S4 gene...

...gt; test to their patch. I see that tests/reg-tests-1e.R is already running >> under options(warn = 2), so if I add the following near line 750 >> ("Deprecation of *direct* calls to as.data.frame.<someVector>")... >> # Should not warn for a call from a derivedDefaultMethod to the raw >> # S3 method -- implementation detail of S4 dispatch >> setGeneric('as.data.frame') >> as.data.frame(factor(1)) >> ...then as.data.frame will remain an S4 generic. Should the test then >> rm(as.data.frame) and keep going? (Or e...

...ense (human reader or R interpreter)? In either > case I'm not convinced. From a developer perspective, especially when debugging, when we do selectMethod("match", ...) and it turns out that this returns the default method, it's good to see: Method Definition (Class "derivedDefaultMethod"): function (x, table, nomatch = NA_integer_, incomparables = NULL, ...) base::match(x, table, nomatch = nomatch, incomparables = incomparables, ...) <environment: namespace:BiocGenerics> Signatures: x table target "DataFrame&quot...

Hi, The acrobatics that as.data.frame.factor() is going thru in order to recognize a direct call don't play nice if as.data.frame() is an S4 generic: ??? df <- as.data.frame(factor(11:12)) ??? suppressPackageStartupMessages(library(BiocGenerics)) ??? isGeneric("as.data.frame") ??? # [1] TRUE ??? df <- as.data.frame(factor(11:12)) ??? # Warning message: ??? # In

There seems to be a bug arising when using multiple S4 generics with "..." as the signature. The following code works as expected: ############################################################## > setGeneric("rbind", function(..., deparse.level=1) standardGeneric("rbind"), + signature = "...") Creating a generic for "rbind" in

On Thu, Jan 22, 2015 at 11:44 AM, <luke-tierney at uiowa.edu> wrote: > > For default methods there ought to be a way to create those so the > default method is computed at creation or load time and stored in an > environment. We had considered that, but we thought the definition of the function would be easier to interpret if it explicitly specified the namespace, instead of