search for: getgeneric

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") getGeneric("sqrt")(4) these are my results, when each is run from a fresh R session [1] > setMethod("Math", signature(x...

Hi, namespaceImportFrom in base/R/namespace.R has the following: fdef <- methods:::getGeneric(genName, impenv) The definition of getGeneric is in methods/R/RMethodUtils.R starts with: getGeneric <- ## return the definition of the function named f as a generic. ## ## If there is no definition, throws an error or returns ## NULL according to the value of mustF...

> setClass('foo') [1] "foo" > setMethod('is.logical', 'foo', function(x) TRUE) [1] "is.logical" > getGeneric('is.integer') Error in options(x) : evaluation is nested too deeply: infinite recursion? > --please do not edit the information below-- Version: platform = i686-pc-linux-gnu arch = i686 os = linux-gnu system = i686, linux-gnu status = major = 1 minor = 8.0 year = 2003...

...: 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 'getGeneric'. It seems that this method is not included in the R Version 1.9.1 (also 1.9.0). See the example code of John Chambers at the end of this email. Why not add the method 'getGroupMembers' as proposed by John Chambers to the methods package? (see reply to mail: "Missing 'getGroup...

...parentenv, handlers) 5: tryCatchOne(expr, names, parentenv, handlers[[1]]) 6: doTryCatch(return(expr), name, parentenv, handler) 7: loadNamespace(package, c(which.lib.loc, lib.loc)) 8: methods:::cacheMetaData(ns, TRUE, ns) 9: .updateMethodsInTable(fdef, where, attach) 10: .updateMethodsInTable(getGeneric(g), where, attach) 11: .setupMethodsTables(generic) ============================================== On a different Linux machine and R version (the standard faculty wide installation), library(pctsData) completes fine but package "grgen" mentioned above still gives the error at installa...

I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to reproduce Jeff's error, though. > library(Matrix) > as.vector function (x, mode = "any") .Internal(as.vector(x,...

...ic only if "..." is an argument to the generic Am I reading the documentation incorrectly? How do I correctly pass the ... object to the method for this "tmp" object? However I note that looking at the generic function, I see no mention of ... (despite the documentation). > getGeneric("as.character") standardGeneric for "as.character" defined from package "base" function (x) standardGeneric("as.character", .Primitive("as.character")) <environment: 0145EDC4> Methods may be defined for arguments: x So, briefly, is the do...

...ic only if "..." is an argument to the generic Am I reading the documentation incorrectly? How do I correctly pass the ... object to the method for this "tmp" object? However I note that looking at the generic function, I see no mention of ... (despite the documentation). > getGeneric("as.character") standardGeneric for "as.character" defined from package "base" function (x) standardGeneric("as.character", .Primitive("as.character")) <environment: 0145EDC4> Methods may be defined for arguments: x So, briefly, is the do...

...mpt", agrep=F) Error: couldn't find function ".class1" > traceback() 12: initialize(value, ...) 11: initialize(value, ...) 10: new("ObjectsWithPackage", value, package = pkg) 9: metaNameUndo(unique(these), prefix = "M", searchForm = searchForm) 8: methods:::getGenerics(ns) 7: unique(c(methods:::getGenerics(ns), methods:::getGenerics(parent.env(ns)))) 6: loadNamespace(name) 5: getNamespace(ns) 4: asNamespace(ns) 3: getExportedValue(pkg, name) 2: tools::fileTest 1: help.search("prompt", agrep = F) > version _ platform i686-pc-linux-gnu arch...

...+++ b/COFF/InputFiles.cpp @@ -229,11 +229,11 @@ Symbol *ObjFile::createRegular(COFFSymbolRef Sym) { if (Sym.isExternal()) { StringRef Name; COFFObj->getSymbolName(Sym, Name); - if (SC) + if (SC && SC != PendingComdat) return Symtab->addRegular(this, Name, Sym.getGeneric(), SC); return Symtab->addUndefined(Name, this, false); } - if (SC) + if (SC && SC != PendingComdat) return make<DefinedRegular>(this, /*Name*/ "", false, /*IsExternal*/ false, Sym.getGeneric(), SC); return nullptr; I ca...

I got the following after running succesfully through this loop 28 million times... the loop opens text files in a directory and inserts line by line into a database... *** caught segfault *** address 0xc0000010, cause 'memory not mapped' Traceback: 1: .getGeneric(f, where, package) 2: getGeneric("coerce", where = where) 3: as(obj, "integer") 4: mysqlConnectionInfo(dbObj, ...) 5: dbGetInfo(conn, "rsId") 6: dbGetInfo(conn, "rsId") 7: dbListResults(con) 8: dbListResults(con) 9: mysqlQuickSQL(conn, statement, ...)...

...] # <environment: R_GlobalEnv> foofunc # nonstandardGenericFunction for "foofunc" defined from package ".GlobalEnv" # # function (object) # { # standardGeneric("foofunc") # } # <environment: 0x293bbb8> # Methods may be defined for arguments: object getGeneric("foofunc") # same result as above #### Now what I suspect is a bug ## Delete the S4-generic and repeat the "forensic" test calls removeGeneric("foofunc") # [1] TRUE ## The following is as expected... foofunc # Fehler: objekt "foofunc" nicht gefunden [~...

...*ObjFile::createRegular(COFFSymbolRef Sym) { >> if (Sym.isExternal()) { >> StringRef Name; >> COFFObj->getSymbolName(Sym, Name); >> - if (SC) >> + if (SC && SC != PendingComdat) >> return Symtab->addRegular(this, Name, Sym.getGeneric(), SC); >> return Symtab->addUndefined(Name, this, false); >> } >> - if (SC) >> + if (SC && SC != PendingComdat) >> return make<DefinedRegular>(this, /*Name*/ "", false, >> /*IsExternal*/...

...t of a trick to find the formal argument list, since R currently just returns NULL for args(f) if f is a primitive. (We may need to make some change here.) Two that are worth noting are "[" and "[[" (and the corresponding "[<-" and "[[<-"): > args(getGeneric("[")) function (x, i = NULL, j = NULL, ..., drop = TRUE) NULL > args(getGeneric("[[")) function (x, i = NULL, ...) NULL The i,j arguments are there so we can, e.g., define methods that dispatch on the column argument for data-frame-like objects in the future. If you'r...

...or. i attempted to do this as I have done it for infix operators like '+' , but am not meeting with success. i am pretty sure this is because '+' has a predefined generic with "dispatchable" formals e1 and e2, whereas no generic is predefined for '@' > getGeneric("+") standardGeneric for "+" defined from package "base" belonging to group(s): Arith function (e1, e2) standardGeneric("+", .Primitive("+")) <environment: 0x169dea44> Methods may be defined for arguments: e1, e2 > getGeneric("@&...

Hi, I'm writing some functions to generate Rd files for a S4 package. I want to have 2 character vectors with the names of the S4 classes and the methods exported by a package. To get the info about methods I'm using "getGenerics(where="package:FLCore")" however I can not find a similar process to get the S4 classes. Are there functions to access this information ? Best and thanks EJ

...uot;, signature=c("numeric", "A"))(e1, e2) print(v) new("B", v, xb=e1*e2 at xb) } ) Results: > t1 <- new("B", new("A", xa=4), xb=2) > t1 An object of class ?B? Slot "xb": [1] 2 Slot "xa": [1] 4 > 3*t1 Error in getGeneric(f, !optional) : no generic function found for "callGeneric" Thanks. Ross Boylan

Hi, I have a BioC infra-structure package that works fine (I can build, check and load it successfully) on revision r53950. The very same package fails on r54591 with the error below: Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space dependency detected when loading ?oligoClasses?, already loading ?oligoClasses? I don't see anything

...itialize (package methods) .Object="mspathCoefficients" (inherited from: .Object="ANY") Function: print (package base) x="mspathCoefficients" Function: show (package methods) object="mspathCoefficients" (inherited from: object="ANY") > getGeneric("print") standardGeneric for "print" defined from package "base" function (x, ...) standardGeneric("print") <environment: 0x84f2d88> Methods may be defined for arguments: x I've looked through the code for promptClass, but nothing popped out at...

...masked from 'package:graphics': plot. And then, I cannot use the classical function plot: plot on object 'A' works, but plot(1) does not. I try, reading some recent post on r-devel to remove the line 'setGeneric' but it does not works (which does not surprise me since getGeneric("plot") gives a NULL results). Any idea of what goes wrong? Christophe -- View this message in context: http://r.789695.n4.nabble.com/Define-S4-methods-for-plot-tp4020750p4020750.html Sent from the R devel mailing list archive at Nabble.com.