search for: showmethods

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", signature("myclass...

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(&quot...

...omewhat related issue: As many of the R-devel readers will know, there has been quite a nice ongoing effort to make S3 and S4 methods and classes more compatible. One issue here, notably for inexperienced programmeRs, is also the fact that methods(f) only tells about S3-methods for 'f', and showMethods(f) only mentions S4 ones. This is not at all design error, as indeed S3 and S4 dispatch is quite different (notably as the latter allows multiple dispatch and hence uses the nice concept of "signature"), used to be more incompatible and, indeed, methods(f) *still* warns, often wrongly, i...

Hi, when running the following on a fresh R, library("IRanges") annotation showMethods("annotation") Biobase:::annotation showMethods("annotation") I get (see the "^^^^^" marked output at the bottom): > library("IRanges") Carico il pacchetto richiesto: 'IRanges' The following object(s) are masked from package:base : cbi...

...y (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 signature of the function with A, but not with B no matter whether I specify 'inherited=TRUE' or not... Any pointer ? Thanks in advance, Laurent -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- R...

Hello list. This is from an R session (admittedly, I''m still using R 2.11.1): > print function (x, ...) UseMethod("print") <environment: namespace:base> > showMethods("print") Function "print": <not a generic function> Don''t the two results contradict each other? Or do I have a terrible misunderstanding of what comprises a generic function? Thx, Nick Sabbe -- ping: nick.sabbe@ugent.be link: <http://biom...

...ards to as.vector. When I looked at the code for as.vector in R-devel it is standardGeneric for "as.vector" defined from package "base" function (x, mode) standardGeneric("as.vector") <environment: 0x0918ad70> Methods may be defined for arguments: x, mode Use showMethods("as.vector") for currently available ones. The code from R3.2.3 is > as.vector function (x, mode = "any") .Internal(as.vector(x, mode)) <bytecode: 0x02dfb858> <environment: namespace:base> > Is default for mode missing as I suspect or will mode be required f...

...is already hard enough. 2/ The note only seems to get generated on the first call and then gets suppressed. This will be nice for users, but makes debugging harder. Is there a way to prevent suppressing the message? 3/ It seems strange that getMethod() cannot find the methods even though showMethods() shows it. (See below.) Paul ________ >showMethods("dbGetQuery") Function: dbGetQuery (package DBI) conn="MySQLConnection", statement="character" > z <- TSget("Series 1", con, TSrepresentation="timeSeries") Note: Method with signatu...

> biplot standardGeneric for "biplot" defined from package "stats" function (x, ...) standardGeneric("biplot") <environment: 0x0d4444d8> Methods may be defined for arguments: x Use showMethods("biplot") for currently available ones. > > > showMethods("biplot") Function: biplot (package stats) x="ANY" x="character" (inherited from: x="ANY") x="Pca" > biplot(resRobPCA) But how do I get the source code of &quo...

...vel version none of these options have the intended effect of making "image" a generic and allowing R to dispatch for matrix.csr objects. When I omit the setGeneric() call, I do get a message at INSTALL time that a generic for image is being created, but then after loading SparseM: > showMethods(image) Function "image": <not an S4 generic function> On the command line, I can make this work: > setGeneric("image") [1] "image" > showMethods(image) Function: image (package graphics) x="ANY" x="matrix.csr" And -- even more irritat...

...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: > library(Biobase) > library(annaffy) > showMethods("[") Function "[": x = "ANY" x = "container" x = "phenoData" x = "exprSet" x = "aafList" x = "aafTable" > library(annaffy) (annaffy loads Biobase in .First.lib) > showMethods("[") Function "[&quo...

...more useful output. You might want to > report the issue on one of the R lists. > >> Since PromptClass() contains a parameter "where" is it possible to use >> it, and how? > > I'm not sure that is relevant here. > > One thing that can be useful here is showMethods(classes="AffyBatch"). > The problem with static documentation for methods is that what methods > are available can change based on what packages are attached. > > If showMethods or a wrapper for it could be convinced to output a link > to a help file, then it might actually...

...> library(RSQLite) > dbDriver('PostgreSQL') Error in function (classes, fdef, mtable) : unable to find an inherited method for function "show", for signature "PostgreSQLDriver" ========================================================== below is the output of showMethods('show') in two scenarios: (1) RPostgreSQL loaded, RSQLite not loaded; (2) RPostgreSQL loaded, RSQLite loaded (in that order). i'd be grateful for any help resolving or working around this issue. if possible, please include my email address in any reply. best jon mcauliffe jon at mcauli...

...class(nancycats) [1] "genind" attr(,"package") [1] "adegenet" > nancycats[1] Error in nancycats[1] : object of type 'S4' is not subsettable # "[" IS NOT USED HERE ### end R code And still, the method is defined in the environment: ### R code > showMethods("[", class="genind") Function: [ (package base) x="genind" > findMethods("[", classes="genind")$genind Method Definition: function (x, i, j, ..., drop = FALSE) { .local <- function (x, i, j, ..., loc = NULL, treatOther = TRUE,...

Any one can explain why this happens or any work arounds? > setClass('foo') [1] "foo" > setAs('foo', 'character', function(from) from) > showMethods('coerce') Function "coerce": from = "ANY", to = "array" from = "ANY", to = "call" from = "ANY", to = "character" from = "ANY", to = "complex" from = "ANY", to = "environment" from...

Any one can explain why this happens or any work arounds? > setClass('foo') [1] "foo" > setAs('foo', 'character', function(from) from) > showMethods('coerce') Function "coerce": from = "ANY", to = "array" from = "ANY", to = "call" from = "ANY", to = "character" from = "ANY", to = "complex" from = "ANY", to = "environment" from...

...e following places package:raster namespace:raster with value standardGeneric for "xyValues" defined from package "raster" function (object, xy, ...) standardGeneric("xyValues") <environment: 0x04daf14c> Methods may be defined for arguments: object, xy Use showMethods("xyValues") for currently available ones. > showMethods("xyValues") Function: xyValues (package raster) object="Raster", xy="data.frame" object="Raster", xy="SpatialPoints" object="Raster", xy="vector" object="...

Hi everyone, I'm sure this has been asked before, but I could not find the right search terms to find it. If I want to see what summarizing a model fit with lm() does, I can write "summary.lm". But what if I want to see what summarizing a model fit with lmer() (lme4 package) does? showMethods(summary) Function: summary (package base) object="ANY" object="character" (inherited from: object="ANY") object="mer" object="sparseMatrix" object="summary.mer" tells me there is a "mer" method, but "summary.mer"...

At the risk of ridicule for my deficient linear algebra skills, I ask for help using the solve.QP function to do portfolio optimization. I am trying to following a textbook example and need help converting the problem into the format required by solve.QP. Below is my sample code if anyone is willing to go through it. This problem will not solve because it is not set up properly. I hope I

...new("A", stuff = as.complex(from)) Signatures: from to target "numeric" "A" defined "ANY" "A" showMethod gives me an overview of the situation (which is much simpler/cleaner than what the note is suggesting): > showMethods("coerce") Function: coerce (package methods) from="ANY", to="A" ... from="integer", to="A" (inherited from: from="ANY", to="A") ... from="numeric", to="A" (inherited from: from=...