similar to: R CMD check thinks my function is an S3 method

Hi Since I believe 3.6, there is a message when loading a package that overwrites S3 methods, reading like "Registered S3 method overwritten by...". Should this message be included in the xxx.Rout.save files saved in the tests/ folder of a package? It seems R CMD check is not happy about it? I simply ran R CMD BATCH xxx.R xxx.Rout.save but running later on R CMD check on the package

I'm getting an R CMD check warning with a package (call it package A) that defines an S3 method but not the generic. The generic is defined in another package (package B). Package A imports the S3 generic from B. And there's one additional detail: the generic overrides a function in the stats package. I've created a minimal test package which reproduces the problem:

I'm trying to R CMD check a package, and I'm getting the 'checking S3 generic/method consistency' warning. I have written a function 'gamma.dist' which is _not_ an S3 method, but happens to collide with the 'gamma' function from the R::base namespace. Is there a way of telling CMD check that the name is intentional and is not meant to be an S3 method? My function

Hi, I'm having some trouble setting methods for the qr family of functions. I believe I have distilled my misunderstanding in the code snippet below: foo <- function(x, ...) UseMethod("foo") foo.default <- function(x) { } # foo setGeneric(name = "foo", useAsDefault = foo) setMethod("foo", signature(x="bar"), function(x, ...) { } )

When creating a package, I would like a way to tell R that a function with a period in its name is not a method. I'm writing a package now with a modified version of qr.R. R CMD check gives warnings: * checking S3 generic/method consistency ... WARNING qr: function(x, ...) qr.R: function(qr, complete, pivot) See section ‘Generic functions and methods’ of the ‘Writing R Extensions’

Hi, I have a 900,000,000*9,000 matrix where I need to calculate the correlation between all entries along the smaller dimension, thus creating a 9k*9k correlation matrix. This matrix is too big to be uploaded in R, and is saved as a binary file. To access the data in the file I use mmap and some api-functions (to get all values in one row, one column, or one particular value). I'm looking for

2017-09-22 19:04 GMT+02:00 Michael Lawrence <lawrence.michael at gene.com>: > The %*% function is a primitive. As it says in the documentation under > ?Methods_Details > > Methods may be defined for most primitives, and corresponding > metadata objects will be created to store them. Calls to the > primitive still go directly to the C code, which will

Hello everyone, I'm trying to update the locfit package so that it passes package check in R 2.6.0. However, the check seems to think some of the functions with dot in the names are S3 methods (thus warns about the format of the \usage{} part) when they are not. Can anyone recommend a workaround for this? I tried reading R-exts, but couldn't find any hint. I'd very much appreciate

> There is formally no such thing as an S3 class. Just S3 objects with a > class attribute. You could extend a base class with an S4 class, like > setClass("IntegerWithUnits", slots=c(units="Units"), > contains="integer"). Sure, that's a disruptive change, but it would be > in the right direction. > > Extending base classes is always a risky

I am trying to extend an S3 method to work with an S4 object as well as the S3 objects it works with, but UseMethod does not seem to recognize the S4 class and dispatches to the default method. Is this to be expected or should I be looking for an error in my code? If it is not an error in my code, is there an easy way to do this, or do I have to convert the generic to S4 and then make those

Dear List, In one of my packages I have an S3 method for the plot3d generic function from package rgl. I am trying to streamline my Depends entries but don't know how to have plot3d(foo) in the examples section for the plot3d method in my package, without rgl being in Depends. Note that I importFrom(rgl, plotd3d) and register my S3 method via S3Method() in the NAMESPACE. If rgl is not in

I have updated the rms package to extensively use NAMESPACE. I cannot get certain S3 methods to dispatch. For example I have in NAMESPACE S3method(anova, rms) S3method(latex, anova.rms) anova.rms produces an object of class "anova.rms" and there is a latex.anova.rms function in rms. But when I do latex(anova(fit)) I get an invocation of latex.default. I have tried using

Hi all, I'm trying to implement the matrix multiplication operator, which is S4 generic, for an old-style S3 class. The following works as expected: x <- 1:10 class(x) <- "myClass" setOldClass("myClass") setGeneric("myMethod", function(x, y) standardGeneric("myMethod")) setMethod("myMethod", c("myClass", "myClass"),

Hi, Let's say one has an object with multiple classes, and a generic function to apply to it has associated S3 methods for more than one of those classes. Further, the method it chooses (I do not know how; some order in the class vector?) is not the suitable one and it produces an error. Would there be some way to make the generic function to choice the correct method, or in case that for

Dear R-devel, Recent versions of R CMD check have been flagging apparent S3 methods that are not registered in the NAMESPACE as such. In most situations this is very helpful. However, I have few cases in existing packages where we have unfortunately named functions using a "." in them that makes them appear as S3 methods when they are not. As there is no existing class

Full_Name: Jerome Asselin Version: 1.7.1 OS: Red Hat Linux 7.2 Submission from: (NULL) (24.77.125.119) Setting the parameter na.action=na.omit should remove incomplete records in princomp. However this does not seem to work as expected. See example below. Sincerely, Jerome Asselin data(USArrests) princomp(USArrests, cor = TRUE) #THIS WORKS USArrests[1,3] <- NA princomp(USArrests, cor =

Hello, I just notice this: > x <- c(1:4,0:5, 4, 11) > library(pastecs) Loading required package: boot > tp <- turnpoints(x) > extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE) [1] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Warning message: arguments after the first two are ignored in: UseMethod("extract", e, n, ...) >

Hey there, I want to stream my app''s media from Amazon S3. I''ve gotten the basics down, having uploaded files, set their permissions for public access, and now can use their S3 URLs wherever I need them. My question is this: can I restrict access to my S3 files to only within the context of the pages that my application serves? I want to avoid people just looking at the

Dear R users: I have some difficulties analizing data with mixed effects NLME and the last version of R. More concretely, I have a repeated measures design with a single group and 2 experimental factors (say A and B) and my interest is to compare additive and nonadditive models. suj rv A B 1 s1 4 a1 b1 2 s1 5 a1 b2 3 s1 7 a1 b3 4 s1 1 a2

If a package defined an S3 generic and an S4 generic for the same function (so as to add methods for S4 classes to the existing code), how do I set up the namespace to have them exported? With import(stats) exportMethods(bigglm) importClassesFrom(DBI) useDynLib(biglm) export(biglm) export(bigglm) in NAMESPACE, the S3 generic is not exported. > methods("bigglm") [1] bigglm.RODBC*