similar to: R CMD check warning message "print.check_code_usage_in_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

Hello, I am a new R user not at ease with installing and updating R package under Ubuntu (Hardy), so that I cannot run R anymore ...! I initially installed r version 2.6.2.2 (amd64) from Intrepid instead of Hardy (!), but it worked. I tried to update to version 2.9, but did not succeeded:    (1) I added to my /etc/apt/sources.list an entry :           deb

Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method markup and not > their full name. > See the chapter 'Writing R documentation files' in manual 'Writing R > Extensions'. The package I'm looking at is one that I did not write which has 34 .Rd files. This warning does not

Hi all, For the R package bujar, the warnings below were generated on CRAN's Windows systems. The package uses some Fortran subroutines. I would appreciate any advice to eliminate the warnings. By the way, similar warnings were generated to some unrelated R packages as well: https://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/imputeTS-00check.html. Thanks in advance. Zhu

The generic stats::median method is defined as median <- function (x, na.rm = FALSE) {UseMethod("median")} I suggest that this should become median <- function (x, na.rm = FALSE, ...) {UseMethod("median")} This would allow additional S3 methods to be developed with additional arguments. Currently I have to over-ride this generic definition in the demography

>>>>> Martin Maechler <maechler at stat.math.ethz.ch> >>>>> on Mon, 27 Feb 2017 10:42:19 +0100 writes: >>>>> Rob J Hyndman <Rob.Hyndman at monash.edu> >>>>> on Wed, 15 Feb 2017 21:48:56 +1100 writes: >> The generic stats::median method is defined as median <- >> function (x, na.rm = FALSE)

Hello! I am working on a package where Enhances field seems to be a plausible option. When I add package, say coda, to this field, I get the following warning with recent R-devel: ---- * checking for working latex ... OK * using log directory '/home/ggorjan/programs/R/devel/test.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-12-06 r40129) * checking for file

I posted on this topic to r-help, but never got a sufficient answer, so I'm reposting here. [Env: R 2.11.1, Win Xp, using Eclipse/StatET] In a package I'm working on, I want to create as.matrix() and as.array() methods for a particular kind of object (log odds ratios). These are returned in a loddsratio object as the $coefficients component, a vector, but really reflect an underlying

* checking S3 generic/method consistency ... WARNING Warning: use of NULL environment is deprecated Warning: use of NULL environment is deprecated See section 'Generic functions and methods' of the 'Writing R Extensions' manual. I don't get any other warnings or errors. Can anyone suggest what the problem might be? (R2.3.0, OS X) Thanks, Hadley

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

CCing r-devel. On Tue, 14 May 2019 at 02:11, Pavel Krivitsky <pavel at uow.edu.au> wrote: > > Dear All, > > I've run into this while updating a package with unfortunately named > legacy functions. It seems like something that might be worth changing > in R, and I want to get a sense of whether this is a problem before > submitting a report to the Bugzilla. > >

Hi all, in my package I have a function with name plot.cor (this function is inherited from another legacy package). According to CRAN package checks reports, the check apparently thinks plot.cor is a method for the plot generic (I hope I'm using the correct terminology). checking Rd \usage sections ... NOTE S3 methods shown with full name in documentation object 'plot.cor':

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

Dear all, "Writing R Extensions" explicitly says that A method must have all the arguments of the generic, including ... if the generic does. A method must have arguments in exactly the same order as the generic. If the generic specifies defaults, all methods should use the same defaults. This is clear. R CMD check even checks for this. But then how is it possible that

Hi, I have a S3 package with namespace called "myS3Pkg". Inside my package I would like to create a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"),

> And in general a developer would avoid masking a function > in a base package, so as not to require the user to distinguish > between stats::density() and igraph::density(). Maybe the > example is not meant literally. The 'filter' function in the popular 'dplyr' package masks the one that has been in the stats package forever, and they have nothing in common, so that

>>>>> Lionel Henry <lionel at rstudio.com> >>>>> on Fri, 1 Sep 2017 13:47:07 +0200 writes: > A package should probably never register a S3 method unless it owns > either the generic or the class. I agree... (and typically it does "own" the class) > Here `formula.tools` owns neither. i.e., it neither defines as.character()

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’

Dear all, in the package its the print() method does not seem to correctly work in all circumstances: > selectMethod(print, "its") Method Definition: function (x, ...) { print(x@.Data <mailto:x@.Data> , ...) } <environment: namespace:its> Signatures: x target "its" defined "its" > fundPME.lst[[1]]$irr An object of