similar to: R-devel Digest, Vol 121, Issue 13

Circa 80 CRAN and core-R packages have duplicate export entries in their NAMESPACE files. E.g., bit 1.1.9 : c("as.bit", "as.bitwhich", "as.which", "physical", "virtual") forecast 4.1 : "forecast.lm" graphics 2.15.3 : "barplot" mcmc 0.9.1 : "morph" RCurl 1.95.3 : "curlOptions" utils 2.15.3 :

parseNamespaceFile() doesn't seem to detect misspelled directives. Looking at its code I see switch(as.character(e[[1L]]), <lots of args omitted here>, stop(gettextf("unknown namespace directive: %s", deparse(e)), call. = FALSE, domain = NA)) but this doesn't seem to function as I expect, viz. to stop with an error if I type a wrong directive.

Dear all, I have defined a generic as.ff(x, ...) and a method as.ff.function(x, ...) which converts a standard R function x into a chunked version operating on large ff objects. Everything works fine, but when registering S3method("as.ff",function) in NAMESPACE, the installation fails with some kind of parsing error: adding build stamp to DESCRIPTION installing NAMESPACE file

Hi, I was trying to get a list of S3 method for a given generic, along with the package in which they are defined, and I came across what looks like an issue in the data.frame returned in attribute 'info'. The column 'from' mostly gets the value "registered S3method for ..." except for visible methods. Is this the expected behavior? See code and output below. Thank you.

I am cleaning up the rms package to not export functions not to be called directly by users. rms uses generic functions defined in other packages. For example there is a latex method in the Hmisc package, and rms has a latex method for objects of class "anova.rms" so there are anova.rms and latex.anova.rms functions in rms. I use:

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

I have defined boolean methods for bit and bitwhich objects, for example |.bit <- function(e1,e2) and |.bitwhich <- function(e1,e2) Both methods coerce their arguments to the respective class, however if I do something like bit_obj | bitwhich_obj then I get a warning Warning message: Incompatible methods ("|.bit", "|.bitwhich") for "|" and none of the

On 15/11/2019 8:42 a.m., Herbert Braselmann wrote: > Hello, > > since Bioconductor devel branch 3.11 started, which is operating with > R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan), > my package CFAssay 1.21.0 is not built on none of all three Systems, > Linux, Windos and Mac. The error message refers to xy.coords which is > called by R function

Travis users are reporting a lot of these errors when testing packages on R 3.5: Error: package or namespace load failed for ?....? in rbind(info, getNamespaceInfo(env, "S3methods")): This problem seems to happen when a c2d4u package was compiled with R 3.6 and is loaded in R 3.5. The problem does not appear when using the same r-cran-xyz package on R 3.6. I'm not entirely sure

Hi, Could R-Core consider adding 'RtangleRuncode' and 'RtangleFinish' to the exports of utils. Their weave equivalent 'makeRweaveLatexCodeRunner' and ?'RweaveLatexFinish' are exported, as well as the other tangle utility functions 'RtangleSetup' and 'RtangleWritedoc'. The rationale is not just symmetry. ;-) I'm finishing a small package that

I find system.file() handy for writing examples, but if the user mistypes its arguments or if a package is not up to date its return value of "" can lead to trouble. This forces the example to be wordier than I'd like. E.g., the following example works > scan(what="", sep="\n", system.file("DESCRIPTION")) Read 9 items [1] "Package:

Hi, I received a bug report from a French user who told me there was something wrong with the function packageVersion(), but packageDescription() worked well. Below is the session info; I'm not sure if other French users can reproduce the error message: > packageVersion('base') Erreur : sp?cification de version incorrecte base > sessionInfo() R version 2.12.1 (2010-12-16)

I'm running R 2.11.1 on 64 bit Debian. I've had no problem installing any other CRAN packages, but installing package "gbm" fails due to: *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : .onAttach failed in attachNamespace() for 'gbm', details: call: NULL error: 'packageVersion' is not an

R-exts.pdf discribes S3method a little bit. But I want to understand more on how it is called, implemented and when to use it. I don't find it in an R session. But I see S3method() in some NAMESPACE files. > S3method Error: object 'S3method' not found > ?S3method No documentation for 'S3method' in specified packages and libraries: you could try '??S3method' I

I am writing my first R package, and I have been getting the following series of errors when I run R CMD check: * checking S3 generic/method consistency ... WARNING Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package,

Hello, since Bioconductor devel branch 3.11 started, which is operating with R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan), my package CFAssay 1.21.0 is not built on none of all three Systems, Linux, Windos and Mac. The error message refers to xy.coords which is called by R function plot.default. I found out that it has to do with the S3 object system. In my package I

Matthew Dowle wrote: > Hi, > > Try package 'data.table'. It has a concept of keys which allows you to do > exactly that. > > http://datatable.r-forge.r-project.org/ > > Matthew > > Hi Matthew, Unfortunately, the load of that library fails (it builds successfully). I'm currently looking into why. Error output looks something similar to: >

On 07/07/2015 02:05 AM, Renaud Gaujoux wrote: > Hi, > > from the man page ?methods, I expected to be able to build pairs > (class,package) for a given S3 method, e.g., print, using > > attr(methods(print), 'info'). > > However all the methods, except the ones defined in base or S4 > methods, get the 'from' value "registered S3method for print",

Thanks Kevin, this indeed clarifies a bit the S3 method registration universe. On 8 July 2015 at 15:48, Kevin Wright <kw.stat at gmail.com> wrote: > Not sure if this answers your question, but you can't unregister a method. See > > http://tolstoy.newcastle.edu.au/R/help/06/07/30791.html > > Kevin Wright > > > On Wed, Jul 8, 2015 at 5:09 AM, Renaud Gaujoux >

[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 (R-1)x(C-1)xstrata array, whose attributes are contained in other components. I define coef,