similar to: Options that are local to the package that sets them

pkgA's NAMESPACE has importFrom(graphics, plot) exportClasses("A") exportMethods("plot") R/foo.R has setClass("A") setMethod("plot", "A", function(x, y, ...) {}) During R CMD INSTALL pkgA_1.0.tar.gz we are told ** preparing package for lazy loading Creating a generic function for 'plot' from package

Hi, SETUP: Consider three packages PkgA, PkgB and PkgC. PkgA defines a generic function foo() and exports it; export(foo) PkgB imports PkgA::foo() and re-exports it; importFrom(PkgA, foo) export(foo) PkgC imports everything from PkgA and PkgB: imports(PkgA, PkgB) PROBLEM: Loading or attaching the namespace of PkgC will generate a warning: replacing previous import by

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

I was wondering: are the downstream dependencies of a package rebuilt when a package is updated on CRAN? (I'm referring to the binary packages, of course.) The reason I ask is because there are cases where this can cause problems. Suppose that when pkgB is built, it calls pkgA::makeClosure(), which returns a closure that refers to a function in pkgA. Suppose this code is in pkgA 1.0:

>>>>> Martin Morgan <mtmorgan at fredhutch.org> >>>>> on Mon, 11 May 2015 10:18:07 -0700 writes: > On 05/10/2015 08:19 AM, Martin Morgan wrote: >> Loading an S4 object from a file without first loading the library sometimes (?, >> the example below and actual example involves a virtual base class and the show >> generic)

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Dear list, // IN SHORT // What are possible workarounds to "consolidate" documentation for S4 methods that are scattered across different packages (generic and some custom methods in one package, additional custom methods in another package) in a *single* Rd help file while using package 'roxygen2' to generate the actual Rd files? // ADDITIONAL INFORMATION // First of, here

I have received three distinct (non-)bug reports where someone claimed a recent package of mine was broken ... simply because the macOS binary was not there. Is there something wrong with the cronjob providing the indices? Why is it pointing people to binaries that do not exist? Concretely, file https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.4/PACKAGES contains Package:

Hi, This strange warning happen sometimes when running 'R CMD check': * checking whether the package can be loaded with stated dependencies ... WARNING Error : .onLoad failed in loadNamespace() for ?pkgB?, details: call: length(new("A")) error: could not find function "loadMethod" Error: package/namespace load failed for ?pkgB? Execution halted

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and exporting a generic in the namespace will also export its methods. and Note that importMethodsFrom will also import any generics defined in

I've installed R-devel R Under development (unstable) (2014-07-09 r66111) Platform: x86_64-apple-darwin13.1.0 (64-bit) and am trying to resolve some problems that I am seeing with my SparseM package. In prior versions I explicitly had: setGeneric("image", function(x, ...) standardGeneric("image")) and then used setMethod to define a method for the class matrix.csr but

> On 30/10/2019 9:08 a.m., peter dalgaard wrote: > > You can fairly easily work around that by saving and restoring .Random.seed. This is actually quite tedious to get correct; it requires you to under how and when .Random.seed is set, and what are valid values on .Random.seed. For instance, a common mistake (me too) is to reset to .GlobalEnv$.Random.seed <- NULL in a fresh R

Hi, I'd like to list all package PkgA functions that another package PkgB use via Depends or Imports (ignoring Suggests for simplicity). As long as PkgB uses importFrom("PkgA", ...) it's just a matter of parsing the NAMESPACE file or inspecting asNamespace("PkgB")$.__NAMESPACE__.$imports. However, what can be done in case PkgB uses import("PkgA")? Is there

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" PkgA promotes 'unique' to a generic and exports that DESCRIPTION: Imports: methods R/f.R: setGeneric("unique") NAMESPACE: export(unique) and PkgB creates and exports a method on unique DESCRIPTION Imports: methods, PkgA R/f.R: setClass("B",

In this post https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html a package author reports that S4 dispatch fails. I can reproduce this with a PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has DESCRIPTION with Depends: intervals Imports: graphics NAMESPACE: importFrom(graphics, "plot") export("plot")

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)

The `-l` option for some `zypper` subcommands is short for `--auto-agree-with-licenses` and not available on the `zypper rm` command. --- customize/customize_run.ml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/customize/customize_run.ml b/customize/customize_run.ml index f92e9a199..3eacdaca0 100644 --- a/customize/customize_run.ml +++ b/customize/customize_run.ml @@ -181,7

I am only reporting this because it is the current release branch and not devel. R-2.13 from svn revision 55957 builds fine, but fails make check. This happened with a fresh svn checkout 12 hours ago and it still happens as of now. Two days ago I could build R-2.13 and it passed make check on the same system, so I doubt it is a system problem. But just in case my system details are a fresh

Dear All, What is the preferred way for Package A, to initialize a cluster, and load Package B on all nodes? I am writing a package that parallelizes some functions through the use of a cluster if useRs are on a Windows machine (using parLapply and family). I also make use of another package in some of my code, so it is necessary to load the required packages on each slave once the cluster is