similar to: S4 NAMESPACE method imports and exports do not include (promoted?) generics

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

Suppose I have a function funcA() in package pkgA that requires function funcB() from another package pkgB under certain circumstances. Those circumstances are rare though, so I put package pkgB under 'Suggests', and use this in funcA() when those circumstances do arise: if (require("pkgB", quietly=TRUE)) { pkgB::funcB(...) } else { stop("Please install package

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:

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

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)

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",

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

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, 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

I am trying to build the latest version of R (3.6.2) on a CentOS system running 7.7.1908. I have been able to build previous versions of R up to and including 3.5.3 successfully. Starting with 3.6.0 the "make check" step fails with errors relating to "pdflatex" being missing. So, I installed texlive-latex (and the 100 other rpm dependencies) then tried rebuilding R.

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

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

Hi Sebastian, On Thursday, 23 August 2018 16:45:27 CEST Sebastian Meyer wrote: > The `-l` option for some `zypper` subcommands is short for > `--auto-agree-with-licenses` and not available on the `zypper rm` command. > No problem with the patch, just one question: can it happen that zypper may decide to install packages when removing others, e.g. to keep some other

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 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

Hi, not sure this is a bug or just an unavoidable undesirable side-effect -- or just me that does not do the right thing. Consider the code and output below. It creates 2 packages: * pkgA * pkgB that creates a method for a generic defined in pkgA Changes in a method for the generic in pkgA (after re-installing pkgA) are not reflected in pkgB, unless pkgB is re-installed against the new

Hi, in 'Writing R Extensions" of R v2.10.0, under Section 'Cross-references' (2009-09-07) it says: 1. "The markup \link{foo} (usually in the combination \code{\link{foo}}) produces a hyperlink to the help for foo. Here foo is a topic, that is the argument of \alias markup in another Rd file (possibly in another package)." 2. "You can specify a link to a different

Hi, Let me justify building R from source. While I can obtain R built for me under Ubuntu, I tend to build it from scratch as we use a NFS-shared build as well as shared R libraries for all the bioinfo staff at this company. Only one build and one set of packages to ensure uniformity across all workstations. My problem is that despite using a pretty standard build process, I am failing at the

Hi ... I came across an old post on R-devel that describes a situation very similar to one I find myself in: https://stat.ethz.ch/pipermail/r-devel/2006-December/043917.html As you can see in Gregor's example, the situation is that if I am writing Pkg A, I want to detect if Pkg B exists - if so use some functionality from there, otherwise do something else. To me this reads as being in

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