similar to: CRAN indices out of whack (for at least macOS)

Dirk, yes, thanks, the edge server that serves the Mac binaries to CRAN has run out of disk space (due to size of CRAN itself) so the sync was incomplete. It is fixed now -- you can try by using the macos master server as mirror: https://r.research.att.com/ and it will propagate through other mirrors as usual. Thanks, Simon > On Jan 31, 2018, at 1:34 PM, Dirk Eddelbuettel <edd at

Although it may not have been the cause of this particular index inconsistency, there are other causes of intermittent index inconsistencies. They could be avoided if there were a different directory structure on CRAN servers. One of the causes of inconsistencies is caching. With cloud.r-project.org (note that this is not cran.r-project.org), the there is a CDN in front of the server; the CDN has

Bumping this as we now have two more issue tickets filed and a fresh SO question. Is anybody looking at this? Simon? Dirk On 30 January 2018 at 15:19, Dirk Eddelbuettel wrote: | | 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

Hi, I am getting an error from one of the test files tests/reg-tests-1.R using the unstable version (r50179). (i've learned my lessons; this is a clean build.) The tail of reg-tests-1.Rout.fail is Loading required package: myTst building package pkgA ... installing package pkgA using file pkgA_1.0.tar.gz ... Error in as.octmode(mode) : invalid digits Error in install.packages(r, lib =

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)" 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",

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

Dear all, In a package, I defined a method for "summary" using setMethod(summary, signature="abc") for my class "abc", but when the package is loaded, the function "summary(x)" where x is of class "abc" seems to have called the default summary function for "ANY" class. Shouldn't it call the method I have defined? How could I get

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",

Dear All, I am trying to do the following, and could use some hints. Suppose I have a package called pkgA. pkgA exposes an API that includes setting some options, e.g. pkgA works with color palettes, and the user of the package can define new palettes. pkgA provides an API to manipulate these palettes, including defining them. pkgA is intended to be used in other packages, e.g. in pkgB1 and

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

I?d like to solicit some advice on a debugging problem I have in the quantreg package. Kurt and Brian have reported to me that on Debian machines with gfortran 9 library(quantreg) f = summary(rq(foodexp ~ income, data = engel, tau = 1:4/5)) plot(f) fails because summary() produces bogus estimates of the coefficient bounds. This example has been around in my R package from the earliest days of 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

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

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

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'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