search for: pkgb

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 'pkgB...

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: makeClosure <- function() { function() { funA() } } funA <- function() "funA was called!" And this is the code in pkgB: foo <- pkgA::make...

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 version of pkgA. I understand this may be linked to lazy-loading, which somehow keeps the old method ver...

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 warni...

...Note that importMethodsFrom will also import any generics defined in the namespace on those methods However, if 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", representation(b="numeric")) setMethod(unique, "B", function(x, incomparables=FALSE, ...) unique(x at b)) NAMESPACE: importFrom(PkgA, uni...

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 It looks like this package (or one of its dependent packages) has an unstated dependence on a standard 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("...

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' dire...

...d 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) exportMethods(unique) PkgB introduces a new class and method setClass("B") unique.B <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "B", unique.B) and in the NAMESPACE has import(methods) importFrom(PkgA, unique) S3method(unique, B) exportMethods(unique) Unfortuan...

...Gaujoux <renaud at mancala.cbio.uct.ac.za> Cc: bioc-devel at r-project.org, dupan.mail at gmail.com I can replicate this with a simpler example, where PkgA has setClass("A", representation(x="numeric")) with NAMESPACE import(methods) exportClasses("A") PkgB has setClass("B", contains="A") NAMESPACE import(methods) importClassesFrom("PkgA", "A") exportClasses("B") and then library(PkgA); library(PkgB) setClassUnion("C", c("matrix", "A")) setGeneric("...

...ring package for lazy loading Creating a generic function for 'plot' from package 'graphics' in package 'pkgA' ** help No man pages found in package ?pkgA? *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pkgA) pkgB has in its DESCRIPTION Depends; pkgA with NAMESPACE importFrom(graphics, plot) exportClasses("B") exportMethods("plot") R/bar.R has setClass("B") setMethod("plot", "B", function(x, y, ...) {}) During R CMD INSTALL pkgB_1.0.ta...

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

...est("-d", pkgSrcPath)) { + ## could use file.copy(recursive = TRUE) + system(paste('cp -r', shQuote(pkgSrcPath), shQuote(tempdir()))) + pkgPath <- file.path(tempdir(), "Pkgs") + op <- options(warn=2) # There should be *NO* warnings here! + ## pkgB tests an empty R directory + dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE, + showWarnings = FALSE) + p.lis <- c("pkgA", "pkgB", "exS4noNS", "exNSS4") + for(p. in p.lis) { + cat("bu...

...tion 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 the wheelhouse of what 'Suggests' is supposed to imply, as per the R Extensions manual. The problem here is that if PkgB is put down as 'Suggests', it is required for R CMD check to pass which seems to defeat the purpose of this exercise a bit. If one puts it as 'Enhances' one gets a NOTE earlier in check but then the WARNING described in this post due to the require() call. Is there a good way ar...

...-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 dependency/relationship satisfied? For example: 1) package PkgA depends on PkgB | PkgC 2) when installing PkgA, PkgB is installed 3) you try to remove PkgB, and zypper decides to install PkgC to keep PkgA installed Of course the example above is overly simplified -- though, can the above happen? Thanks, -- Pino Toscano

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

...scenario that some package (say 'pkga') contains the *generic* method/function 'foo()' as well as *some* custom methods (for different data types of the available signature arguments). Now, let's suppose that someone using 'pkga' and building a new package (say 'pkgb') would like to build upon the generic method 'pkga::foo()' and provide some more custom methods for it. When he sticks to the suggested workflow (especially with respect to the way the roxygen2 code is written), then R CMD check will rightly(!) complain that an Rd file with the res...

...9; make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/opt/apps/x86_64/R/src/R-3.2.5/tests' make: *** [check] Error 2 > cd tests > tail -30 reg-packages.Rout.fail *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pkgB) Loading required package: pkgB building package exNSS4 ... installing package exNSS4 using file exNSS4_1.1.tar.gz ... * installing *source* package 'exNSS4' ... ** R ** preparing package for lazy loading Creating a generic function for 'plot' from package 'graphics' in pac...

...;, shQuote(pkgSrcPath), shQuote(tempdir()))) + } > pkgPath <- file.path(tempdir(), "Pkgs") > if(!dir.exists(pkgPath)) { + message("No valid 'pkgPath' (from 'pkgSrcPath') - exit this test") + if(!interactive()) q("no") + } > > ## pkgB tests an empty R directory > dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE, + showWarnings = FALSE) > p.lis <- c(if("Matrix" %in% row.names(installed.packages(.Library))) + c("pkgA", "pkgB", "pkgC&quot...

...s] Error 1 make: *** [check] Error 2 Looking at reg-packages.Rout.fail shows: > > ## else w/o clause: > ## could use file.copy(recursive = TRUE) > system(paste('cp -R', shQuote(pkgSrcPath), shQuote(tempdir()))) > pkgPath <- file.path(tempdir(), "Pkgs") > ## pkgB tests an empty R directory > dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE, + showWarnings = FALSE) > p.lis <- if("Matrix" %in% row.names(installed.packages(.Library))) + c("pkgA", "pkgB", "exNSS4")...