search for: exportclasses

Hello, I have a question concerning "setClassUnion". I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. I tried to use "setClassUnion" in a package I am currently working on. The situation is similar to the following example: The DESCRIPTION file has entries: Depends: R (>= 2.0.0), methods Imports: methods LazyLoad: yes The NAMESPACE file has

Hello, I have a question concerning "setClassUnion". I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. I tried to use "setClassUnion" in a package I am currently working on. The situation is similar to the following example: The DESCRIPTION file has entries: Depends: R (>= 2.0.0), methods Imports: methods LazyLoad: yes The NAMESPACE file has

...ds for union class To: Renaud 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")...

...it should be back compatible, and it passes the checks (on linux). But approach with caution, namespaces do change the language semantics, and we will likely encounter some surprises. The new directives, in addition to those described in Luke Tierney's article in the June, 2003 R News, are: exportClasses(...) exportMethods(...) importClassesFrom(package, ...) importMethodsFrom(package, ...) The `...' arguments are the names of classes or of generic functions as appropriate. The exportClasses and exportMethods directives export the corresponding class definitions and all the methods for the f...

...t;setClass("rpa", contains = "list", where=topenv(parent.frame())) Use package skeleton to create directory structure: >package.skeleton(name = "test",list=c("tmp")) Edit man files, add test/NAMESPACE file with the following contents: >export(tmp) >exportClasses("rpa") Use R CMD check and R CMD build to create tarball. -> No error messages. Start R, install the created package: >install.packages("test_1.0.tar.gz",repos=NULL) Test the new package: >require(test) >my.object = new("rpa") This gives the error messa...

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' fr...

...ntains = "track") setMethod( ".DollarNames", signature( x = "track", pattern = "character" ), function(x, pattern){ grep( pattern, c("foo", "bar"), value = TRUE ) } ) and the NAMESPACE : import( utils ) exportMethods( .DollarNames ) exportClasses( track, trackCurve ) When I load the package, I can call .DollarNames explicitely : > require( foo ) > x <- new( "trackCurve", x = 1:10, y = 1:10, smooth = 1:10 ) > .DollarNames( x, "f" ) [1] "foo" but completion does not work : > x$f<TAB>...

...library('woof1') Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'woof1' classes for export not defined: dog Error: package/namespace load failed for 'woof1' Execution halted Here's the NAMESPACE importFrom(graphics,plot) exportClasses("dog") exportMethods("plot","show") thanks yet again, Sincerely, Erin mailto: hodgess at gator.uhd.edu

Dear Michael, my package has setOldClass("inla") and the NAMESPACE contains exportClasses(inla) and importFrom(INLA, inla.posterior.sample) the old version of INLA uses the S3 class "inla" but does not export it. the new version of INLA has setOldClass("inla") and the NAMESPACE contains exportClasses(inla) installing my package in combination with an older INLA ver...

...eproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A", function(object) cat("A\n")) setMethod("show", "B", function(object) cat("B\n")) with NAMESPACE import(methods) exportClasses(A, B) exportMethods(show) This creates the object and illustrated expected behavior ~/tmp$ R --vanilla --slave -e "library(PkgA); b = new('B'); save(b, file='b.Rda'); b" B Loading PkgA before the object leads to correct dispatch ~/tmp$ R --vanilla --slave -e...

I'm creating a package for my own use that uses some S4 classes but no methods. I have a file called NAMESPACE it contains the line: exportClasses("foo") and at the top of the R file I have setClass("foo", representation(x="numeric") and the line: .onLoad<-function(libname,pkgname) When I run R CMD check I get Syntax error in the only R file. If I comment out the .onLoad function I get a package/namespac...

...such... ## From various other R files... setMethod("image", signature(x="RPPA"), ... setMethod("image", signature(x="RPPADesign"), ... And then exported them for use outside the package. ## NAMESPACE import(methods) importFrom("graphics", image) exportClasses(....) exportMethods(image) If the problem is because of the exportMethods(), I'm left stumped as to how to work around this. Making our S4 objects useable externally was kind of the point. Source package available, if needed. oompa <- "http://bioinformatics.mdanderson.org/OOMPA/2.1...

...atchSignature(signature, fdef, where) : in the method signature for function "plot" no definition for class: "validation" ** help *** installing help indices ... Maybe my NAMESPACE file looks wrong. Has anybody an idea how it has to look like to solve this problem? ( I use exportClasses(...), exportMethods(...). ) I have 3 classes: 'prediction', 'validation', 'nvalidation' which have a plot function. There's no warning for class 'nvalidation' but for the other two. Any suggestions? Greetings. Dan

...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, unique) exportClasses(B) exportMethods(unique) There is a man/ page for each package, but no other documentation. Yet R CMD check PkgA_1.0.tar.gz says * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK and for Pkg B we only get * checking for missing docu...

...t;NAMESPACE") [1] "blah( nada )" "blee( nil )" "export( outDS )" > parseNamespaceFile("",".") # now parse it $imports list() $exports [1] "outDS" $exportPatterns character(0) $importClasses list() $importMethods list() $exportClasses character(0) $exportMethods character(0) $exportClassPatterns character(0) $dynlibs character(0) $nativeRoutines list() $S3methods [,1] [,2] [,3] > So, it picked up 'export' and ignored the other two lines. Chuck p.s. > sessionInfo() R version 2.12.0 (2010-10-15) Plat...

...g lines in the zzz.R file in the R directory while creating an R package. >setClass("rpa", contains="list") >show.rpa <- function (...) {cat("rpa object \n")} The corresponding lines were also added to NAMESPACE file: >importMethodsFrom(methods,show) >exportClasses(rpa) >S3method(show,rpa) The CMD check and CMD build do not produce warning messages related to this issue (only warnings are about missing .Rd files). After installing the package ('test' is the package name) I start R and require the new package: > require(test) Loading required...

...kage A defines an S4 generic 'foo' and as well as S4 methods for 'foo' and has exportMethods("foo") in its NAMESPACE file. Package B defines another method for 'foo' for class "bar" and has importFrom(A, "foo") exportMethods("foo") exportClasses("bar") in its NAMESPACE file. Should Package B also have Package A in the 'Depends:' field of the DESCRIPTION file or is it correct to import Package A only? Finally, Package C has a single exported function named 'myfunc' which needs to use the method for 'foo...

...tFrom("KernSmooth", "bkde2D") importFrom("RColorBrewer", "brewer.pal") importFrom("utils", "getFromNamespace", "assignInNamespace") importFrom("MASS", "cov.rob") S3method("$", "cytoFrame") exportClasses("cytoFrame", "cytoSet") exportMethods("colnames", "colnames<-", "description", "description<-", "exprs", "exprs<-", "length", "[", "[[", &...

...tFrom("KernSmooth", "bkde2D") importFrom("RColorBrewer", "brewer.pal") importFrom("utils", "getFromNamespace", "assignInNamespace") importFrom("MASS", "cov.rob") S3method("$", "cytoFrame") exportClasses("cytoFrame", "cytoSet") exportMethods("colnames", "colnames<-", "description", "description<-", "exprs", "exprs<-", "length", "[", "[[", &...

...lid' Execution halted ERROR: lazy loading failed for package 'clValid' ** Removing '/Users/guybrock/Documents/projects/DattaPackages/Cluster/clValid_0.5-4.Rcheck/clValid' The NAMESPACE file is below, .onLoad <- function(lib, pkg) require(methods) importFrom(graphics, plot) exportClasses(clValid) exportMethods(clusters, clusterMethods, nClusters, measNames, measures, optimalScores, plot, print, show, summary) S3method(print,sota) S3method(plot,sota) export(clValid, sota, dunn, connectivity, BHI, BSI, stability, matchGO) My question is - how can I locate the source of the cyclic de...