search for: allgeneric

I've attached a script I wrote that pulls all the setGeneric definitions out of a set of R files and puts them in a separate file, default allGenerics.R. I thought it might help others who find themselves in a similar situation. The "situation" was that I had to change the order in which files in my package were parsed; the scheme in which the generic definition is in the "first" file that has the corresponding setMethod br...

Where should the setClass() ('methods' package) calls be placed in a package? I try to follow a one-class-one-file principe, but since setClass("ClassA", "ClassB") has to come a after setClass("ClassB", [snip]) it is not possible to fully follow this rule. So the best I can do now is to put all setClass() calls in a file named "000.R" (I know this

...> setClass("track", representation(x="numeric", y="character")) [1] "track" > setGeneric("max", group="Summary") [1] "max" > setMethod("Summary", signature(x="track"), function(x, ..., na.rm) callGeneric(x at x, ..., na.rm)) [1] "Summary" > dd<-new("track", x=c(1,2), y="abc") > max(dd) [1] -Inf Warning message: no finite arguments to max; returning -Inf > showMethods("max") Function "max": na.rm = "ANY" na.rm = &quo...

...r production packages no longer builds under R-2.15.0 with the following message. ** testing if installed package can be loaded Error: Function found when exporting methods from the namespace 'SuperCurve' which is not S4 generic: 'image' Possibly relevant clues follow: ## From R/AllGenerics.R if (!isGeneric("image")) { setGeneric("image", function(x, ...) standardGeneric("image")) } We have done the same for many S3 generics, converting them to S4 and adding specific method-combinations as such... ## From various other R files... set...

Hi, I have a BioC infra-structure package that works fine (I can build, check and load it successfully) on revision r53950. The very same package fails on r54591 with the error below: Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space dependency detected when loading ?oligoClasses?, already loading ?oligoClasses? I don't see anything

Hello R-Team, May you help me to post a 'S4-creating Package Problem'? Thanks already now for supporting. The problem sounds like: Hello R forum, while compiling my R-package these 'Warnings' occur: ... Warnung in matchSignature(signature, fdef, where) : in the method signature for function "plot" no definition for class: "prediction" Warnung in

Hello everyone. R-2.12.0, suse linux 11.3. I am debugging a package that uses S4 methods and R CMD check gives the following warning: > Warning in methods::findMethods(g, env) : > non-generic function 'mdm' given to findMethods() > See the information on DESCRIPTION files in the chapter 'Creating R > packages' of the 'Writing R Extensions' manual. I

...getVirtual(), mlistMetaName(), removeMethodsObject() and seemsS4Object() are defunct. o Use of a non-integer .Random.seed is now an error. (R itself has never generated such values, but user code has, and R >= 2.6.0 has given a warning.) o methods::allGenerics() is deprecated. o In package installation, SaveImage: yes is now ignored, and any use of the field will give a warning. o unserialize() no longer accepts character strings as input. o The C macro 'allocString' has been removed -- use 'mkChar' and...

...getVirtual(), mlistMetaName(), removeMethodsObject() and seemsS4Object() are defunct. o Use of a non-integer .Random.seed is now an error. (R itself has never generated such values, but user code has, and R >= 2.6.0 has given a warning.) o methods::allGenerics() is deprecated. o In package installation, SaveImage: yes is now ignored, and any use of the field will give a warning. o unserialize() no longer accepts character strings as input. o The C macro 'allocString' has been removed -- use 'mkChar' and...

...to specify restricted models. o A new function smoothScatter has been added to package 'graphics'. It is appropriate for very dense scatter plots and uses density estimation and color to reflect density of plotting. DEPRECATED & DEFUNCT o allGenerics() is defunct. o Use of allocVector(CHARSXP ...) is defunct and gives an error. o The compatibility define for graphics structure NewDevDesc in GraphicsDevice.h has been removed. o Support for versioned installs (R CMD INSTALL --with-package-versions and install...

...to specify restricted models. o A new function smoothScatter has been added to package 'graphics'. It is appropriate for very dense scatter plots and uses density estimation and color to reflect density of plotting. DEPRECATED & DEFUNCT o allGenerics() is defunct. o Use of allocVector(CHARSXP ...) is defunct and gives an error. o The compatibility define for graphics structure NewDevDesc in GraphicsDevice.h has been removed. o Support for versioned installs (R CMD INSTALL --with-package-versions and install...

...FCPIFCPLAGS, nor CXX98 and similar. * Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20-8.31 has been removed. * Defunct functions mem.limits(), .readRDS(), .saveRDS(),..find.package(), and .path.package() from package base and allGenerics(), getAccess(), getAllMethods(), getClassName(), getClassPackage(), getExtends(), getProperties(), getPrototype(), getSubclasses(), getVirtual(), mlistMetaName(), removeMethodsObject(), seemsS4Object(), traceOff(), and traceOn() from methods have been removed. C-LEVEL FA...

...FCPIFCPLAGS, nor CXX98 and similar. * Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20-8.31 has been removed. * Defunct functions mem.limits(), .readRDS(), .saveRDS(),..find.package(), and .path.package() from package base and allGenerics(), getAccess(), getAllMethods(), getClassName(), getClassPackage(), getExtends(), getProperties(), getPrototype(), getSubclasses(), getVirtual(), mlistMetaName(), removeMethodsObject(), seemsS4Object(), traceOff(), and traceOn() from methods have been removed. C-LEVEL FA...

...FCPIFCPLAGS, nor CXX98 and similar. * Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20-8.31 has been removed. * Defunct functions mem.limits(), .readRDS(), .saveRDS(),..find.package(), and .path.package() from package base and allGenerics(), getAccess(), getAllMethods(), getClassName(), getClassPackage(), getExtends(), getProperties(), getPrototype(), getSubclasses(), getVirtual(), mlistMetaName(), removeMethodsObject(), seemsS4Object(), traceOff(), and traceOn() from methods have been removed. C-LEVEL FA...