search for: allclass

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

...oesn't correspond to the default collation of R (alphabetically). I've tried to pick up on how to ensure the right collation when building R Packages by reading some previous posts and as far as I understand I've basically got two options here: 1) Put all class defs in one script, e.g. allClasses.R. 2) Manually specify the collation via the "Collate" field in the DESCRIPTION file. I'm used to organizing my classes, generics, methods etc. on a "one-per-script" basis in various subdirectories (e.g. R/classes, R/methods etc.) and try automate manual steps wherever po...

Hi, ExonFeatureSet I have an object of the above class. The following document mentioned it. http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf But I would like to see its defintion. I'm wondering if there is a way in R to give me the definition of any class? Regards, Peng

...nfirm that this is in fact an issue as I believe it to be? 2. If it is a legitimate issue, have others seen it manifested working with other packages that are not Matrix? In this case, I believe that the class union I defied is somehow interfering with the "index" class union in Matrix, R/AllClass.R, line 809 3. Why should the class union I defined interfere with the inner workings of a separate package? 4. Is this a bug in Base or Methods? Thank you for your time! Sincerely, Ezra [[alternative HTML version deleted]]

...the copy method: assign("theta",get("theta",envir=selfEnv)+0, envir=vEnv) ... but (a) this is very ugly and (b) it seems very unsafe -- as R gets smarter it should start to recognize trivial changes like x+0 and x*1 and *not* copy in these cases ... Method details: ## from R/AllClass.R, merPredD RC definition ptr = function() { 'returns the external pointer, regenerating if necessary' if (length(theta)) { if (.Call(isNullExtPtr, Ptr)) initializePtr() } Ptr }, ## ditto initializePtr = function() { Ptr <<- .Call(me...

Hi the list, Using S4, how can we create a package? In "S4 Classes in 15 pages, more or less", they put all the classes definition in a function that will be called at the opening of the library and they add "by hand" a Rd file. Is it the only way ? Is there something like "S4.package.skeleton"? Thanks Christophe

Hi R lovers, I'm looking for more information about, and implementations of abstract classes. After reading "Head First Design Patterns" (O'Reilly). I want to know whether I could use this to build an interface, i.e. a placeholder for all possible methods in the underlying subclasses. The final goal is to end up with a more flexible/extensible design than could be achieved with

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, I am trying to make a R package with S4 classes. To do so, i do as usual (when no S4 were involved, i.e without NAMESPACE file) and I've got errors in class refering to other classes in the package. So I use a NAMESPACE file to declare classes, it works fine, but now I have to declare each functions in the NAMESPACE file. Since I have a lot of functions, it's not very easy.

...luding a simple reproducible example. > 2. If it is a legitimate issue, have others seen it manifested working with > other packages that are not Matrix? In this case, I believe that the class > union I defied is somehow interfering with the "index" class union in > Matrix, R/AllClass.R, line 809 > 3. Why should the class union I defined interfere with the inner workings > of a separate package? There is no good reason ... > 4. Is this a bug in Base or Methods? This is a bug in "base R", in package 'methods'. The R core team had taken the issue up...

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

The methods package ?cbind2 includes the instruction to use via methods:::bind_activation(TRUE). This changes the default definition of cbind globally, disrupting proper evaluation in packages not using cbind2. Is cbind2 a hold-over from a time when ... could not be used for dispatch? What is a safe way for a package to use cbind2? This came up in the context of complex package dependencies

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.2.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.6.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.7.21.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.cla...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.2.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.6.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.1.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.0.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...

...tree.html... Generating api/constant-values.html... Generating api/serialized-form.html... Building index for all the packages and classes... Generating api/overview-tree.html... Generating api/index-all.html... Generating api/deprecated-list.html... Building index for all classes... Generating api/allclasses-frame.html... Generating api/allclasses-noframe.html... Generating api/index.html... Generating api/help-doc.html... Generating api/stylesheet.css... touch doc-stamp /usr/lib/jvm/java-6-openjdk/bin/jar cf libguestfs-1.9.2.jar com/redhat/et/libguestfs/IntBool.class com/redhat/et/libguestfs/PV.clas...