search for: classrepresentation

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

...any help resolving or working around this issue. if possible, please include my email address in any reply. best jon mcauliffe jon at mcauliffe.com (1) > showMethods('show') Function: show (package methods) object="ANY" object="classGeneratorFunction" object="classRepresentation" object="dbObjectId" object="envRefClass" object="function" (inherited from: object="ANY") object="genericFunction" object="genericFunctionWithTrace" object="MethodDefinition" object="MethodDefinitionWithTrace"...

...dArgs2", function( .Object, f, ...) callNextMethod( .Object, function( x, y ) f( x, y, ... ) )) Everything works well within a R session but I can build the package. If I look at the internal R file that this created I get `.__C__BindArgs` <- <S4 object of class structure("classRepresentation", package = "methods")> `.__C__BindArgs2` <- <S4 object of class structure("classRepresentation", package = "methods")> `.__M__initialize:methods` <- <S4 object of class structure("MethodsList", package = "methods")> `.__T_...

...Data) design <- cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- lmFit(eset,design)   But I keep getting an eroor message after "lmFit" that says: Error in possibleExtends(cl, class2, class1Def, class2Def) : trying to get slot "subclasses" from an object (class "classRepresentation") that is not an S4 object   I am using R-2.9.2. Whats happening now? I have done exactly the same commands in another computer and it works fine. I forgot which R version it was. But after installing the latest version nothing works. Pls advice...   Regards, Wendy [[alternative HTM...

'?removeClass' shows that 'removeClass' is from package 'package:methods'. Is there a command which can show me all the functions and the classed defined in a package such as 'package:methods'?

...class instances. How is the version argument to setClass is intended to work? It appears to want an externalptr, but that seems odd to me. setClass("FOO", representation(x="numeric"), version="1.2.3") Error in validObject(.Object) : invalid class "classRepresentation" object: invalid object for slot "versionKey" in class "classRepresentation": got class "character", should be or extend class "externalptr" The use case I'm interested in is: A user has a serialized instance foo of class FOO in old.rda....

...shared BLAS, R profiling Capabilities skipped: ICU Options not enabled: memory profiling make fails at: byte-compiling 'methods' initializing class and method definitions ...Error: .onLoad failed in loadNamespace() for 'methods', details: call: new("classRepresentation") error: could not find function "isVirtualClass" The only other oddity of my system/potential clue is that symbolic links sometimes behave strangely because I am working on a VirtualBox virtual machine with a virtual Linux filesystem layered over an HGFS filesystem. -----BEGIN PG...

.../include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c RtreeApply.c -o RtreeApply.o gcc -shared -L/usr/local/lib -o OOP.so RtreeApply.o ** R ** inst ** save image [1] TRUE Initializing OOP objects in database 1 [1] "initialize" Error in .identC(class(Class), "classRepresentation") : couldn't find function ".traceClassName" Execution halted ERROR: execution of package source for 'OOP' failed ** Removing '/usr/local/lib/R/library/OOP' Anyone got a fix? Cheers, Sam.

Hi there, Installation error was given when I tried to install pmg (Poor mans GUI) http://wiener.math.csi.cuny.edu/pmg/index.html. $ LANG=C sudo R CMD INSTALL pmg_0.6.tar.gz * Installing *source* package 'gtkpmg' ... ** R ** save image Error in library(OOP) : There is no package called 'OOP' Execution halted /usr/lib/R/bin/INSTALL: line -116: 20554 Broken pipe cat

...kage attribute is there (possible, but hard to see why anyone would do this). It can make the opposite mistake, though, UNLESS the package generating the object is reinstalled with the current version of R, because older versions failed to put the attribute on some of the basic S4 classes (esp. classRepresentation). This is not by itself the right test for intercepting S3 code for certain primitives (c(), match(), [, for example), as was being discussed earlier. Only S4 objects that do not inherit from "vector" should be blocked. So the suitable test, in R code, is something like: if(seemsS...

...image by save.image(), although an existing class definition will not be overwritten. So when load()ing an (old) S4 object, by default there will be no information about the class definition at save() time available. Of course, conceptually, such information would best be stored in the respective classRepresentation object; however, as this one does not get save()d automatically along with an object, we might think of alternatives. It might at least be a compromise to store the some version information as a special slot to every object of any S4 class. For S4 classes defined in packages (which should make fo...

Hi, I get the following error when trying to remove a union class: > setClassUnion('a', c('matrix', 'numeric')) > removeClass('a') > sessionInfo() R version 2.15.3 (2013-03-01) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8

...ese two topics. The downside (perhaps) of the change is that class() and data.class() will now occasionally be inconsistent when methods is attached. class(1:1) is "integer", but data.class(1:1) is "numeric". 2. The representation of classes is now via an actual class, "classRepresentation". The metadata objects for class definitions are objects from this class. (Before, the class representation was a special-purpose hack, partly to avoid bootstrapping problems.) *** This means that packages using methods need to be installed from source to make their metadata objects correct...

...nd method information. pkg <- getPackageName(where) classes <- getClasses(where) for(cl in classes) { cldef <- (if(attach) get(classMetaName(cl), where) # NOT getClassDef, it will use cache else getClassDef(cl, searchWhere)) if(is(cldef, "classRepresentation")) { if(attach) { .cacheClass(cl, cldef, is(cldef, "ClassUnionRepresentation"), where) } else if(identical(cldef at package, pkg)) { .uncacheClass(cl, cldef) .removeSuperclassBackRefs(cl, cldef, searc...

...stored. ? prompt() did not backquote some default arguments in the \usage section. (Reported by Claudia Beleites.) ? writeBin() disallows attempts to write 2GB or more in a single call. (PR#14362) ? new() and getClass() will now work if Class is a subclass of "classRepresentation" and should also be faster in typical calls. ? The summary() method for data frames makes a better job of names containing characters invalid in the current locale. ? [[ sub-assignment for factors could create an invalid factor (reported by Bill Dunlap). ? Negate(f)...

...stored. ? prompt() did not backquote some default arguments in the \usage section. (Reported by Claudia Beleites.) ? writeBin() disallows attempts to write 2GB or more in a single call. (PR#14362) ? new() and getClass() will now work if Class is a subclass of "classRepresentation" and should also be faster in typical calls. ? The summary() method for data frames makes a better job of names containing characters invalid in the current locale. ? [[ sub-assignment for factors could create an invalid factor (reported by Bill Dunlap). ? Negate(f)...

...he caller of the generic function rather than the environment where the generic is defined. o The objects created in the methods package to represent classes, generic functions, method definitions, and inheritance relations now themselves belong to true classes. In particular, the "classRepresentation" objects follow the description in "Programming with Data" (section 7.6). o Other additions and changes to the methods package: - The function setOldClass() has been added, following the description on page 450 of "Programming with Data". Use it if old-style...

...he caller of the generic function rather than the environment where the generic is defined. o The objects created in the methods package to represent classes, generic functions, method definitions, and inheritance relations now themselves belong to true classes. In particular, the "classRepresentation" objects follow the description in "Programming with Data" (section 7.6). o Other additions and changes to the methods package: - The function setOldClass() has been added, following the description on page 450 of "Programming with Data". Use it if old-style...

...ional now, notably for large |dig|. * Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker). * is() behaves more robustly when its argument class2 is a classRepresentation object. * The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem. * choose() misbehaved in corner cases where it switched n - k for k and n was only _nearly_ integer (report from Eri...

...ional now, notably for large |dig|. * Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker). * is() behaves more robustly when its argument class2 is a classRepresentation object. * The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem. * choose() misbehaved in corner cases where it switched n - k for k and n was only _nearly_ integer (report from Eri...