search for: topenv

I was surprised just now to find out that `topenv(emptyenv())` equals ? `.GlobalEnv`, not `emptyenv()`. From my understanding of the description of `topenv`, it should walk up the chain of enclosing environments (as if by calling `e = parent.env(e)` repeatedly; in fact, that is almost exactly its implementation in envir.c) until it hits a top leve...

>>>>> Konrad Rudolph >>>>> on Sat, 23 Mar 2019 14:26:40 +0000 writes: >>>>> Konrad Rudolph >>>>> on Sat, 23 Mar 2019 14:26:40 +0000 writes: > I was surprised just now to find out that `topenv(emptyenv())` equals > ? `.GlobalEnv`, not `emptyenv()`. From my understanding of the > description of `topenv`, it should walk up the chain of enclosing > environments (as if by calling `e = parent.env(e)` repeatedly; in > fact, that is almost exactly its implementation...

...ear all, I have been trying to create an R package. This has been successfull until I tried to define classes. Currently, my procedure is the following: Start R, load the function and class definition >tmp <- function (x) {x} >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 cr...

...s should be independent of user customisations. For instance a package author might gather tabular data in a matrix or data frame and print() it as part of a larger print method. In that case, user customisations might cause a mess. Would it make sense to resort to autoprint customisation when the topenv() of the parent.frame() of print() is the global environment, and ignore the customisation otherwise? This should ensure consistent printing behaviour at the REPL and in scripts. Checking the topenv() allows print() calls inserted to debug lapply'd functions to behave the same as when called fr...

Hi, I would like to know how to capture the console output from running an algorithm for further analysis. I can capture this using capture.output() but that yields a character vector. I would like to extract the actual numeric values. Here is an example of what I am trying to do. fr <- function(x) { ## Rosenbrock Banana function on.exit(print(f)) x1 <- x[1] x2 <- x[2]

...te a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"), where = topenv()) I get: Error in assign(classMetaName(Class), def, where) : cannot add bindings to a locked environment I understand the fact that after "myPkg" is loaded, its namespace is sealed, but I was hoping to find a way around it. I would appreciate any comment on this. thank...

...) setClass("Class3", representation("Class2")) setClass("Class4", representation("Class3")) setClass("Class5", representation("Class4")) getClass("Class3") # as I expected Class3Def <- getClassDef("Class3", where = topenv(parent.frame())) ## the following is called in setValidity() via resetClass() ## (further explanations, see below) completeClassDefinition("Class3", Class3Def, where = topenv(parent.frame()), doExtends = TRUE) ## 'Extends' includs only "Class2" ## ## would give...

Doing it like this: genericForPrimitive <- function(f, where = topenv(parent.frame()), mustFind = TRUE) { ans = .BasicFunsList[[f]] ## this element may not exist (yet, during loading), dom't test null if(mustFind && identical(ans, FALSE)) stop(gettextf("methods may not be defined for primitive function %s in this version of R&...

...tephan Steinhaus (stst at informatik.uni-frankfurt.de) # Reference for Escoufier's equivalents vectors (test III.5): # Escoufier Y., 1970. Echantillonnage dans une population de variables # aleatoires r??les. Publ. Inst. Statis. Univ. Paris 19 Fasc 4, 1-47. ... Error in getClass(Class, where = topenv(parent.frame())) : "geMatrix" is not a defined class Calls: new -> getClass Execution halted

...s sealed; new superclasses can not be defined, except by setClassUnion Error in setIs("character", "characterORMIAME", where = where) : Class "character" is sealed; new superclasses can not be defined, except by setClassUnion Error in getClass(Class, where = topenv(parent.frame())) : "MIAME" is not a defined class Error in library(affy) : .First.lib failed Is someone still have this problem ? Ghislaine GUIGON Biostatisticienne

...BioC CVS) fails to load. annaffy 1.0 (on the BioC web site) has the same problem. It looks like the load is failing because of a bug in completeSubclasses() in r-devel. It calls setIs() and doesn't specify an environment via the "where" argument. setIs() "where" defaults to topEnv() and fails because "aafGO" doesn't exist in that environment and "list" is sealed. completeSubclasses should be specifying my package for "where" instead of using the default. > library(annaffy) Error in setIs(class2, obji@superClass, extensionObject = obji,...

...be available in the > environment of the call to the generic, or they must be registered. (It does > not matter whether they are visible in the environment in which the generic is > defined.) As from R 3.5.0, the registration data base is searched after the > top level environment (see ?topenv?) of the calling environment (but before > the parents of the top level environment). This used to work but it stopped working in R 3.6.1 and I cannot figure out (a) why, and (b) how to fix it. Unfortunately I am unable to find the relevant information by reading the R source code, even when ?d...

Dear List, I tested the example in the reposTools vignette: library(reposTools); Loading required package: tools genRepos("Test Repository", "http://biowww.dfci.harvard.edu/~jgentry/","newRepos"); Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in 'rep' Could someone help me out with this one? I'd appreciate all help.... I am

...ts, [1] "ProgressBarText" [1] "initialize" [1] "open" [1] "open" [1] "update" [1] "update" [1] "close" [1] "close" Error in getClass(Class, where = topenv(parent.frame())) : "MIAME" is not a defined class Execution halted /bioinfo/apps/lib/R/bin/INSTALL: line 1: 761 Broken pipe cat "/home/sxv6413/rstuffs/lib/affy/R/affy" ERROR: execution of package source for 'affy' failed...

...l(ans, FALSE) should be is.null(ans). So no error is thrown: > methods:::genericForPrimitive("foo") NULL Will fix. On Wed, Jan 21, 2015 at 3:13 PM, Peter Haverty <haverty.peter at gene.com> wrote: > Doing it like this: > > genericForPrimitive <- function(f, where = topenv(parent.frame()), mustFind > = TRUE) { > > ans = .BasicFunsList[[f]] > > ## this element may not exist (yet, during loading), dom't test null > > if(mustFind && identical(ans, FALSE)) > > stop(gettextf("methods may not be defined for pr...

...one: ------------------------------------------------------------------------ r75127 | hornik | 2018-08-13 09:58:47 -0400 (Mon, 13 Aug 2018) | 2 lines Changed paths: M /trunk/src/main/objects.c M /trunk/tests/reg-tests-1a.R Have S3 methods lookup by default look for the S3 registry in the topenv of the generic. ------------------------------------------------------------------------ Duncan Murdoch > > I am implementing S3 dispatch for generic methods in environments that are > not > packages. I am trying to emulate the R package namespace mechanism by > having a > ?nam...

Hello, the last command (isGeneric) in following R-code (attached) produces different output, depending on wheter 1.8.0 alpha or 1.7.1 is used. Is that to be expected ? Both R Versions were started with option vanilla --------------------------------------------------- R.1.7.1: --------------------------------------------------- > version _ platform i686-pc-linux-gnu arch i686

...CMD check ./anRpackage * checking for working pdflatex ... OK [snip] * checking data for non-ASCII characters ... NOTE Error: "foo" is not a defined class Call sequence: 8: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA) 7: getClass(Class, where = topenv(parent.frame())) 6: new("foo", x = rep(2, 7)) 5: eval(expr, envir, enclos) 4: eval(i, envir) 3: sys.source(zfile, chdir = TRUE, envir = envir) 2: switch(ext, R = , r = { library("utils") sys.source(zfile, chdir = TRUE, envir = envir) }, RData = , rdata = , rda = load(zfile, envi...

...x: RMethodUtils.R =================================================================== --- RMethodUtils.R (revision 41719) +++ RMethodUtils.R (working copy) @@ -621,7 +621,7 @@ getMethodsMetaData <- ## get the methods meta-data for function f on database where function(f, where = topenv(parent.frame())) { - mname <- mlistMetaName(f, where) + mname <- mlistMetaName(f, getPackageName(where)) if(exists(mname, where = where, inherits = missing(where))) get(mname, where) else Seth Falcon <sfalcon at fhcrc.org> writes: > cstr...

Hi all, The function call series genericForPrimitive -> .findBasicFuns -> .findAll happens 4400 times while the GenomicRanges package is loading. Each time .findAll follows a chain of environments to determine that the methods namespace is the only one that holds a variable called .BasicFunsList. This accounts for ~10% of package loading time. I'm sure there is some history to that