Actually, after reading the comment about it being OK for it being NULL, it's not a bug after all.
On Thu, Jan 22, 2015 at 5:57 AM, Michael Lawrence <micha...@gene.com> wrote: > I also just noticed that there is a bug: identical(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.pe...@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 primitive function %s >> in this version of R", >> >> sQuote(f)), >> >> domain = NA) >> >> ans >> >> } >> >> or this: >> >> genericForPrimitive <- function(f, where = topenv(parent.frame()), mustFind >> = TRUE) { >> >> env = asNamespace("methods") >> >> funs <- env[[".BasicFunsList"]] >> >> ans = funs[[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", >> >> sQuote(f)), >> >> domain = NA) >> >> ans >> >> } >> >> Seems to work just fine. >> >> Yes, "el" and "elNamed" can probably go now. >> >> >> Pete >> >> ____________________ >> Peter M. Haverty, Ph.D. >> Genentech, Inc. >> phave...@gene.com >> >> On Wed, Jan 21, 2015 at 2:26 PM, Michael Lawrence >> <lawrence.mich...@gene.com> wrote: >>> >>> Note that setMethod() resolves .BasicFunsList in the methods namespace >>> directly when setting a method on a primitive. Somehow there should be >>> consistency between genericForPrimitive() and the check in setMethod(). >>> >>> Also, we can probably step away from the use of elNamed(), given that [[ >>> now uses exact matching. >>> >>> Have you tried patching methods to use .BasicFunsList directly as in >>> setMethod? >>> >>> >>> On Wed, Jan 21, 2015 at 10:41 AM, Peter Haverty <haverty.pe...@gene.com> >>> wrote: >>>> >>>> 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 design, but would it be possible shortcut this operation? Could >>>> .BasicFunsList be initialized in the methods namespace at startup and >>>> might >>>> genericForPrimitive just go straight there? >>>> >>>> Does anyone on the list know why it works this way? >>>> >>>> There are some other cases of seemingly redundant work, but this seems >>>> like >>>> an easy one to address. >>>> >>>> I have included some code below that was used to investigate some of the >>>> above. >>>> >>>> # Try this to count calls to a function >>>> >>>> .count <- 0; trace(methods:::.findBasicFuns,tracer=function() { .count >>>> <<- >>>> .count + 1 }); library(GenomicRanges); print(.count) >>>> >>>> # Try this to capture the input and output of a set of functions you wish >>>> to refactor >>>> >>>> .init_test_data_collection <- function(ns = asNamespace("methods")) { >>>> >>>> funs = c("isClassUnion", "getClass", "genericForPrimitive", >>>> "possibleExtends", ".dataSlot", ".requirePackage", ".classEnv", >>>> "getClassDef", "outerLabels", ".getClassFromCache", "getFunction") >>>> >>>> message(paste0("\nCollecting data for unit tests on ", paste(funs, >>>> collapse=", "), " ...\n")) >>>> >>>> # Make env with list to hold test input/output >>>> >>>> TEST_ENV <- new.env() >>>> >>>> for (fname in funs) { >>>> >>>> # Make placeholder for input/output for future runs of this >>>> function >>>> >>>> TEST_ENV[[fname]] = list() # Actually probably not necessary, >>>> will >>>> just be c(NULL, list(first result)) the first time >>>> >>>> # Construct test version of function >>>> >>>> unlockBinding(fname, ns) >>>> >>>> fun = get(fname, envir=ns, mode="function") >>>> >>>> funbody = deparse(body(fun)) >>>> >>>> newfun <- fun >>>> >>>> newfun.body = c( >>>> >>>> sprintf("fname = '%s'", fname), >>>> >>>> "TEST_INFO = list()", >>>> >>>> "TEST_INFO$input = mget(names(formals(fname)))", >>>> >>>> c("realfun <- function()", funbody), >>>> >>>> "TEST_INFO$output = realfun()", >>>> >>>> "TEST_ENV[[fname]] = c(TEST_ENV[[fname]], list(TEST_INFO))", >>>> >>>> "return(TEST_INFO$output)") >>>> >>>> body(newfun) = as.call(c(as.name("{"), >>>> as.list(parse(text=newfun.body)))) >>>> >>>> assign(fname, newfun, envir=ns) >>>> >>>> } >>>> >>>> return(TEST_ENV) >>>> >>>> } >>>> # run code, print items in TEST_ENV >>>> >>>> The relevant code is in methods/R/BasicFunsList.R and >>>> methods/R/ClassExtensions.R >>>> Pete >>>> >>>> ____________________ >>>> Peter M. Haverty, Ph.D. >>>> Genentech, Inc. >>>> phave...@gene.com >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> R-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >>> >> ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel