CRAN Package Check Results for Package jomo

Last updated on 2018-11-24 00:51:11 CET.

Check Details

Version: 2.6-5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64

Version: 2.6-5
Check: examples
Result: ERROR
    Running examples in ‘jomo-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: jomo.clmm
    > ### Title: Joint Modelling Imputation Compatible with Cumulative Link Mixed
    > ### Model
    > ### Aliases: jomo.clmm
    >
    > ### ** Examples
    >
    >
    >
    > # make sure social is a factor:
    >
    > cldata<-within(cldata, social<-factor(social))
    >
    > # we define the data frame with all the variables
    >
    > data<-cldata[,c("measure","age", "social", "city")]
    >
    > # And the formula of the substantive lm model
    > # social as an outcome only because it is the only ordinal variable in the dataset...
    >
    > formula<-as.formula(social~age+measure+(1|city))
    >
    > #And finally we run the imputation function:
    >
    > imp<-jomo.clmm(formula,data, nburn=2, nbetween=2, nimp=2)
    This function is beta software. Please use carefully and report any bug to the package mantainer
    
     *** caught segfault ***
    address 70a, cause 'memory not mapped'
    
    Traceback:
     1: lapply(findLocals1(e, shadowed, cntxt, vars), function(x) if (typeof(x) == "language") newtodo <<- append(newtodo, x))
     2: FUN(X[[i]], ...)
     3: lapply(todo, function(e) lapply(findLocals1(e, shadowed, cntxt, vars), function(x) if (typeof(x) == "language") newtodo <<- append(newtodo, x)))
     4: findLocalsList1(elist, sf, cntxt)
     5: findLocalsList(c(forms, body), cntxt)
     6: funEnv(forms, body, cntxt)
     7: make.functionContext(cntxt, formals(f), body(f))
     8: cmpfun(f)
     9: doTryCatch(return(expr), name, parentenv, handler)
    10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    11: tryCatchList(expr, classes, parentenv, handlers)
    12: tryCatch(cmpfun(f), error = function(e) { notifyCompilerError(paste(e$message, "at", deparse(e$call))) f})
    13: compiler:::tryCmpfun(new("MethodDefinition", .Data = function (from, to = "MethodDefinition", value) { for (what in c(".Data", "target", "defined", "generic")) slot(from, what) <- slot(value, what) from}, target = new("signature", .Data = c("MethodWithNext", "MethodDefinition"), names = c("from", "to"), package = c("methods", "methods")), defined = new("signature", .Data = c("MethodWithNext", "MethodDefinition" ), names = c("from", "to"), package = c("methods", "methods" )), generic = "coerce<-"))
    14: asMethod(object, Class, value)
    15: `as<-`(`*tmp*`, Classi, value = obj)
    16: initialize(value, ...)
    17: initialize(value, ...)
    18: new("MethodWithNext", method, nextMethod = methods[[1L]], excluded = as.list(excluded))
    19: .findNextFromTable(method, f, optional, envir)
    20: addNextMethod(method, f, envir = methodEnv)
    21: addNextMethod(method, f, envir = methodEnv)
    22: callNextMethod()
    23: methods:::loadMethod(new("MethodWithNext", .Data = function (.Object, ...) { .Object <- callNextMethod() if (length(args <- list(...)) && any(nzchar(snames <- names(args))) && "Dimnames" %in% snames) .Object@Dimnames <- .fixupDimnames(.Object@Dimnames) .Object}, nextMethod = new("derivedDefaultMethod", .Data = function (.Object, ...) { args <- list(...) if (length(args)) { Class <- class(.Object) if (!is.na(match(Class, .BasicClasses))) return(newBasic(Class, ...)) ClassDef <- getClass(Class) snames <- allNames(args) which <- nzchar(snames) elements <- args[which] supers <- args[!which] thisExtends <- names(ClassDef@contains) slotDefs <- ClassDef@slots dataPart <- slotDefs[[".Data"]] if (is.null(dataPart)) dataPart <- "missing" if (length(supers)) { for (i in rev(seq_along(supers))) { obj <- supers[[i]] Classi <- class(obj) if (length(Classi) > 1L) Classi <- Classi[[1L]] if (.identC(Classi, Class)) .Object <- obj else if (extends(Classi, Class)) .Object <- as(obj, Class, strict = FALSE) else if (extends(Class, Classi)) as(.Object, Classi) <- obj else if (extends(Classi, dataPart)) .Object@.Data <- obj else { extendsi <- extends(Classi)[-1L] which <- match(thisExtends, extendsi) which <- seq_along(which)[!is.na(which)] if (length(which)) { Classi <- thisExtends[which[1L]] as(.Object, Classi) <- obj } else stop(gettextf("cannot use object of class %s in new(): class %s does not extend that class", dQuote(Classi), dQuote(Class)), domain = NA) } } } if (length(elements)) { snames <- names(elements) if (anyDuplicated(snames)) stop(gettextf("duplicated slot names: %s", paste(sQuote(snames[duplicated(snames)]), collapse = ", ")), domain = NA) which <- match(snames, names(slotDefs)) if (anyNA(which)) stop(sprintf(ngettext(sum(is.na(which)), "invalid name for slot of class %s: %s", "invalid names for slots of class %s: %s"), dQuote(Class), paste(snames[is.na(which)], collapse = ", ")), domain = NA) firstTime <- TRUE for (i in seq_along(snames)) { slotName <- snames[[i]] slotClass <- slotDefs[[slotName]] slotClassDef <- getClassDef(slotClass, package = ClassDef@package) slotVal <- elements[[i]] if (!.identC(class(slotVal), slotClass) && !is.null(slotClassDef)) { valClass <- class(slotVal) valClassDef <- getClassDef(valClass, package = ClassDef@package) if (!identical(possibleExtends(valClass, slotClass, valClassDef, slotClassDef), FALSE)) slotVal <- as(slotVal, slotClass, strict = FALSE) } if (firstTime) { slot(.Object, slotName, check = FALSE) <- slotVal firstTime <- FALSE } else { `slot<-`(.Object, slotName, check = FALSE, slotVal) } } } validObject(.Object) } .Object}, target = new("signature", .Data = "Matrix", names = ".Object", package = "Matrix"), defined = new("signature", .Data = "ANY", names = ".Object", package = "methods"), generic = "initialize"), excluded = list("Matrix"), target = new("signature", .Data = "dgTMatrix", names = ".Object", package = "methods"), defined = new("signature", .Data = "Matrix", names = ".Object", package = "Matrix"), generic = "initialize"), "initialize", <environment>)
    24: methods:::loadMethod(new("MethodWithNext", .Data = function (.Object, ...) { .Object <- callNextMethod() if (length(args <- list(...)) && any(nzchar(snames <- names(args))) && "Dimnames" %in% snames) .Object@Dimnames <- .fixupDimnames(.Object@Dimnames) .Object}, nextMethod = new("derivedDefaultMethod", .Data = function (.Object, ...) { args <- list(...) if (length(args)) { Class <- class(.Object) if (!is.na(match(Class, .BasicClasses))) return(newBasic(Class, ...)) ClassDef <- getClass(Class) snames <- allNames(args) which <- nzchar(snames) elements <- args[which] supers <- args[!which] thisExtends <- names(ClassDef@contains) slotDefs <- ClassDef@slots dataPart <- slotDefs[[".Data"]] if (is.null(dataPart)) dataPart <- "missing" if (length(supers)) { for (i in rev(seq_along(supers))) { obj <- supers[[i]] Classi <- class(obj) if (length(Classi) > 1L) Classi <- Classi[[1L]] if (.identC(Classi, Class)) .Object <- obj else if (extends(Classi, Class)) .Object <- as(obj, Class, strict = FALSE) else if (extends(Class, Classi)) as(.Object, Classi) <- obj else if (extends(Classi, dataPart)) .Object@.Data <- obj else { extendsi <- extends(Classi)[-1L] which <- match(thisExtends, extendsi) which <- seq_along(which)[!is.na(which)] if (length(which)) { Classi <- thisExtends[which[1L]] as(.Object, Classi) <- obj } else stop(gettextf("cannot use object of class %s in new(): class %s does not extend that class", dQuote(Classi), dQuote(Class)), domain = NA) } } } if (length(elements)) { snames <- names(elements) if (anyDuplicated(snames)) stop(gettextf("duplicated slot names: %s", paste(sQuote(snames[duplicated(snames)]), collapse = ", ")), domain = NA) which <- match(snames, names(slotDefs)) if (anyNA(which)) stop(sprintf(ngettext(sum(is.na(which)), "invalid name for slot of class %s: %s", "invalid names for slots of class %s: %s"), dQuote(Class), paste(snames[is.na(which)], collapse = ", ")), domain = NA) firstTime <- TRUE for (i in seq_along(snames)) { slotName <- snames[[i]] slotClass <- slotDefs[[slotName]] slotClassDef <- getClassDef(slotClass, package = ClassDef@package) slotVal <- elements[[i]] if (!.identC(class(slotVal), slotClass) && !is.null(slotClassDef)) { valClass <- class(slotVal) valClassDef <- getClassDef(valClass, package = ClassDef@package) if (!identical(possibleExtends(valClass, slotClass, valClassDef, slotClassDef), FALSE)) slotVal <- as(slotVal, slotClass, strict = FALSE) } if (firstTime) { slot(.Object, slotName, check = FALSE) <- slotVal firstTime <- FALSE } else { `slot<-`(.Object, slotName, check = FALSE, slotVal) } } } validObject(.Object) } .Object}, target = new("signature", .Data = "Matrix", names = ".Object", package = "Matrix"), defined = new("signature", .Data = "ANY", names = ".Object", package = "methods"), generic = "initialize"), excluded = list("Matrix"), target = new("signature", .Data = "dgTMatrix", names = ".Object", package = "methods"), defined = new("signature", .Data = "Matrix", names = ".Object", package = "Matrix"), generic = "initialize"), "initialize", <environment>)
    25: initialize(value, ...)
    26: (function (Class, ...) { ClassDef <- getClass(Class, where = topenv(parent.frame())) value <- .Call(C_new_object, ClassDef) initialize(value, ...)})(Class = "dgTMatrix", Dim = c(10L, 637L), Dimnames = list(c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9"), NULL), i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L), j = 0:636, x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
    27: do.call(new, c(list(Class = paste0(to, "gTMatrix"), Dim = c(length(levs), n), Dimnames = list(levs, names(fact))), df))
    28: fac2sparse(from, to = "d")
    29: asMethod(object)
    30: as(ff, "sparseMatrix")
    31: FUN(X[[i]], ...)
    32: lapply(barlist, function(x) { ff <- eval(substitute(as.factor(fac)[, drop = TRUE], list(fac = x[[3]])), fullmf) Zti <- as(ff, "sparseMatrix") mm <- model.matrix(eval(substitute(~expr, list(expr = x[[2]]))), fullmf) Zt = do.call(rbind, lapply(seq_len(ncol(mm)), function(j) { Zti@x <- mm[, j] Zti })) ST <- matrix(0, ncol(mm), ncol(mm), dimnames = list(colnames(mm), colnames(mm))) list(f = ff, Zt = Zt, ST = ST)})
    33: getREterms(frames = frames, formulae$formula)
    34: ordinal::clmm(formula, data = data, na.action = na.omit, Hess = T, link = "probit")
    35: jomo.clmm(formula, data, nburn = 2, nbetween = 2, nimp = 2)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86