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 ...