Running examples in ‘mvSLOUCH-Ex.R’ failed
The error most likely occurred in:

> ### Name: BrownianMotionModel
> ### Title: Estimate parameters under a Brownian motion model of evolution
> ### Aliases: BrownianMotionModel
> ### Keywords: models multivariate htest
> 
> ### ** Examples
> 
> RNGversion(min(as.character(getRversion()),"3.6.1"))
> set.seed(12345, kind = "Mersenne-Twister", normal.kind = "Inversion")
> ### We will first simulate a small phylogenetic tree  using functions from ape. 
> ### For simulating the tree one could also use alternative functions, eg. sim.bd.taxa 
> ### from the TreeSim package
> phyltree<-ape::rtree(5)
> 
> ## The line below is not necessary but advisable for speed
> phyltree<-phyltree_paths(phyltree)
> 
> ### Define Brownian motion parameters to be able to simulate data under 
> ### the Brownian motion model.
> BMparameters<-list(vX0=matrix(0,nrow=3,ncol=1),
+ Sxx=rbind(c(1,0,0),c(0.2,1,0),c(0.3,0.25,1)))
> 
> ### Now simulate the data.
> BMdata<-simulBMProcPhylTree(phyltree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
> BMdata<-BMdata[phyltree$tip.label,,drop=FALSE]
> 
> ### Recover the parameters of the Brownian motion.
> BMestim<-BrownianMotionModel(phyltree,BMdata)
> 
> ### And finally obtain bootstrap condfidence intervals for some parameters
> BMbootstrap<-parametric.bootstrap(estimated.model=BMestim,phyltree=phyltree,
+ values.to.bootstrap=c("vX0","StS"),M.error=NULL,numboot=2)
Doing bootstrap iteration: 1. Start time: 2020-01-04 20:03:41
Doing bootstrap iteration: 2. Start time: 2020-01-04 20:03:41

 *** caught segfault ***
address 0x7f3546a462c8, cause 'invalid permissions'

Traceback:
 1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x242a4e0>,     dll = list(name = "Rcpp", path = "/data/gannet/ripley/R/test-clang/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x47226b0>,         info = <pointer: 0x228a640>), numParameters = -1L), <pointer: 0x86e4ff0>,     <pointer: 0x9b2fad0>, .pointer, ...)
 2: metaI$TraverseTree(par, mode = getOption("PCMBase.Lmr.mode",     as.integer(11)))
 3: PCMLmr.PCMInfoCpp(X = X, tree = tree, model = model, SE = SE,     metaI = metaI, verbose = verbose, root.only = TRUE)
 4: PCMLmr(X = X, tree = tree, model = model, SE = SE, metaI = metaI,     verbose = verbose, root.only = TRUE)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
 9: try(PCMLmr(X = X, tree = tree, model = model, SE = SE, metaI = metaI,     verbose = verbose, root.only = TRUE), silent = TRUE)
10: PCMLik.GaussianPCM(X, tree, model, SE, metaI, log = log)
11: PCMLik(X, tree, model, SE, metaI, log = log)
12: phyltree_org$likFun_BM_kX(v_pcmbasemodelparams)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch({    if (!b_useLikFunc) {        if (isTRUE(phyltree_org$b_usePCMBaseCpp)) {            phylLogLik <- PCMBase::PCMLik(X = t(mData), tree = phyltree,                 model = pcmbase_model_box, log = b_islog, metaI = PCMBaseCpp::PCMInfoCpp)        }        else {            phylLogLik <- PCMBase::PCMLik(X = t(mData), tree = phyltree,                 model = pcmbase_model_box, log = b_islog)        }    }    else {        v_pcmbasemodelparams <- double(PCMBase::PCMParamCount(o = pcmbase_model_box))        PCMBase::PCMParamLoadOrStore(o = pcmbase_model_box, vecParams = v_pcmbasemodelparams,             offset = 0, load = FALSE)        if (modelclass == "OU") {            phylLogLik <- phyltree_org$likFun_OU(v_pcmbasemodelparams)        }        if (modelclass == "BM") {            if (ncol(mData) == phyltree_org$kX) {                phylLogLik <- phyltree_org$likFun_BM_kX(v_pcmbasemodelparams)            }            else {                phylLogLik <- phyltree_org$likFun_BM_all(v_pcmbasemodelparams)            }        }    }    bno_error <- TRUE}, logic_error = function(e) {    .my_message(paste("Error in call to PCMBaseCpp : \n", e,         "\n", sep = ""), FALSE)}, `std::logic_error` = function(e) {    .my_message(paste("Error in call to PCMBaseCpp : \n", e,         "\n", sep = ""), FALSE)}, `C++Error` = function(e) {    .my_message(paste("Error in call to PCMBaseCpp : \n", e,         "\n", sep = ""), FALSE)}, error = function(e) {    .my_message(paste("Error in call to PCMBase::PCMLik : \n",         e, "\n", sep = ""), FALSE)}, warning = function(e) {    .my_message(paste("Error in call to PCMBase::PCMLik : \n",         e, "\n", sep = ""), FALSE)})
29: .callPCMBase_mvlik(mX, phyltree, pcmbase_model_box, b_islog = TRUE,     minLogLik = minLogLik)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch({    LogLik <- .callPCMBase_mvlik(mX, phyltree, pcmbase_model_box,         b_islog = TRUE, minLogLik = minLogLik)}, error = function(e) {    .my_message(paste("Error in BM optim when calling PCMBse::mvlik",         e), FALSE)    .my_message("\n", FALSE)})
34: .bm.estim(mData, PhylTree, modelParams$pcmbase_model_box, modelParams$regimes.types.orig,     minLogLik = minLogLik)
35: .maxlik.estim(mData = mData, EvolModel = params$EvolModel, method = params$method,     regimes = regimes, regimeTypes = regimes.types, EstimationParams = params$EstimParams,     PhylTree = phyltree, regimeTimes = regimes.times, bShouldPrint = params$bShouldPrint,     tol = params$tol, maxIter = params$maxIter, maxTries = params$maxTries,     minLogLik = params$minLogLik, regimes.types.orig = regimes.types.orig)
36: .PhyloSDEestim(phyltree, mData, kY = NULL, regimes = NULL, regimes.times = NULL,     root.regime = NULL, params = list(EvolModel = EvolModel,         EstimParams = list(calcCI = FALSE)), predictors = predictors,     M.error = M.error)
37: .internal_BrownianMotionModel(phyltree, mData, predictors, M.error,     min_bl)
38: BrownianMotionModel(phyltree, mData = simres, predictors = predictors,     M.error = M.error, min_bl = min_bl)
39: .bm.sim.est(phyltree, modelParams, M.error, predictors, min_bl)
40: FUN(X[[i]], ...)
41: lapply(X = X, FUN = FUN, ...)
42: sapply(1:numboot, function(i, evolmodel, phyltree, modelParams,     M.error, predictors, regimes, regimes.times, root.regime,     kY, Atype, Syytype, diagA, values.to.bootstrap, parameter_signs,     start_point_for_optim, parscale) {    .my_message(paste("Doing bootstrap iteration: ", i, ". Start time: ",         Sys.time(), sep = ""), TRUE)    if (!is.null(start_point_for_optim)) {        orgnames <- names(start_point_for_optim)        start_point_for_optim <- sapply(start_point_for_optim,             function(x) {                y <- matrix(jitter(c(x)), nrow = nrow(x), ncol = ncol(x))                colnames(y) <- colnames(x)                rownames(y) <- rownames(x)                y            }, simplify = FALSE)        names(start_point_for_optim) <- orgnames    }    estres <- switch(evolmodel, bm = .bm.sim.est(phyltree, modelParams,         M.error, predictors, min_bl), ouch = .ouou.sim.est(phyltree,         modelParams, regimes, regimes.times, root.regime, Atype,         Syytype, diagA, M.error, predictors, parameter_signs,         start_point_for_optim, parscale, min_bl, maxiter[c(1,             3)]), slouch = .oubm.sim.est(phyltree, modelParams,         regimes, regimes.times, root.regime, Atype, Syytype,         diagA, M.error, predictors, kY, parameter_signs, start_point_for_optim,         min_bl, maxiter), mvslouch = .oubm.sim.est(phyltree,         modelParams, regimes, regimes.times, root.regime, Atype,         Syytype, diagA, M.error, predictors, kY, parameter_signs,         start_point_for_optim, parscale, min_bl, maxiter))    .boot.extract(estres, values.to.bootstrap)}, evolmodel = evolmodel, phyltree = phyltree, modelParams = modelParams,     M.error = M.error, predictors = predictors, regimes = regimes,     regimes.times = NULL, root.regime = root.regime, kY = kY,     Atype = Atype, Syytype = Syytype, diagA = diagA, values.to.bootstrap = values.to.bootstrap,     parameter_signs = parameter_signs, start_point_for_optim = start_point_for_optim,     parscale = parscale, simplify = FALSE)
43: parametric.bootstrap(estimated.model = BMestim, phyltree = phyltree,     values.to.bootstrap = c("vX0", "StS"), M.error = NULL, numboot = 2)
An irrecoverable exception occurred. R is aborting now ...