Error(s) in re-building vignettes:
  ...
--- re-building 'an_introduction_to_markovchain_package.Rmd' using rmarkdown
Package:  markovchain
Version:  0.8.0
Date:     2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: TraMineR

TraMineR stable version 2.0-13 (Built: 2019-11-26)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.

Loading required package: colorspace
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
markovchain
 --- call from context --- 
verifyHomogeneity(inputList = kullback, verbose = TRUE)
 --- call from argument --- 
if (class(inputList[[i]]) == "matrix") {
    checks <- .checkMatrix4Homogeneity(inputList[[i]])
    if (!checks) 
        stop("Error! Element ", i, " to be checked")
} else {
    inputList[[i]] <- createSequenceMatrix(stringchar = inputList[[i]])
}
 --- R stacktrace ---
where 1: verifyHomogeneity(inputList = kullback, verbose = TRUE)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("an_introduction_to_markovchain_package.Rmd", 
    "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/markovchain.Rcheck/vign_test/markovchain", 
    TRUE, FALSE, "an_introduction_to_markovchain_package", "UTF-8", 
    "/tmp/RtmpI1PrXD/file4e003eb38e61.rds")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (inputList, verbose = TRUE) 
{
    warning("The accuracy of the statistical inference functions has been questioned. It will be thoroughly investigated in future versions of the package.")
    if (class(inputList) != "list") 
        stop("Error! inputList should be a string")
    if (length(inputList) < 2) 
        stop("Error! inputList length lower than 2")
    for (i in 1:length(inputList)) {
        if (class(inputList[[i]]) == "matrix") {
            checks <- .checkMatrix4Homogeneity(inputList[[i]])
            if (!checks) 
                stop("Error! Element ", i, " to be checked")
        }
        else {
            inputList[[i]] <- createSequenceMatrix(stringchar = inputList[[i]])
        }
    }
    all.names <- character()
    for (i in 1:length(inputList)) {
        all.names <- c(all.names, rownames(inputList[[i]]))
    }
    all.names <- sort(unique(all.names))
    PooledRawTransitionMatrix <- matrix(0, nrow = length(all.names), 
        ncol = length(all.names), dimnames = list(all.names, 
            all.names))
    RowSumsMatrix <- matrix(0, nrow = length(inputList), ncol = length(all.names), 
        dimnames = list(1:length(inputList), all.names))
    for (k in 1:length(inputList)) {
        current_support = rownames(inputList[[k]])
        current_dim = dim(inputList[[k]])
        for (i in 1:current_dim[1]) {
            for (j in 1:current_dim[2]) {
                num_trans <- inputList[[k]][i, j]
                which_row_trans <- current_support[i]
                which_col_trans <- current_support[j]
                row_to_write <- match(x = which_row_trans, table = all.names)
                col_to_write <- match(x = which_col_trans, table = all.names)
                PooledRawTransitionMatrix[row_to_write, col_to_write] = PooledRawTransitionMatrix[row_to_write, 
                  col_to_write] + num_trans
            }
        }
    }
    for (k in 1:length(inputList)) {
        my_row_sums <- rowSums(inputList[[k]])
        current_support = names(my_row_sums)
        for (i in 1:length(current_support)) {
            my_element <- my_row_sums[i]
            col_to_write <- match(x = current_support[i], table = all.names)
            RowSumsMatrix[k, col_to_write] <- RowSumsMatrix[k, 
                col_to_write] + my_element
        }
    }
    statistic <- 0
    newInputList <- lapply(inputList, .addNamedColumns, fullnames = all.names)
    number_of_transitions <- sapply(newInputList, sum)
    total_transitions <- sum(number_of_transitions)
    for (s in 1:length(inputList)) {
        for (j in 1:length(all.names)) {
            for (k in 1:length(all.names)) {
                if (any(newInputList[[s]][j, k] == 0, number_of_transitions[s] == 
                  0, PooledRawTransitionMatrix[j, k] == 0)) {
                  statistic <- statistic + 0
                }
                else {
                  statistic <- statistic + newInputList[[s]][j, 
                    k] * log((total_transitions * newInputList[[s]][j, 
                    k])/(number_of_transitions[s] * PooledRawTransitionMatrix[j, 
                    k]))
                }
            }
        }
    }
    statistic <- statistic * 2
    degrees_of_freedom <- (length(inputList) - 1) * (length(all.names)^2 - 
        1)
    p.value <- 1 - pchisq(q = statistic, df = degrees_of_freedom)
    if (verbose == TRUE) {
        cat("Testing homogeneity of DTMC underlying input list \n")
        cat("ChiSq statistic is", statistic, "d.o.f are", degrees_of_freedom, 
            "corresponding p-value is", p.value, "\n")
    }
    out <- list(statistic = statistic, dof = degrees_of_freedom, 
        pvalue = p.value)
    return(out)
}
<bytecode: 0xb87ebc8>
<environment: namespace:markovchain>
 --- function search by body ---
Function verifyHomogeneity in namespace markovchain has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building 'gsoc_2017_additions.Rmd' using rmarkdown
Package:  markovchain
Version:  0.8.0
Date:     2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'gsoc_2017_additions.Rmd'

--- re-building 'higher_order_markov_chains.Rmd' using rmarkdown
Loading required package: markovchain
Package:  markovchain
Version:  0.8.0
Date:     2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues

This function is experimental
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
markovchain
 --- call from context --- 
fitHighOrderMultivarMC(sales, order = 8, Norm = 2)
 --- call from argument --- 
if (class(seqMat) == "data.frame") {
    seqMat <- as.matrix(seqMat)
}
 --- R stacktrace ---
where 1: fitHighOrderMultivarMC(sales, order = 8, Norm = 2)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("higher_order_markov_chains.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/markovchain.Rcheck/vign_test/markovchain", 
    TRUE, FALSE, "higher_order_markov_chains", "UTF-8", "/tmp/RtmpI1PrXD/file4e007275e87.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (seqMat, order = 2, Norm = 2) 
{
    message("This function is experimental")
    if (class(seqMat) == "data.frame") {
        seqMat <- as.matrix(seqMat)
    }
    seqMat <- t(seqMat)
    allTmat <- .allTransMat(seqMat, order = order)
    freqMat <- .allFreqProbMat(seqMat)
    n <- order
    uelement <- sort(unique(as.character(seqMat)))
    m <- length(uelement)
    s <- nrow(seqMat)
    lmbda <- rep(1/(n * s), n * s * s)
    fit <- Rsolnp::solnp(pars = lmbda, fun = .fn3, eqfun = .eqn3, 
        eqB = rep(1, s), LB = rep(0, n * s * s), control = list(trace = 0), 
        allTmat = allTmat, freqMat = freqMat, n = n, m = m, s = s, 
        Norm = Norm)
    return(new("hommc", order = order, Lambda = fit$pars, P = allTmat, 
        states = uelement, byrow = FALSE))
}
<bytecode: 0xcbd6608>
<environment: namespace:markovchain>
 --- function search by body ---
Function fitHighOrderMultivarMC in namespace markovchain has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building 'markvochain_crash_intro.Rmd' using rmarkdown
--- finished re-building 'markvochain_crash_intro.Rmd'

SUMMARY: processing the following files failed:
  'an_introduction_to_markovchain_package.Rmd'
  'higher_order_markov_chains.Rmd'

Error: Vignette re-building failed.
Execution halted