Last updated on 2019-11-26 00:51:57 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.0 | 156.10 | 151.59 | 307.69 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.8.0 | 124.31 | 118.54 | 242.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.8.0 | 564.74 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 0.8.0 | 550.98 | WARN | |||
| r-devel-windows-ix86+x86_64 | 0.8.0 | 385.00 | 405.00 | 790.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.8.0 | 394.00 | 369.00 | 763.00 | OK | |
| r-patched-linux-x86_64 | 0.8.0 | 131.61 | 293.31 | 424.92 | OK | |
| r-patched-solaris-x86 | 0.8.0 | 569.00 | OK | |||
| r-release-linux-x86_64 | 0.8.0 | 129.74 | 290.00 | 419.74 | OK | |
| r-release-windows-ix86+x86_64 | 0.8.0 | 362.00 | 484.00 | 846.00 | OK | |
| r-release-osx-x86_64 | 0.8.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.8.0 | 274.00 | 446.00 | 720.00 | OK | |
| r-oldrel-osx-x86_64 | 0.8.0 | NOTE |
Version: 0.8.0
Check: examples
Result: ERROR
Running examples in 'markovchain-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitHighOrderMultivarMC
> ### Title: Function to fit Higher Order Multivariate Markov chain
> ### Aliases: fitHighOrderMultivarMC
>
> ### ** Examples
>
> data <- matrix(c('2', '1', '3', '3', '4', '3', '2', '1', '3', '3', '2', '1',
+ c('2', '4', '4', '4', '4', '2', '3', '3', '1', '4', '3', '3')),
+ ncol = 2, byrow = FALSE)
>
> fitHighOrderMultivarMC(data, order = 2, Norm = 2)
This function is experimental
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
markovchain
--- call from context ---
fitHighOrderMultivarMC(data, order = 2, Norm = 2)
--- call from argument ---
if (class(seqMat) == "data.frame") {
seqMat <- as.matrix(seqMat)
}
--- R stacktrace ---
where 1: fitHighOrderMultivarMC(data, order = 2, Norm = 2)
--- 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: 0x7f4f9b8>
<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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.0
Check: tests
Result: ERROR
Running 'testthat.R' [19s/20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(markovchain)
Package: markovchain
Version: 0.8.0
Date: 2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues
> test_check("markovchain")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
markovchain
--- call from context ---
markovchainListFit(data = myHolson)
--- call from argument ---
if (class(data) == "list") {
markovchains <- list()
freqMatrixes <- .mcListFitForList(data)
} else {
if (is.data.frame(data)) {
data <- unname(as.matrix(data))
}
if (!byrow) {
data <- t(data)
}
nCols <- ncol(data)
freqMatrixes <- lapply(seq_len(nCols - 1), function(i) {
matrData <- data[, c(i, i + 1)]
matrData[1, ] <- as.character(matrData[1, ])
validTransition <- any(apply(matrData, 1, function(x) {
!any(is.na(x))
}))
if (validTransition)
createSequenceMatrix(matrData, toRowProbs = FALSE,
sanitize = TRUE)
})
freqMatrixes <- freqMatrixes[!sapply(freqMatrixes, is.null)]
}
--- R stacktrace ---
where 1: markovchainListFit(data = myHolson)
where 2: eval_bare(expr, quo_get_env(quo))
where 3: quasi_label(enquo(object), label, arg = "object")
where 4 at testthat/testFits.R#19: expect_equal(markovchainListFit(data = myHolson), checkmarkovchainFitList)
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/testFits.R#17: test_that("Check markovchainFit & listFit", {
expect_equal(markovchainFit(ciao), simpleMcCiaoFit)
expect_equal(markovchainListFit(data = myHolson), checkmarkovchainFitList)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("markovchain")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data, byrow = TRUE, laplacian = 0, name)
{
if (!any((class(data) %in% c("data.frame", "matrix", "list")))) {
stop("Error: data must be either a matrix or a data.frame or a list")
}
freqMatrixes <- list()
if (class(data) == "list") {
markovchains <- list()
freqMatrixes <- .mcListFitForList(data)
}
else {
if (is.data.frame(data)) {
data <- unname(as.matrix(data))
}
if (!byrow) {
data <- t(data)
}
nCols <- ncol(data)
freqMatrixes <- lapply(seq_len(nCols - 1), function(i) {
matrData <- data[, c(i, i + 1)]
matrData[1, ] <- as.character(matrData[1, ])
validTransition <- any(apply(matrData, 1, function(x) {
!any(is.na(x))
}))
if (validTransition)
createSequenceMatrix(matrData, toRowProbs = FALSE,
sanitize = TRUE)
})
freqMatrixes <- freqMatrixes[!sapply(freqMatrixes, is.null)]
}
if (length(freqMatrixes) == 0) {
return(list())
}
markovchains <- lapply(freqMatrixes, function(freqMatrix) {
freqMatrix <- freqMatrix + laplacian
rSums <- rowSums(freqMatrix)
tMatrix <- freqMatrix/rSums
estMc <- new("markovchain", transitionMatrix = tMatrix)
estMc
})
outMcList <- new("markovchainList", markovchains = markovchains)
out <- list(estimate = outMcList)
if (!missing(name)) {
out$estimate@name <- name
}
return(out)
}
<bytecode: 0xaf893f8>
<environment: namespace:markovchain>
--- function search by body ---
Function markovchainListFit in namespace markovchain has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.0
Check: re-building of vignette outputs
Result: WARN
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: 2019-11-24)
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/RtmpYpC1Os/file47e660d78679.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: 0xa60edd0>
<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/RtmpYpC1Os/file47e64c957999.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: 0xc5be2f0>
<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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.0
Check: examples
Result: ERROR
Running examples in ‘markovchain-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitHighOrderMultivarMC
> ### Title: Function to fit Higher Order Multivariate Markov chain
> ### Aliases: fitHighOrderMultivarMC
>
> ### ** Examples
>
> data <- matrix(c('2', '1', '3', '3', '4', '3', '2', '1', '3', '3', '2', '1',
+ c('2', '4', '4', '4', '4', '2', '3', '3', '1', '4', '3', '3')),
+ ncol = 2, byrow = FALSE)
>
> fitHighOrderMultivarMC(data, order = 2, Norm = 2)
This function is experimental
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
markovchain
--- call from context ---
fitHighOrderMultivarMC(data, order = 2, Norm = 2)
--- call from argument ---
if (class(seqMat) == "data.frame") {
seqMat <- as.matrix(seqMat)
}
--- R stacktrace ---
where 1: fitHighOrderMultivarMC(data, order = 2, Norm = 2)
--- 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: 0x5630e16aa2d0>
<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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(markovchain)
Package: markovchain
Version: 0.8.0
Date: 2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues
> test_check("markovchain")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
markovchain
--- call from context ---
markovchainListFit(data = myHolson)
--- call from argument ---
if (class(data) == "list") {
markovchains <- list()
freqMatrixes <- .mcListFitForList(data)
} else {
if (is.data.frame(data)) {
data <- unname(as.matrix(data))
}
if (!byrow) {
data <- t(data)
}
nCols <- ncol(data)
freqMatrixes <- lapply(seq_len(nCols - 1), function(i) {
matrData <- data[, c(i, i + 1)]
matrData[1, ] <- as.character(matrData[1, ])
validTransition <- any(apply(matrData, 1, function(x) {
!any(is.na(x))
}))
if (validTransition)
createSequenceMatrix(matrData, toRowProbs = FALSE,
sanitize = TRUE)
})
freqMatrixes <- freqMatrixes[!sapply(freqMatrixes, is.null)]
}
--- R stacktrace ---
where 1: markovchainListFit(data = myHolson)
where 2: eval_bare(expr, quo_get_env(quo))
where 3: quasi_label(enquo(object), label, arg = "object")
where 4 at testthat/testFits.R#19: expect_equal(markovchainListFit(data = myHolson), checkmarkovchainFitList)
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/testFits.R#17: test_that("Check markovchainFit & listFit", {
expect_equal(markovchainFit(ciao), simpleMcCiaoFit)
expect_equal(markovchainListFit(data = myHolson), checkmarkovchainFitList)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("markovchain")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data, byrow = TRUE, laplacian = 0, name)
{
if (!any((class(data) %in% c("data.frame", "matrix", "list")))) {
stop("Error: data must be either a matrix or a data.frame or a list")
}
freqMatrixes <- list()
if (class(data) == "list") {
markovchains <- list()
freqMatrixes <- .mcListFitForList(data)
}
else {
if (is.data.frame(data)) {
data <- unname(as.matrix(data))
}
if (!byrow) {
data <- t(data)
}
nCols <- ncol(data)
freqMatrixes <- lapply(seq_len(nCols - 1), function(i) {
matrData <- data[, c(i, i + 1)]
matrData[1, ] <- as.character(matrData[1, ])
validTransition <- any(apply(matrData, 1, function(x) {
!any(is.na(x))
}))
if (validTransition)
createSequenceMatrix(matrData, toRowProbs = FALSE,
sanitize = TRUE)
})
freqMatrixes <- freqMatrixes[!sapply(freqMatrixes, is.null)]
}
if (length(freqMatrixes) == 0) {
return(list())
}
markovchains <- lapply(freqMatrixes, function(freqMatrix) {
freqMatrix <- freqMatrix + laplacian
rSums <- rowSums(freqMatrix)
tMatrix <- freqMatrix/rSums
estMc <- new("markovchain", transitionMatrix = tMatrix)
estMc
})
outMcList <- new("markovchainList", markovchains = markovchains)
out <- list(estimate = outMcList)
if (!missing(name)) {
out$estimate@name <- name
}
return(out)
}
<bytecode: 0x5645e7b8d3f8>
<environment: namespace:markovchain>
--- function search by body ---
Function markovchainListFit in namespace markovchain has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘an_introduction_to_markovchain_package.Rmd’ using rmarkdown
Package: markovchain
Version: 0.8.0
Date: 2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues
Loading required package: TraMineR
TraMineR stable version 2.0-13 (Built: 2019-11-25)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.
Loading required package: colorspace
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
markovchain
--- call from context ---
verifyHomogeneity(inputList = kullback, verbose = TRUE)
--- call from argument ---
if (class(inputList[[i]]) == "matrix") {
checks <- .checkMatrix4Homogeneity(inputList[[i]])
if (!checks)
stop("Error! Element ", i, " to be checked")
} else {
inputList[[i]] <- createSequenceMatrix(stringchar = inputList[[i]])
}
--- R stacktrace ---
where 1: verifyHomogeneity(inputList = kullback, verbose = TRUE)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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-gcc/Work/PKGS/markovchain.Rcheck/vign_test/markovchain",
TRUE, FALSE, "an_introduction_to_markovchain_package", "UTF-8",
"/home/hornik/tmp/scratch/RtmplIWTOq/file71ea5028b91c.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: 0x56309277efe0>
<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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("higher_order_markov_chains.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/markovchain.Rcheck/vign_test/markovchain",
TRUE, FALSE, "higher_order_markov_chains", "UTF-8", "/home/hornik/tmp/scratch/RtmplIWTOq/file71ea3b17cef7.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (seqMat, order = 2, Norm = 2)
{
message("This function is experimental")
if (class(seqMat) == "data.frame") {
seqMat <- as.matrix(seqMat)
}
seqMat <- t(seqMat)
allTmat <- .allTransMat(seqMat, order = order)
freqMat <- .allFreqProbMat(seqMat)
n <- order
uelement <- sort(unique(as.character(seqMat)))
m <- length(uelement)
s <- nrow(seqMat)
lmbda <- rep(1/(n * s), n * s * s)
fit <- Rsolnp::solnp(pars = lmbda, fun = .fn3, eqfun = .eqn3,
eqB = rep(1, s), LB = rep(0, n * s * s), control = list(trace = 0),
allTmat = allTmat, freqMat = freqMat, n = n, m = m, s = s,
Norm = Norm)
return(new("hommc", order = order, Lambda = fit$pars, P = allTmat,
states = uelement, byrow = FALSE))
}
<bytecode: 0x5586a54cacd8>
<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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.0
Check: installed package size
Result: NOTE
installed size is 11.1Mb
sub-directories of 1Mb or more:
libs 9.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.8.0
Check: re-building of vignette outputs
Result: WARN
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: 2019-11-23)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.
Loading required package: colorspace
Warning: LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
Warning: LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
--- finished re-building ‘an_introduction_to_markovchain_package.Rmd’
--- 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
! LaTeX Error: Environment cslreferences undefined.
Error: processing vignette 'gsoc_2017_additions.Rmd' failed with diagnostics:
Failed to compile gsoc_2017_additions.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See gsoc_2017_additions.log for more info.
--- failed 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
--- finished re-building ‘higher_order_markov_chains.Rmd’
--- re-building ‘markvochain_crash_intro.Rmd’ using rmarkdown
--- finished re-building ‘markvochain_crash_intro.Rmd’
SUMMARY: processing the following file failed:
‘gsoc_2017_additions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.0
Check: re-building of vignette outputs
Result: WARN
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: 2019-11-24)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.
Loading required package: colorspace
Warning: LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
Warning: LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
LaTeX Warning: `h' float specifier changed to `ht'.
--- finished re-building ‘an_introduction_to_markovchain_package.Rmd’
--- 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
! LaTeX Error: Environment cslreferences undefined.
Error: processing vignette 'gsoc_2017_additions.Rmd' failed with diagnostics:
Failed to compile gsoc_2017_additions.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See gsoc_2017_additions.log for more info.
--- failed 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
--- finished re-building ‘higher_order_markov_chains.Rmd’
--- re-building ‘markvochain_crash_intro.Rmd’ using rmarkdown
--- finished re-building ‘markvochain_crash_intro.Rmd’
SUMMARY: processing the following file failed:
‘gsoc_2017_additions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc