CRAN Package Check Results for Package multistateutils

Last updated on 2020-04-25 07:49:56 CEST.

Check Details

Version: 1.2.4
Check: examples
Result: ERROR
    Running examples in ‘multistateutils-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cohort_simulation
    > ### Title: Runs a cohort discrete event simulation
    > ### Aliases: cohort_simulation
    >
    > ### ** Examples
    >
    > library(multistateutils)
    > library(mstate)
    Loading required package: survival
    > library(flexsurv)
    >
    > # Convert data to long
    > data(ebmt3)
    > tmat <- trans.illdeath()
    > long <- msprep(time=c(NA, 'prtime', 'rfstime'),
    + status=c(NA, 'prstat', 'rfsstat'),
    + data=ebmt3,
    + trans=tmat,
    + keep=c('age', 'dissub'))
    >
    > # Fit parametric models
    > models <- lapply(1:3, function(i) {
    + flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
    + })
    >
    > sim <- cohort_simulation(models, ebmt3, tmat)
    
     *** caught illegal operation ***
    address 0x10947c8e0, cause 'illegal opcode'
    
    Traceback:
     1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs)
     2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs))
     3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times, start_states)
     4: state_occupancy(models, trans_mat, newdata, tcovs, start_time, start_state, ci, M, agelimit, agecol, agescale)
     5: cohort_simulation(models, ebmt3, tmat)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-osx-x86_64

Version: 1.2.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [3s/5s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     32: withOneRestart(expr, restarts[[1L]])
     33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     34: 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() })
     35: FUN(X[[i]], ...)
     36: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     37: force(code)
     38: doWithOneRestart(return(expr), restart)
     39: withOneRestart(expr, restarts[[1L]])
     40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     41: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     43: 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)
     44: 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)
     45: test_check("multistateutils")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-osx-x86_64

Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Examples.Rmd’ using rmarkdown
    
     *** caught illegal operation ***
    address 0x10a9608e0, cause 'illegal opcode'
    
    Traceback:
     1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs)
     2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs))
     3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times, start_states)
     4: state_occupancy(models, trans_mat, newdata_ext, tcovs, initial_times, start_states, ci, M, agelimit, agecol, agescale)
     5: predict_transitions(models, newdata, tmat, times = 365)
     6: eval(expr, envir, enclos)
     7: eval(expr, envir, enclos)
     8: withVisible(eval(expr, envir, enclos))
     9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    13: evaluate::evaluate(...)
    14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    15: 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$render, options)))
    16: block_exec(params)
    17: call_block(x)
    18: process_group.block(group)
    19: process_group(group)
    20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    21: process_file(text, output)
    22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
    24: vweave_rmarkdown(...)
    25: engine$weave(file, quiet = quiet, encoding = enc)
    26: doTryCatch(return(expr), name, parentenv, handler)
    27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    28: tryCatchList(expr, classes, parentenv, handlers)
    29: tryCatch({ engine$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) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    30: tools:::buildVignettes(dir = "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/multistateutils.Rcheck/vign_test/multistateutils", ser_elibs = "/var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T//RtmpNBPtbl/file154df10e09141.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-osx-x86_64

Version: 1.2.4
Check: examples
Result: ERROR
    Running examples in ‘multistateutils-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cohort_simulation
    > ### Title: Runs a cohort discrete event simulation
    > ### Aliases: cohort_simulation
    >
    > ### ** Examples
    >
    > library(multistateutils)
    > library(mstate)
    Loading required package: survival
    > library(flexsurv)
    >
    > # Convert data to long
    > data(ebmt3)
    > tmat <- trans.illdeath()
    > long <- msprep(time=c(NA, 'prtime', 'rfstime'),
    + status=c(NA, 'prstat', 'rfsstat'),
    + data=ebmt3,
    + trans=tmat,
    + keep=c('age', 'dissub'))
    >
    > # Fit parametric models
    > models <- lapply(1:3, function(i) {
    + flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
    + })
    >
    > sim <- cohort_simulation(models, ebmt3, tmat)
    
     *** caught illegal operation ***
    address 0x10ac9c042, cause 'illegal opcode'
    
    Traceback:
     1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs)
     2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs))
     3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times, start_states)
     4: state_occupancy(models, trans_mat, newdata, tcovs, start_time, start_state, ci, M, agelimit, agecol, agescale)
     5: cohort_simulation(models, ebmt3, tmat)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-osx-x86_64

Version: 1.2.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [4s/5s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     32: withOneRestart(expr, restarts[[1L]])
     33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     34: 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() })
     35: FUN(X[[i]], ...)
     36: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     37: force(code)
     38: doWithOneRestart(return(expr), restart)
     39: withOneRestart(expr, restarts[[1L]])
     40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     41: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     43: 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)
     44: 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)
     45: test_check("multistateutils")
     An irrecoverable exception occurred. R is aborting now ...
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Examples.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
     *** caught illegal operation ***
    address 0x11500c042, cause 'illegal opcode'
    
    Traceback:
     1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs)
     2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs))
     3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times, start_states)
     4: state_occupancy(models, trans_mat, newdata_ext, tcovs, initial_times, start_states, ci, M, agelimit, agecol, agescale)
     5: predict_transitions(models, newdata, tmat, times = 365)
     6: eval(expr, envir, enclos)
     7: eval(expr, envir, enclos)
     8: withVisible(eval(expr, envir, enclos))
     9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    13: evaluate::evaluate(...)
    14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    15: 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$render, options)))
    16: block_exec(params)
    17: call_block(x)
    18: process_group.block(group)
    19: process_group(group)
    20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    21: process_file(text, output)
    22: knit(input, text = text, envir = envir, quiet = quiet)
    23: knit2html(..., force_v1 = TRUE)
    24: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    25: vweave(...)
    26: engine$weave(file, quiet = quiet, encoding = enc)
    27: doTryCatch(return(expr), name, parentenv, handler)
    28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    29: tryCatchList(expr, classes, parentenv, handlers)
    30: tryCatch({ engine$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) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    31: tools:::buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/multistateutils.Rcheck/vign_test/multistateutils", ser_elibs = "/tmp/RtmpybPbXs/file140427b1135c.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-osx-x86_64

Version: 1.2.4
Check: examples
Result: ERROR
    Running examples in ‘multistateutils-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cohort_simulation
    > ### Title: Runs a cohort discrete event simulation
    > ### Aliases: cohort_simulation
    >
    > ### ** Examples
    >
    > library(multistateutils)
    > library(mstate)
    Loading required package: survival
    > library(flexsurv)
    >
    > # Convert data to long
    > data(ebmt3)
    > tmat <- trans.illdeath()
    > long <- msprep(time=c(NA, 'prtime', 'rfstime'),
    + status=c(NA, 'prstat', 'rfsstat'),
    + data=ebmt3,
    + trans=tmat,
    + keep=c('age', 'dissub'))
    >
    > # Fit parametric models
    > models <- lapply(1:3, function(i) {
    + flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
    + })
    >
    > sim <- cohort_simulation(models, ebmt3, tmat)
    
     *** caught illegal operation ***
    address 0x10fdd78d0, cause 'illegal opcode'
    
    Traceback:
     1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs)
     2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat, start_times, start_states - 1, tcovs))
     3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times, start_states)
     4: state_occupancy(models, trans_mat, newdata, tcovs, start_time, start_state, ci, M, agelimit, agecol, agescale)
     5: cohort_simulation(models, ebmt3, tmat)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-osx-x86_64

Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     8: withVisible(eval(expr, envir, enclos))
     9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    13: evaluate::evaluate(...)
    14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    15: 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$render, options)))
    16: block_exec(params)
    17: call_block(x)
    18: process_group.block(group)
    19: process_group(group)
    20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    21: process_file(text, output)
    22: knit(input, text = text, envir = envir, quiet = quiet)
    23: knit2html(..., force_v1 = TRUE)
    24: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    25: vweave(...)
    26: engine$weave(file, quiet = quiet, encoding = enc)
    27: doTryCatch(return(expr), name, parentenv, handler)
    28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    29: tryCatchList(expr, classes, parentenv, handlers)
    30: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
    31: buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/multistateutils.Rcheck/vign_test/multistateutils")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-osx-x86_64