Check results for 'cbcTools'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:26:05 UTC
checking for file ‘cbcTools/DESCRIPTION’ ... OK
this is package ‘cbcTools’ version ‘0.7.1’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘cbcTools’ can be installed ... [2s/2s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking whether startup messages can be suppressed ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [4s/2s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [2s/2s] OK Running ‘testthat.R’ [2s/2s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [24s/17s] ERROR Error(s) in re-building vignettes: --- re-building ‘choices.Rmd’ using rmarkdown --- finished re-building ‘choices.Rmd’ --- re-building ‘d_error.Rmd’ using rmarkdown --- finished re-building ‘d_error.Rmd’ --- re-building ‘design.Rmd’ using rmarkdown --- finished re-building ‘design.Rmd’ --- re-building ‘encoding.Rmd’ using rmarkdown --- finished re-building ‘encoding.Rmd’ --- re-building ‘getting-started.Rmd’ using rmarkdown *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: getV(coefs, data$X, data$scalePar) 2: getMnlProbs(object, data, obsID, interval, level, numDrawsCI, getV, getVDraws) 3: predict.logitr(model) 4: stats::predict(model) 5: logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ model <- logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) model$sample_size <- unique(data_subset$sample_size) return(model)}, error = function(e) { return(NULL)}) 10: FUN(X[[i]], ...) 11: lapply(X = S, FUN = FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: 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, nlines = 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))}) 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 18: FUN(X[[i]], ...) 19: lapply(seq_len(cores), inner.do) 20: parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores) 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 22: suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)}) 23: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 24: suppressMessages(suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)})) 25: estimate_models_parallel_internal(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 26: estimate_models_parallel(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 27: cbc_power(choices) 28: eval(expr, envir) 29: eval(expr, envir) 30: withVisible(eval(expr, envir)) 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 32: eval(call) 33: eval(call) 34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestartList(expr, restarts[-nr]) 38: doWithOneRestart(return(expr), restart) 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 40: withRestartList(expr, restarts) 41: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 42: evaluate::evaluate(...) 43: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 44: in_dir(input_dir(), expr) 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 46: eng_r(options) 47: block_exec(params) 48: call_block(x) 49: process_group(group) 50: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 51: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 52: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 53: process_file(text, output) 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 56: vweave_rmarkdown(...) 57: engine$weave(file, quiet = quiet, encoding = enc) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch({ engine$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)))}) 62: tools:::.buildOneVignette("getting-started.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/cbcTools.Rcheck/vign_test/cbcTools", TRUE, FALSE, "getting-started", "UTF-8", "/Volumes/Temp/tmp/Rtmp3zu2vE/file9fd26d44d773.rds") An irrecoverable exception occurred. R is aborting now ... Warning in file("", "w+b") : cannot open file '/Volumes/Temp/tmp/RtmpobLhIo/Rfa23a13a0e657': No such file or directory Quitting from getting-started.Rmd:178-181 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cannot open the connection ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from getting-started.Rmd:178-181 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ file("", "w+b") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'getting-started.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘getting-started.Rmd’ --- re-building ‘power.Rmd’ using rmarkdown *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: getV(coefs, data$X, data$scalePar) 2: getMnlProbs(object, data, obsID, interval, level, numDrawsCI, getV, getVDraws) 3: predict.logitr(model) 4: stats::predict(model) 5: logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ model <- logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) model$sample_size <- unique(data_subset$sample_size) return(model)}, error = function(e) { return(NULL)}) 10: FUN(X[[i]], ...) 11: lapply(X = S, FUN = FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: 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, nlines = 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))}) 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 18: FUN(X[[i]], ...) 19: lapply(seq_len(cores), inner.do) 20: parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores) 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 22: suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)}) 23: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 24: suppressMessages(suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)})) 25: estimate_models_parallel_internal(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 26: estimate_models_parallel(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 27: cbc_power(data = choices, outcome = "choice", obsID = "obsID", n_q = 6, n_breaks = 10) 28: eval(expr, envir) 29: eval(expr, envir) 30: withVisible(eval(expr, envir)) 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 32: eval(call) 33: eval(call) 34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestartList(expr, restarts[-nr]) 38: doWithOneRestart(return(expr), restart) 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 40: withRestartList(expr, restarts) 41: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 42: evaluate::evaluate(...) 43: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 44: in_dir(input_dir(), expr) 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 46: eng_r(options) 47: block_exec(params) 48: call_block(x) 49: process_group(group) 50: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 51: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 52: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 53: process_file(text, output) 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 56: vweave_rmarkdown(...) 57: engine$weave(file, quiet = quiet, encoding = enc) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch({ engine$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)))}) 62: tools:::.buildOneVignette("power.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/cbcTools.Rcheck/vign_test/cbcTools", TRUE, FALSE, "power", "UTF-8", "/Volumes/Temp/tmp/Rtmp3zu2vE/file9fd255e1520b.rds") An irrecoverable exception occurred. R is aborting now ... Traceback: 1: getV(coefs, data$X, data$scalePar) 2: getMnlProbs(object, data, obsID, interval, level, numDrawsCI, getV, getVDraws) 3: predict.logitr(model) 4: stats::predict(model) 5: logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ model <- logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) model$sample_size <- unique(data_subset$sample_size) return(model)}, error = function(e) { return(NULL)}) 10: FUN(X[[i]], ...) 11: lapply(X = S, FUN = FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: 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, nlines = 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))}) 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 18: FUN(X[[i]], ...) 19: lapply(seq_len(cores), inner.do) 20: parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores) 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 22: suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)}) 23: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 24: suppressMessages(suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)})) 25: estimate_models_parallel_internal(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 26: estimate_models_parallel(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 27: cbc_power(data = choices, outcome = "choice", obsID = "obsID", n_q = 6, n_breaks = 10) 28: eval(expr, envir) 29: eval(expr, envir) 30: withVisible(eval(expr, envir)) 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 32: eval(call) 33: eval(call) 34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestartList(expr, restarts[-nr]) 38: doWithOneRestart(return(expr), restart) 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 40: withRestartList(expr, restarts) 41: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 42: evaluate::evaluate(...) 43: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 44: in_dir(input_dir(), expr) 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 46: eng_r(options) 47: block_exec(params) 48: call_block(x) 49: process_group(group) 50: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 51: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 52: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 53: process_file(text, output) 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 56: vweave_rmarkdown(...) 57: engine$weave(file, quiet = quiet, encoding = enc) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch({ engine$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)))}) 62: tools:::.buildOneVignette("power.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/cbcTools.Rcheck/vign_test/cbcTools", TRUE, FALSE, "power", "UTF-8", "/Volumes/Temp/tmp/Rtmp3zu2vE/file9fd255e1520b.rds") An irrecoverable exception occurred. R is aborting now ... *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: getV(coefs, data$X, data$scalePar) 2: getMnlProbs(object, data, obsID, interval, level, numDrawsCI, getV, getVDraws) 3: predict.logitr(model) 4: stats::predict(model) 5: logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ model <- logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) model$sample_size <- unique(data_subset$sample_size) return(model)}, error = function(e) { return(NULL)}) 10: FUN(X[[i]], ...) 11: lapply(X = S, FUN = FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: 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, nlines = 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))}) 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 18: FUN(X[[i]], ...) 19: lapply(seq_len(cores), inner.do) 20: parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores) 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 22: suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)}) 23: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 24: suppressMessages(suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)})) 25: estimate_models_parallel_internal(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 26: estimate_models_parallel(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 27: cbc_power(data = choices, outcome = "choice", obsID = "obsID", n_q = 6, n_breaks = 10) 28: eval(expr, envir) 29: eval(expr, envir) 30: withVisible(eval(expr, envir)) 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 32: eval(call) 33: eval(call) 34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestartList(expr, restarts[-nr]) 38: doWithOneRestart(return(expr), restart) 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 40: withRestartList(expr, restarts) 41: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 42: evaluate::evaluate(...) 43: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 44: in_dir(input_dir(), expr) 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 46: eng_r(options) 47: block_exec(params) 48: call_block(x) 49: process_group(group) 50: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 51: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 52: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 53: process_file(text, output) 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 56: vweave_rmarkdown(...) 57: engine$weave(file, quiet = quiet, encoding = enc) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch({ engine$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)))}) 62: tools:::.buildOneVignette("power.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/cbcTools.Rcheck/vign_test/cbcTools", TRUE, FALSE, "power", "UTF-8", "/Volumes/Temp/tmp/Rtmp3zu2vE/file9fd255e1520b.rds") An irrecoverable exception occurred. R is aborting now ... *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: getV(coefs, data$X, data$scalePar) 2: getMnlProbs(object, data, obsID, interval, level, numDrawsCI, getV, getVDraws) 3: predict.logitr(model) 4: stats::predict(model) 5: logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch({ model <- logitr::logitr(data = data_subset, outcome = outcome, obsID = obsID, pars = pars, randPars = randPars, panelID = panelID, ...) model$sample_size <- unique(data_subset$sample_size) return(model)}, error = function(e) { return(NULL)}) 10: FUN(X[[i]], ...) 11: lapply(X = S, FUN = FUN, ...) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: 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, nlines = 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))}) 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 18: FUN(X[[i]], ...) 19: lapply(seq_len(cores), inner.do) 20: parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores) 21: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 22: suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)}) 23: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 24: suppressMessages(suppressWarnings({ models <- parallel::mclapply(data_list, estimate_single_model, mc.cores = n_cores)})) 25: estimate_models_parallel_internal(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 26: estimate_models_parallel(data_list, outcome, obsID, pars, randPars, panelID, n_cores, ...) 27: cbc_power(data = choices, outcome = "choice", obsID = "obsID", n_q = 6, n_breaks = 10) 28: eval(expr, envir) 29: eval(expr, envir) 30: withVisible(eval(expr, envir)) 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 32: eval(call) 33: eval(call) 34: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestartList(expr, restarts[-nr]) 38: doWithOneRestart(return(expr), restart) 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 40: withRestartList(expr, restarts) 41: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 42: evaluate::evaluate(...) 43: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 44: in_dir(input_dir(), expr) 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 46: eng_r(options) 47: block_exec(params) 48: call_block(x) 49: process_group(group) 50: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 51: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 52: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 53: process_file(text, output) 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 55: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 56: vweave_rmarkdown(...) 57: engine$weave(file, quiet = quiet, encoding = enc) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch({ engine$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)))}) 62: tools:::.buildOneVignette("power.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/cbcTools.Rcheck/vign_test/cbcTools", TRUE, FALSE, "power", "UTF-8", "/Volumes/Temp/tmp/Rtmp3zu2vE/file9fd255e1520b.rds") An irrecoverable exception occurred. R is aborting now ... Warning in file("", "w+b") : cannot open file '/Volumes/Temp/tmp/Rtmp8jH4z0/Rfa2e8459f2e9': No such file or directory Quitting from power.Rmd:114-127 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cannot open the connection ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from power.Rmd:114-127 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ file("", "w+b") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'power.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘power.Rmd’ --- re-building ‘priors.Rmd’ using rmarkdown --- finished re-building ‘priors.Rmd’ --- re-building ‘profiles.Rmd’ using rmarkdown --- finished re-building ‘profiles.Rmd’ SUMMARY: processing the following files failed: ‘getting-started.Rmd’ ‘power.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [2s/2s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '