CRAN Package Check Results for Package rEDM

Last updated on 2026-08-19 10:56:17 CEST.

Check Details

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown 2026-08-19 19:42:47.204 R[42033:61120] XType: Using static font registry. *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: ComputeError(predictions$Observations, predictions$Predictions) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: 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))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) 22: unlist(SweepApply(theta, worker, numProcess)) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: eval(expr, envir) 25: eval(expr, envir) 26: withVisible(eval(expr, envir)) 27: Traceback: 1: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, withCallingHandlers(code, error = function (e) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") } 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: ComputeError(predictions$Observations, predictions$Predictions) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) }, 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)}) 6: FUN(X[[i]], ...) 28: eval(call) 7: lapply(X = S, FUN = FUN, ...) 8: 29: eval(call) 30: with_handlers({ for (expr in tle$exprs) {doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart) 35: call <- conditionCall(e) if (!is.null(call)) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) Traceback: 1: RowCumsum(valid) 2: prefix <- paste("Error in", dcall, ": ") LONG <- 75LFindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 4: ComputeError(predictions$Observations, predictions$Predictions) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ignoreNan = ignoreNan, backend = backend)$predictions) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() Traceback: type = "b") if (w > LONG) watcher$print_value(ev$value, ev$visible, envir) 6: 1: prefix <- paste0(prefix, "\n ") }FUN(X[[i]], ...) }RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose) 7: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: ComputeError(predictions$Observations, predictions$Predictions) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 38: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, evaluate::evaluate(...) 39: embedded = embedded, validLib = validLib, noTime = noTime, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) keep_message = if (is.numeric(options$message)) TRUE else options$message, ignoreNan = ignoreNan, backend = backend)$predictions) stop_on_error = if (is.numeric(options$error)) options$error else { } if (options$error && options$include) invisible(structure(msg, class = "try-error", condition = e))})lapply(X = S, FUN = FUN, ...) 6: 0L else 2L }, output_handler = knit_handlers(options$render, options))FUN(X[[i]], ...) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 7: 8: 40: lapply(X = S, FUN = FUN, ...)doTryCatch(return(expr), name, parentenv, handler)in_dir(input_dir(), expr) 9: 13: 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))doTryCatch(return(expr), name, parentenv, handler) 9: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))) 42: eng_r(options) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers)14: 11: 43: tryCatch(expr, error = function(e) {block_exec(params)FUN(X[[i]], ...) call <- conditionCall(e) if (!is.null(call)) { 15: if (identical(call[[1L]], quote(doTryCatch))) 10: tryCatchList(expr, classes, parentenv, handlers) call <- sys.call(-4L)44: lapply(seq_len(cores), inner.do)call_block(x) 45: process_group(group) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 16: dcall <- deparse(call, nlines = 1L) if (progress && is.function(pb$interrupt)) prefix <- paste("Error in", dcall, ": ") pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) error <<- format(e) })11: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {19: if (progress && is.function(pb$interrupt)) tryCatch(expr, error = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 20: call <- conditionCall(e) if (!is.null(call)) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) if (identical(call[[1L]], quote(doTryCatch))) 21: pb$interrupt()SweepApply(theta, worker, numProcess) if (is_R_CMD_build() || is_R_CMD_check()) call <- sys.call(-4L) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]22: unlist(SweepApply(theta, worker, numProcess)) 23: type = "b")PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (w > LONG) prefix <- paste0(prefix, "\n ") if (progress && is.function(pb$interrupt)) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) pb$interrupt() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (is_R_CMD_build() || is_R_CMD_check()) .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)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) type = "b")24: error <<- format(e) eval(expr, envir) }), 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)) if (w > LONG) 12: prefix <- paste0(prefix, "\n ")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 25: 16: paste0("\n", rule(), error, "\n", rule()))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) } 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) eval(expr, envir)49: process_file(text, output) else prefix <- "Error : "50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 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))}) output_dir = getwd(), ...) 52: vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) SweepApply(theta, worker, numProcess) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 22: 13: unlist(SweepApply(theta, worker, numProcess)) 26: withVisible(eval(expr, envir)) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 54: E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler) watcher$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) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$push(cnd)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$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) switch(on_error, continue = invokeRestart("eval_continue"), }14: 24: FUN(X[[i]], ...)eval(expr, envir) stop = invokeRestart("eval_stop"), error = NULL) })25: 15: outputs <- c(outputs, output) 28: eval(expr, envir) eval(call) }, error = function(e) {29: 26: eval(call)lapply(seq_len(cores), inner.do)withVisible(eval(expr, envir)) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) 30: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: }doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: with_handlers({ if (on_message$silence) {tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) { thisOK <<- FALSE ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) fails <<- c(fails, file) invokeRestart("muffleMessage") 20: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 31: file, conditionMessage(e))) }doWithOneRestart(return(expr), restart)}, warning = function (cnd) })tryCatch(parallel::mclapply(values, worker, mc.cores = cores, { 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp7iRwHB/file69ae55857466.rds") An irrecoverable exception occurred. R is aborting now ... if (getOption("warn") >= 2 || getOption("warn") < 0) {32: return() } watcher$capture_plot_and_output() if (on_warning$capture) {withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart) cnd <- sanitize_call(cnd)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() mc.preschedule = TRUE), error = function(e) NULL) watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir) } if (on_warning$silence) { } TRUE invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)21: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 28: eval(call) 29: eval(call)SweepApply(theta, worker, numProcess) 38: evaluate::evaluate(...) 39: 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, 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))}, handlers) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 40: in_dir(input_dir(), expr) 41: 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$render, options))) 42: eng_r(options) 43: block_exec(params) 44: call_block(x) 45: process_group(group) 46: 22: unlist(SweepApply(theta, worker, numProcess))37: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 47: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", withRestarts(with_handlers({ E = E, showPlot = TRUE) 24: eval(expr, envir) 25: eval(expr, envir) 26: withVisible(eval(expr, envir)) 27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withCallingHandlers(code, error = function (e) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() for (expr in tle$exprs) { if (on_message$capture) { watcher$push(cnd) } ev <- withVisible(eval(expr, envir)) if (on_message$silence) { invokeRestart("muffleMessage") } }), list(rlang_trace_top_env = knit_global())) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, warning = function (cnd) { 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) { } TRUE setwd(wd) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 49: process_file(text, output)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) output_dir = getwd(), ...) 52: vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)54: 38: }) doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({28: engine$weave(file, quiet = quiet, encoding = enc)eval(call) setwd(startdir) evaluate::evaluate(...)29: eval(call) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) texi2pdf(file = output, clean = FALSE, quiet = quiet)31: doWithOneRestart(return(expr), restart) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } 32: withOneRestart(expr, restarts[[1L]]) outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)33: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 39: withRestartList(expr, restarts[-nr])58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp7iRwHB/file69ae55857466.rds") An irrecoverable exception occurred. R is aborting now ... 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))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$render, options)) 40: in_dir(input_dir(), expr) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 38: evaluate::evaluate(...) 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L else 2L 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { }, output_handler = knit_handlers(options$render, options)) 40: in_dir(input_dir(), expr) if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options) 43: block_exec(params) 44: call_block(x) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 45: process_group(group) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 43: block_exec(params) 44: error = function(e) {call_block(x) 45: process_group(group) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 47: 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()))46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 48: 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) 49: process_file(text, output) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 47: 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())) 48: 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())) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: vweave_rmarkdown(...) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 49: process_file(text, output) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 53: engine$weave(file, quiet = quiet, encoding = enc) 52: vweave_rmarkdown(...) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 53: 56: engine$weave(file, quiet = quiet, encoding = enc) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { 57: tryCatch({ engine$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) 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)))}) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp7iRwHB/file69ae55857466.rds") An irrecoverable exception occurred. R is aborting now ... message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp7iRwHB/file69ae55857466.rds") An irrecoverable exception occurred. R is aborting now ... Quitting from rEDM-tutorial.Rmd:466-469 [smap_thrips] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `data.frame()`: ! arguments imply differing number of rows: 15, 0 --- Backtrace: ▆ 1. └─rEDM::PredictNonlinear(...) 2. └─base::data.frame(Theta = theta, rho = rho) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rEDM-tutorial.Rmd' failed with diagnostics: arguments imply differing number of rows: 15, 0 --- failed re-building ‘rEDM-tutorial.Rmd’ SUMMARY: processing the following file failed: ‘rEDM-tutorial.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-arm64