CRAN Package Check Results for Package rEDM

Last updated on 2026-08-31 23:50:12 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.0.1	3.45	222.09	225.54	OK
r-devel-linux-x86_64-debian-gcc	2.0.1	2.45	228.69	231.14	OK
r-devel-linux-x86_64-fedora-clang	2.0.2			183.45	OK
r-devel-linux-x86_64-fedora-gcc	2.0.2			186.30	OK
r-devel-windows-x86_64	2.0.1	5.00	132.00	137.00	OK
r-patched-linux-x86_64	2.0.1	3.38	211.41	214.79	OK
r-release-linux-x86_64	2.0.1	3.39	203.63	207.02	OK
r-release-macos-arm64	2.0.2	1.00	56.00	57.00	OK
r-release-macos-x86_64	2.0.2	3.00	208.00	211.00	OK
r-release-windows-x86_64	2.0.2	7.00	137.00	144.00	OK
r-oldrel-macos-arm64	2.0.2	1.00	22.00	23.00	ERROR
r-oldrel-macos-x86_64	2.0.2	3.00	201.00	204.00	OK
r-oldrel-windows-x86_64	2.0.2	8.00	164.00	172.00	OK

Check Details

Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown 2026-09-01 05:34:56.589 R[49198:77620] 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, Traceback: 1: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, 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, ComputeError(predictions$Observations, predictions$Predictions) 5: ignoreNan = ignoreNan, backend = backend) 4: 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, 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)$predictions) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 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") 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)) 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"))) { 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) Traceback: Traceback: 1: RowCumsum(valid) 1: 17: 13: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, 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)14: 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: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: 10: tryCatchList(expr, classes, parentenv, handlers) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)11: tryCatch(expr, error = function(e) {17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: call <- conditionCall(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 3: 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", 20: E = E, showPlot = TRUE)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: if (!is.null(call)) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, SweepApply(theta, worker, numProcess) tau = tau, theta = th, exclusionRadius = exclusionRadius, 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) embedded = embedded, validLib = validLib, noTime = noTime, 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) 22: ignoreNan = ignoreNan, backend = backend) 4: ComputeError(predictions$Observations, predictions$Predictions) 5: .Internal(printDeferredWarnings())unlist(SweepApply(theta, worker, numProcess)) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)13: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) 6: FUN(X[[i]], ...) 14: 24: eval(expr, envir) 25: eval(expr, envir)FUN(X[[i]], ...) 26: 24: 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {15: lapply(seq_len(cores), inner.do) 16: eval(expr, envir) watcher$push(cnd) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) } if (on_message$silence) { invokeRestart("muffleMessage") }25: 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) eval(expr, envir)24: 26: eval(expr, envir) withVisible(eval(expr, envir)) 11: 25: }, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {27: return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) }tryCatch(expr, error = function(e) { if (on_warning$silence) { call <- conditionCall(e) invokeRestart("muffleWarning")withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { }eval(expr, envir)}, error = function (cnd) 26: withVisible(eval(expr, envir)){ watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_message$capture) {27: watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") } cnd <- sanitize_call(cnd)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) watcher$capture_plot_and_output()}, warning = function (cnd) {}) if (on_message$capture) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()28: eval(call) watcher$push(cnd) if (!is.null(call)) { } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) {{ if (identical(call[[1L]], quote(doTryCatch))) if (getOption("warn") >= 2 || getOption("warn") < 0) { call <- sys.call(-4L) invokeRestart("muffleWarning")29: dcall <- deparse(call, nlines = 1L)eval(call) } prefix <- paste("Error in", dcall, ": ") return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) 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], }, error = function (cnd) type = "b") if (w > LONG) watcher$push(cnd)30: { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 28: eval(call) prefix <- paste0(prefix, "\n ") } } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) if (on_warning$silence) { invokeRestart("muffleWarning")29: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE }eval(call) }, error = function (cnd) 30: {with_handlers({}, handlers) } invisible(structure(msg, class = "try-error", condition = e))}) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 28: eval(call) for (expr in tle$exprs) {31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) ev <- withVisible(eval(expr, envir))29: eval(call)12: 34: doWithOneRestart(return(expr), restart) 35: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$print_value(ev$value, ev$visible, envir)36: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)withRestartList(expr, restarts) 37: 30: 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: withRestarts(with_handlers({with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) } TRUE}, handlers) 31: lapply(seq_len(cores), inner.do) 16: for (expr in tle$exprs) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: 17: doTryCatch(return(expr), name, parentenv, handler) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEwithRestartList(expr, restarts[-nr])18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 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 }, output_handler = knit_handlers(options$render, options)) 40: in_dir(input_dir(), expr) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {34: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options) }, handlers)doWithOneRestart(return(expr), restart)19: 43: block_exec(params) 44: call_block(x) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: 45: withRestartList(expr, restarts[-nr]) process_group(group) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) tryCatchList(expr, classes, parentenv, handlers)36: withRestartList(expr, restarts) 37: 34: withRestarts(with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) ev <- withVisible(eval(expr, envir)) 20: 47: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$exprs) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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) error = function(e) { watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$print_value(ev$value, ev$visible, envir) } TRUE mc.preschedule = TRUE), error = function(e) NULL) 21: 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, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L 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: else 2L }, output_handler = knit_handlers(options$render, options)) 40: in_dir(input_dir(), expr) 41: 22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, unlist(SweepApply(theta, worker, numProcess))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) keep_warning = if (is.numeric(options$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$error else { 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: if (options$error && options$include) eval(expr, envir)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 38: 0Levaluate::evaluate(...) else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options) }), list(rlang_trace_top_env = knit_global())), function(loc) {39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, setwd(wd) 25: 43: write_utf8(res, output %n% stdout())eval(expr, envir) paste0("\nQuitting from ", loc, if (!is.null(error)) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { paste0("\n", rule(), error, "\n", rule())) if (options$error && options$include) 0L else 2Lblock_exec(params)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }, output_handler = knit_handlers(options$render, options))26: 44: call_block(x) 45: 49: process_group(group)withVisible(eval(expr, envir))process_file(text, output) 27: withCallingHandlers(code, error = function (e) 50: 40: rlang::entrace(e), message = function (cnd) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), {in_dir(input_dir(), expr) watcher$capture_plot_and_output()46: output_dir = getwd(), ...) 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$render, options))) 42: eng_r(options) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 52: if (on_message$capture) {vweave_rmarkdown(...) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 47: watcher$push(cnd) }53: 43: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt()block_exec(params) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) engine$weave(file, quiet = quiet, encoding = enc)44: call_block(x) 54: doTryCatch(return(expr), name, parentenv, handler) 45: process_group(group) 46: 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()) }), list(rlang_trace_top_env = knit_global())), function(loc) { if (on_message$silence) { error <<- format(e) setwd(wd) invokeRestart("muffleMessage") write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 49: process_file(text, output) }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } 55: 50: })tryCatchOne(expr, names, parentenv, handlers[[1L]])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$capture_plot_and_output()56: 51: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: }vweave_rmarkdown(...) if (on_warning$silence) { invokeRestart("muffleWarning")47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { } if (progress && is.function(pb$interrupt)) }, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)53: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) }), list(rlang_trace_top_env = knit_global()))engine$weave(file, quiet = quiet, encoding = enc)}, error = function(e) { 28: thisOK <<- FALSE48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), fails <<- c(fails, file)eval(call) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) file, conditionMessage(e))) error = function(e) {})57: tryCatch({29: 58: eval(call)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (progress && is.function(pb$interrupt)) pb$interrupt()30: with_handlers({ if (is_R_CMD_build() || is_R_CMD_check()) engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e) setwd(startdir) }), list(rlang_trace_top_env = knit_global())), function(loc) { output <- find_vignette_product(name, by = "weave", engine = engine) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpoA0Cgq/file99924ed7157c.rds") for (expr in tle$exprs) { if (!have.makefile && vignette_is_tex(output)) { ev <- withVisible(eval(expr, envir)) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }An irrecoverable exception occurred. R is aborting now ... outputs <- c(outputs, output)}, error = function(e) { setwd(wd) thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 58: write_utf8(res, output %n% stdout()) watcher$capture_plot_and_output() paste0("\nQuitting from ", loc, if (!is.null(error)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", watcher$print_value(ev$value, ev$visible, envir) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpoA0Cgq/file99924ed7157c.rds") An irrecoverable exception occurred. R is aborting now ... paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 49: process_file(text, output) 50: } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: doWithOneRestart(return(expr), restart)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) 54: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 38: evaluate::evaluate(...) 39: 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L engine$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)))}) 58: else 2L }, output_handler = knit_handlers(options$render, options)) 40: in_dir(input_dir(), expr) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpoA0Cgq/file99924ed7157c.rds") An irrecoverable exception occurred. R is aborting now ... keep_message = if (is.numeric(options$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: 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) }) 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()))}, 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(), ...) 52: vweave_rmarkdown(...) 53: engine$weave(file, quiet = quiet, encoding = enc) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$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) 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/RtmpoA0Cgq/file99924ed7157c.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