CRAN Package Check Results for Package rEDM

Last updated on 2026-08-11 12:50:10 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.0.1	3.35	222.44	225.79	OK
r-devel-linux-x86_64-debian-gcc	2.0.1	2.33	221.60	223.93	OK
r-devel-linux-x86_64-fedora-clang	2.0.1			180.02	OK
r-devel-linux-x86_64-fedora-gcc	2.0.1			180.83	OK
r-devel-windows-x86_64	2.0.1	5.00	131.00	136.00	OK
r-patched-linux-x86_64	2.0.1	3.74	206.25	209.99	OK
r-release-linux-x86_64	2.0.1	3.45	205.25	208.70	OK
r-release-macos-arm64	2.0.1	1.00	67.00	68.00	OK
r-release-macos-x86_64	2.0.1	3.00	195.00	198.00	OK
r-release-windows-x86_64	2.0.1	6.00	128.00	134.00	OK
r-oldrel-macos-arm64	2.0.1	1.00	217.00	218.00	ERROR
r-oldrel-macos-x86_64	2.0.1	3.00	199.00	202.00	OK
r-oldrel-windows-x86_64	2.0.1	5.00	164.00	169.00	OK

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 2026-08-11 18:43:53.731 R[39678:58403] 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]], ...) Traceback: 1: RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) 4: 15: lapply(seq_len(cores), inner.do) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) ComputeError(predictions$Observations, predictions$Predictions) Traceback: Traceback: 1: RowCumsum(valid)22: 1: RowCumsum(valid) 2: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 5: unlist(SweepApply(theta, worker, numProcess)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose) verbose = verbose) 3: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 3: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 23: ignoreNan = ignoreNan, backend = backend)$predictions)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)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)$predictions) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) tau = tau, theta = th, exclusionRadius = exclusionRadius, 24: dcall <- deparse(call, nlines = 1L) 6: prefix <- paste("Error in", dcall, ": ") embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) eval(expr, envir) 4: FUN(X[[i]], ...) LONG <- 75L25: sm <- strsplit(conditionMessage(e), "\n")[[1L]]eval(expr, envir)ComputeError(predictions$Observations, predictions$Predictions) 5: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")26: withVisible(eval(expr, envir)) 27: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 7: withCallingHandlers(code, error = function (e) lapply(X = S, FUN = FUN, ...) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 8: embedded = embedded, validLib = validLib, noTime = noTime, if (is.na(w)) rlang::entrace(e), message = function (cnd) ignoreNan = ignoreNan, backend = backend)$predictions){ doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 6: if (w > LONG) if (on_message$capture) {FUN(X[[i]], ...) watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") 7: }lapply(X = S, FUN = FUN, ...) 8: 11: }, warning = function (cnd) prefix <- paste0(prefix, "\n ") }doTryCatch(return(expr), name, parentenv, handler){tryCatch(expr, error = function(e) { else prefix <- "Error : " 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], 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: if (getOption("warn") >= 2 || getOption("warn") < 0) { type = "b") msg <- paste0(prefix, conditionMessage(e), "\n")tryCatchList(expr, classes, parentenv, handlers) if (w > LONG) return() prefix <- paste0(prefix, "\n ") } watcher$capture_plot_and_output()11: if (on_warning$capture) { .Internal(seterrmessage(msg[1L])) cnd <- sanitize_call(cnd) watcher$push(cnd) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {}) if (identical(call[[1L]], quote(doTryCatch))) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) .Internal(printDeferredWarnings())12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$push(cnd) }14: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 28: eval(call) 29: eval(call) 30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart) 32: withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) call <- sys.call(-4L)FUN(X[[i]], ...)34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]15: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")lapply(seq_len(cores), inner.do)36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } invisible(structure(msg, class = "try-error", condition = e))16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) TRUE if (is.na(w)) }) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) type = "b") 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (w > LONG) 14: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) FUN(X[[i]], ...) prefix <- paste0(prefix, "\n ") } 19: 38: 15: else prefix <- "Error : "lapply(seq_len(cores), inner.do)evaluate::evaluate(...) 39: 16: tryCatchList(expr, classes, parentenv, handlers)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, msg <- paste0(prefix, conditionMessage(e), "\n") stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) mc.preschedule = TRUE), error = function(e) NULL) .Internal(seterrmessage(msg[1L])) 21: 17: doTryCatch(return(expr), name, parentenv, handler) SweepApply(theta, worker, numProcess) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) else 2L 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 19: }, output_handler = knit_handlers(options$render, options))22: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) 22: unlist(SweepApply(theta, worker, numProcess)) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: eval(expr, envir) 25: eval(expr, envir) 26: withVisible(eval(expr, envir))13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage")FUN(X[[i]], ...) } 15: 40: }, warning = function (cnd) unlist(SweepApply(theta, worker, numProcess)){in_dir(input_dir(), expr)lapply(seq_len(cores), inner.do) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: eval(expr, envir) 25: eval(expr, envir) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 26: 16: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {withVisible(eval(expr, envir)) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } watcher$capture_plot_and_output() if (on_message$silence) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } if (on_warning$capture) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) if (on_warning$capture) { watcher$push(cnd) if (options$error && options$include) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) }{ if (on_warning$silence) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})17: invokeRestart("muffleWarning")28: eval(call) 29: eval(call) 30: with_handlers({ }}, error = function (cnd) doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) { 0L for (expr in tle$exprs) { watcher$capture_plot_and_output() else 2L }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options) 43: block_exec(params) cnd <- sanitize_call(cnd)22: unlist(SweepApply(theta, worker, numProcess)) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 44: call_block(x) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 24: watcher$push(cnd)eval(expr, envir) 45: switch(on_error, continue = invokeRestart("eval_continue"), 25: eval(expr, envir) stop = invokeRestart("eval_stop"), error = NULL) process_group(group) 46: ev <- withVisible(eval(expr, envir))26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withVisible(eval(expr, envir)) 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {}) watcher$capture_plot_and_output() error = function(e) { watcher$capture_plot_and_output() 28: if (on_message$capture) { watcher$push(cnd) }eval(call) 29: eval(call) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (on_message$silence) { watcher$print_value(ev$value, ev$visible, envir) invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() error <<- format(e) }30: }) }with_handlers({ for (expr in tle$exprs) { watcher$capture_plot_and_output() TRUE if (on_warning$capture) { ev <- withVisible(eval(expr, envir)) cnd <- sanitize_call(cnd) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) watcher$push(cnd) }}, handlers) 31: 47: if (on_warning$silence) { with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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)}) 28: eval(call) 31: doWithOneRestart(return(expr), restart) error = function(e) {29: eval(call) 30: with_handlers({ 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) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart) 32: doWithOneRestart(return(expr), restart)51: withOneRestart(expr, restarts[[1L]]) 32: 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 32: output_dir = getwd(), ...)withRestartList(expr, restarts[-nr]) withOneRestart(expr, restarts[[1L]])withOneRestart(expr, restarts[[1L]]) 33: withRestartList(expr, restarts[-nr]) 34: 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 52: 37: 33: withRestartList(expr, restarts[-nr]) vweave_rmarkdown(...)34: withRestarts(with_handlers({doWithOneRestart(return(expr), restart) doWithOneRestart(return(expr), restart)53: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) } 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) TRUE } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({ for (expr in tle$exprs) { }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) ev <- withVisible(eval(expr, envir))38: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 38: evaluate::evaluate(...) evaluate::evaluate(...) 54: 39: doTryCatch(return(expr), name, parentenv, handler)39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 38: evaluate::evaluate(...) 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 0L keep_message = if (is.numeric(options$message)) TRUE else options$message, 57: else 2L }, output_handler = knit_handlers(options$render, options))tryCatch({ 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$error else { if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L40: 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, setwd(startdir) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) }, output_handler = knit_handlers(options$render, options)) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))40: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE 0Lin_dir(input_dir(), expr) 42: eng_r(options) else 2L fails <<- c(fails, file) }, output_handler = knit_handlers(options$render, options)))43: block_exec(params) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 42: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L file, conditionMessage(e)))}) else 2L }, output_handler = knit_handlers(options$render, options)))eng_r(options)44: call_block(x)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/Rtmp6mBeul/file6aea1f53ede3.rds") 45: process_group(group) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), An irrecoverable exception occurred. R is aborting now ... error = function(e) {42: eng_r(options) 43: 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) {block_exec(params) 44: call_block(x) 45: process_group(group) 46: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 43: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()block_exec(params) 44: call_block(x) 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), 45: process_group(group) 46: if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(e)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)47: if (progress && is.function(pb$interrupt)) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 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())) 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()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) } 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) outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) write_utf8(res, output %n% stdout()) }), list(rlang_trace_top_env = knit_global())) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 49: }, error = function(e) { 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), process_file(text, output) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) error = function(e) { 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: thisOK <<- FALSEvweave_rmarkdown(...) if (progress && is.function(pb$interrupt)) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)53: }), 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)) file, conditionMessage(e)))}) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", engine$weave(file, quiet = quiet, encoding = enc) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6mBeul/file6aea1f53ede3.rds") 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)49: process_file(text, output) 50: 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", 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$weave(file, quiet = quiet, encoding = enc) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: engine = engine)tryCatchList(expr, classes, parentenv, handlers)An irrecoverable exception occurred. R is aborting now ... } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) 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/Rtmp6mBeul/file6aea1f53ede3.rds") 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) An irrecoverable exception occurred. R is aborting now ... } 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/Rtmp6mBeul/file6aea1f53ede3.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