• using R version 4.5.2 Patched (2026-01-31 r89382)
• using platform: aarch64-apple-darwin20
• R was compiled by     Apple clang version 16.0.0 (clang-1600.0.26.6)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.7.8
• using session charset: UTF-8
• checking for file ‘rEDM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rEDM’ version ‘2.0.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘rEDM’ can be installed ... [1s/1s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [1s/1s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [8s/8s] ERROR Error(s) in re-building vignettes: --- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown 2026-09-03 15:01:24.877 R[47178:69669] 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)  3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)  4: ComputeError(predictions$Observations, predictions$Predictions)  5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)  6: FUN(X[[i]], ...)  7: lapply(X = S, FUN = FUN, ...)  8: doTryCatch(return(expr), name, parentenv, handler) Traceback:  1: RowCumsum(valid)  9: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)  3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { Traceback:  1: tau = tau, theta = th, exclusionRadius = exclusionRadius, RowCumsum(valid) if (identical(call[[1L]], quote(doTryCatch)))  2: embedded = embedded, validLib = validLib, noTime = noTime, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ignoreNan = ignoreNan, backend = backend) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) tieBreak = FALSE, verbose = verbose)  3: 4: prefix <- paste("Error in", dcall, ": ")ComputeError(predictions$Observations, predictions$Predictions)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")  5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 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])) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)  6: FUN(X[[i]], ...)  7: ignoreNan = ignoreNan, backend = backend) if (!silent && isTRUE(getOption("show.error.messages"))) {lapply(X = S, FUN = FUN, ...) cat(msg, file = outFile) .Internal(printDeferredWarnings())     } invisible(structure(msg, class = "try-error", condition = e)) 4: ComputeError(predictions$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: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)FUN(X[[i]], ...)  7: 8: lapply(X = S, FUN = FUN, ...)doTryCatch(return(expr), name, parentenv, handler)  9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...)10: tryCatchList(expr, classes, parentenv, handlers) 11: 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) Traceback:  9: if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 1: 15: lapply(seq_len(cores), inner.do) 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]))RowCumsum(valid) if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchOne(expr, names, parentenv, handlers[[1L]])         cat(msg, file = outFile) 2:         .Internal(printDeferredWarnings()) }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, invisible(structure(msg, class = "try-error", condition = e))10: tryCatchList(expr, classes, parentenv, handlers) 11: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)}) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) tryCatch(expr, error = function(e) { 3: 17: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, call <- conditionCall(e) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, doTryCatch(return(expr), name, parentenv, handler)12: if (!is.null(call)) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)         dcall <- deparse(call, nlines = 1L) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) ignoreNan = ignoreNan, backend = backend) 18: 14: prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...) 15: LONG <- 75LtryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, sm <- strsplit(conditionMessage(e), "\n")[[1L]] mc.preschedule = TRUE), error = function(e) NULL) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")lapply(seq_len(cores), inner.do) if (is.na(w)) 4: ComputeError(predictions$Observations, predictions$Predictions) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],  5: 21: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, type = "b") embedded = embedded, validLib = validLib, noTime = noTime, if (w > LONG) prefix <- paste0(prefix, "\n ")16: SweepApply(theta, worker, numProcess) }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)     else prefix <- "Error : "17: ignoreNan = ignoreNan, backend = backend)$predictions) 22: unlist(SweepApply(theta, worker, numProcess))  6: 23: FUN(X[[i]], ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",  7: msg <- paste0(prefix, conditionMessage(e), "\n")doTryCatch(return(expr), name, parentenv, handler)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) .Internal(seterrmessage(msg[1L])) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (!silent && isTRUE(getOption("show.error.messages"))) {18:         cat(msg, file = outFile)tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(printDeferredWarnings()) } E = E, showPlot = TRUE)11: tryCatch(expr, error = function(e) {24: invisible(structure(msg, class = "try-error", condition = e)) call <- conditionCall(e)})19:     if (!is.null(call)) {eval(expr, envir) 12: tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)25: if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)13: eval(expr, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))         dcall <- deparse(call, nlines = 1L)26: 20: withVisible(eval(expr, envir))         prefix <- paste("Error in", dcall, ": ")14: 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], 27: FUN(X[[i]], ...)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 15: watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { type = "b")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: invokeRestart("muffleMessage") if (w > LONG) } prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))}, warning = function (cnd) mc.preschedule = TRUE), error = function(e) NULL){ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchOne(expr, names, parentenv, handlers[[1L]])         return() cat(msg, file = outFile)19: } watcher$capture_plot_and_output() if (on_warning$capture) { .Internal(printDeferredWarnings())tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } mc.preschedule = TRUE), error = function(e) NULL) cnd <- sanitize_call(cnd) 21:         watcher$push(cnd) }SweepApply(theta, worker, numProcess)21:     if (on_warning$silence) {22: SweepApply(theta, worker, numProcess) invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffleWarning")}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: 22: }unlist(SweepApply(theta, worker, numProcess))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: unlist(SweepApply(theta, worker, numProcess))23: FUN(X[[i]], ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", }, error = function (cnd) {     target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)15: 24: eval(expr, envir) watcher$capture_plot_and_output()lapply(seq_len(cores), inner.do) 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 17: doTryCatch(return(expr), name, parentenv, handler) 18: E = E, showPlot = TRUE) 25: eval(expr, envir) 26: withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]])     cnd <- sanitize_call(cnd)24: 27: eval(expr, envir)withCallingHandlers(code, error = function (e)     watcher$push(cnd)rlang::entrace(e), message = function (cnd) { switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})25: 19: eval(expr, envir)     watcher$capture_plot_and_output()28: eval(call)26: 29: eval(call)withVisible(eval(expr, envir)) 30: if (on_message$capture) {with_handlers({ watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) }27: withCallingHandlers(code, error = function (e) if (on_message$silence) { invokeRestart("muffleMessage") for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)rlang::entrace(e), message = function (cnd) } TRUE}, handlers) 31: doWithOneRestart(return(expr), restart)     }32: }, warning = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) withOneRestart(expr, restarts[[1L]])20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 21: SweepApply(theta, worker, numProcess) 22: {     } if (on_message$silence) { invokeRestart("muffleMessage") }33: if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }unlist(SweepApply(theta, worker, numProcess)) watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr]) 34: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } }, warning = function (cnd) if (on_warning$silence) {{ invokeRestart("muffleWarning") if (getOption("warn") >= 2 || getOption("warn") < 0) { }doWithOneRestart(return(expr), restart) return() 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts) 37: }23: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, error = function (cnd) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output() target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) if (on_warning$capture) { {24: eval(expr, envir)         cnd <- sanitize_call(cnd)25: watcher$capture_plot_and_output()eval(expr, envir) cnd <- sanitize_call(cnd) watcher$push(cnd)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)     watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)38: } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)26: evaluate::evaluate(...) withVisible(eval(expr, envir))}) 28: eval(call)39:     watcher$push(cnd)27: 29: withCallingHandlers(code, error = function (e) switch(on_error, continue = invokeRestart("eval_continue"), 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, eval(call) stop = invokeRestart("eval_stop"), error = NULL)rlang::entrace(e), message = function (cnd) }){     stop_on_error = if (is.numeric(options$error)) options$error else {28: 30: eval(call) watcher$capture_plot_and_output()with_handlers({ if (on_message$capture) { watcher$push(cnd)     } if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) if (on_message$silence) { invokeRestart("muffleMessage")29:     }40: }, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }eval(call) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output()in_dir(input_dir(), expr) if (on_warning$capture) { } TRUE         cnd <- sanitize_call(cnd)}, handlers) watcher$push(cnd)30: with_handlers({ for (expr in tle$exprs) { } if (on_warning$silence) { 31: invokeRestart("muffleWarning")doWithOneRestart(return(expr), restart) 32: }withOneRestart(expr, restarts[[1L]]) ev <- withVisible(eval(expr, envir))         watcher$capture_plot_and_output()}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)33: withRestartList(expr, restarts[-nr]) watcher$push(cnd) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 31: switch(on_error, continue = invokeRestart("eval_continue"), doWithOneRestart(return(expr), restart)     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 36: withRestartList(expr, restarts)     keep_message = if (is.numeric(options$message)) TRUE else options$message, 32: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L37: stop = invokeRestart("eval_stop"), error = NULL)}) }, output_handler = knit_handlers(options$render, options))) 42: eng_r(options)withOneRestart(expr, restarts[[1L]])28: eval(call)withRestarts(with_handlers({     for (expr in tle$exprs) {43: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()         watcher$print_value(ev$value, ev$visible, envir) } TRUE }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 29: eval(call)33: withRestartList(expr, restarts[-nr])30: block_exec(params) 44: call_block(x) 45: 38: with_handlers({process_group(group) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()         watcher$print_value(ev$value, ev$visible, envir)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), evaluate::evaluate(...)     error = function(e) { 39: if (progress && is.function(pb$interrupt)) }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 34: doWithOneRestart(return(expr), restart) 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) TRUE}, handlers) pb$interrupt()         if (is_R_CMD_build() || is_R_CMD_check()) 36: withRestartList(expr, restarts) 37: withRestarts(with_handlers({     keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) if (options$error && options$include) 0L }), list(rlang_trace_top_env = knit_global())) 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { else 2L31: doWithOneRestart(return(expr), restart) 32: }, output_handler = knit_handlers(options$render, options)) if (progress && is.function(pb$interrupt))             pb$interrupt()40: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {withOneRestart(expr, restarts[[1L]]) setwd(wd)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 { watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) write_utf8(res, output %n% stdout()) } TRUE paste0("\nQuitting from ", loc, if (!is.null(error)) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)         if (options$error && options$include) 0L33: 38: evaluate::evaluate(...) 39: else 2Levaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, output_handler = knit_handlers(options$render, options))) withRestartList(expr, restarts[-nr]) paste0("\n", rule(), error, "\n", rule()))42: 34: keep_message = if (is.numeric(options$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)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) eng_r(options)doWithOneRestart(return(expr), restart) 43: 49: block_exec(params) process_file(text, output) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)41: 44: 51: call_block(x) 45: process_group(group) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (progress && is.function(pb$interrupt)) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])     output_dir = getwd(), ...) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message, pb$interrupt()52: stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)vweave_rmarkdown(...) })         if (options$error && options$include) 36: 0L47: else 2Lwith_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { }, output_handler = knit_handlers(options$render, options)))withRestartList(expr, restarts)53: 42: eng_r(options) 43: if (progress && is.function(pb$interrupt)) block_exec(params) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) engine$weave(file, quiet = quiet, encoding = enc) 37: withRestarts(with_handlers({48: 44: for (expr in tle$exprs) {call_block(x) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {45: 54: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) ev <- withVisible(eval(expr, envir))process_group(group) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) setwd(wd) doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()47: watcher$print_value(ev$value, ev$visible, envir)     write_utf8(res, output %n% stdout()) }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), paste0("\nQuitting from ", loc, if (!is.null(error)) 55: error = function(e) { paste0("\n", rule(), error, "\n", rule()))tryCatchOne(expr, names, parentenv, handlers[[1L]])}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)         if (progress && is.function(pb$interrupt)) pb$interrupt()49: TRUEprocess_file(text, output)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (is_R_CMD_build() || is_R_CMD_check()) 38: evaluate::evaluate(...) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 52: 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({vweave_rmarkdown(...) error <<- format(e) engine$weave(file, quiet = quiet, encoding = enc) 53: setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) }), list(rlang_trace_top_env = knit_global()))39: if (!have.makefile && vignette_is_tex(output)) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, engine$weave(file, quiet = quiet, encoding = enc) texi2pdf(file = output, clean = FALSE, quiet = quiet)     keep_message = if (is.numeric(options$message)) TRUE else options$message, 54: stop_on_error = if (is.numeric(options$error)) options$error else {48: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "texi2pdf", xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))             pb$interrupt() if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 40: in_dir(input_dir(), expr)56: 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()) engine = engine) paste0("\nQuitting from ", loc, if (!is.null(error)) } tryCatchList(expr, classes, parentenv, handlers) 57: outputs <- c(outputs, output)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) setwd(startdir) paste0("\n", rule(), error, "\n", rule())) output <- find_vignette_product(name, by = "weave", engine = engine)})}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)41:     if (!have.makefile && vignette_is_tex(output)) {49: process_file(text, output) texi2pdf(file = output, clean = FALSE, quiet = quiet) 50: in_input_dir(evaluate(code, envir = env, new_device = FALSE, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 51: output <- find_vignette_product(name, by = "texi2pdf", rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), keep_message = if (is.numeric(options$message)) TRUE else options$message, output_dir = getwd(), ...) engine = engine) } stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 42: outputs <- c(outputs, output)eng_r(options) 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, error = function(e) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp8rPcYh/file800b372687b0.rds") 43: thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 58: An irrecoverable exception occurred. R is aborting now ... block_exec(params)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 52: vweave_rmarkdown(...)     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp8rPcYh/file800b372687b0.rds")53: engine$weave(file, quiet = quiet, encoding = enc) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 44: 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)An irrecoverable exception occurred. R is aborting now ...     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)))})call_block(x) 45: 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/Rtmp8rPcYh/file800b372687b0.rds") An irrecoverable exception occurred. R is aborting now ... 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/Rtmp8rPcYh/file800b372687b0.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
• checking PDF version of manual ... [3s/3s] OK
• DONE

Status: 1 ERROR