Last updated on 2026-09-12 04:51:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.43 | 222.55 | 225.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.73 | 235.84 | 238.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 177.28 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 184.77 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 7.00 | 136.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.64 | 210.51 | 214.15 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.44 | 203.68 | 207.12 | 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 | 6.00 | 131.00 | 137.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 33.00 | 34.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 163.00 | 170.00 | OK |
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
2026-09-12 10:42:49.592 R[46465:70379] 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)
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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
9: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 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)
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)tryCatch(expr, error = function(e) {
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)$predictions)
4: 6: ComputeError(predictions$Observations, predictions$Predictions) call <- conditionCall(e) if (!is.null(call)) {
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) embedded = embedded, validLib = validLib, noTime = noTime, dcall <- deparse(call, nlines = 1L) ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 7: lapply(X = S, FUN = FUN, ...)
8: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
11: tryCatch(expr, error = function(e) { call <- conditionCall(e)10: if (w > LONG) prefix <- paste0(prefix, "\n ") 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)) } else prefix <- "Error : "tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) 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)) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") .Internal(printDeferredWarnings()) if (w > LONG) } invisible(structure(msg, class = "try-error", condition = e)) 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) type = "b") if (w > LONG) }) prefix <- paste0(prefix, "\n ")
.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)) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
14: cat(msg, file = outFile)FUN(X[[i]], ...)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)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: .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)19:
Traceback:
tryCatchList(expr, classes, parentenv, handlers)
17: 15:
doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
1: RowCumsum(valid)lapply(seq_len(cores), inner.do)
2: 19:
tryCatchList(expr, classes, parentenv, handlers)16: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
tieBreak = FALSE, verbose = verbose)20: mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)17:
mc.preschedule = TRUE), error = function(e) NULL) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 26:
doTryCatch(return(expr), name, parentenv, handler)21: tau = tau, theta = th, exclusionRadius = exclusionRadius, SweepApply(theta, worker, numProcess)withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) embedded = embedded, validLib = validLib, noTime = noTime, rlang::entrace(e), message = function (cnd) { ignoreNan = ignoreNan, backend = backend) watcher$capture_plot_and_output() if (on_message$capture) {22: watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output()
unlist(SweepApply(theta, worker, numProcess)) 4: ComputeError(predictions$Observations, predictions$Predictions) if (on_warning$capture) {
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 5: 24: eval(expr, envir)
25: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, eval(expr, envir)
26: withVisible(eval(expr, envir))
27: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)withCallingHandlers(code, error = function (e) cnd <- sanitize_call(cnd)
watcher$push(cnd) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
rlang::entrace(e), message = function (cnd) 6: {21: watcher$capture_plot_and_output() }FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: if (on_warning$silence) { invokeRestart("muffleWarning") } if (on_message$capture) {tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function (cnd) SweepApply(theta, worker, numProcess)
{22: unlist(SweepApply(theta, worker, numProcess)) watcher$capture_plot_and_output()
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd) return() switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
23: }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output()
if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", } E = E, showPlot = TRUE)
24: eval(expr, envir) if (!is.null(call)) {28: if (identical(call[[1L]], quote(doTryCatch))) eval(call)
29: eval(call)
if (on_warning$silence) { invokeRestart("muffleWarning") call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
25: }eval(expr, envir)
LONG <- 75L30: 26: with_handlers({}, error = function (cnd) withVisible(eval(expr, envir))
sm <- strsplit(conditionMessage(e), "\n")[[1L]]27: withCallingHandlers(code, error = function (e) 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() cnd <- sanitize_call(cnd) watcher$push(cnd) } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$push(cnd) TRUE 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))}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])})
33: withRestartList(expr, restarts[-nr])
}
34: if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) switch(on_error, continue = invokeRestart("eval_continue"), doWithOneRestart(return(expr), restart)
12: {35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL)})
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)28:
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$print_value(ev$value, ev$visible, envir) if (getOption("warn") >= 2 || getOption("warn") < 0) {
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) } 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 {28: eval(call) if (options$error && options$include)
0L29: eval(call)eval(call)
17:
else 2L }, output_handler = knit_handlers(options$render, options))30:
doTryCatch(return(expr), name, parentenv, handler)
with_handlers({ for (expr in tle$exprs) {
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])29: 40: ev <- withVisible(eval(expr, envir))eval(call) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])31: doWithOneRestart(return(expr), restart)19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) keep_message = if (is.numeric(options$message)) TRUE else options$message,
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)32: stop_on_error = if (is.numeric(options$error)) options$error else {withOneRestart(expr, restarts[[1L]]) if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: 21:
SweepApply(theta, worker, numProcess)
35: 33: withRestartList(expr, restarts[-nr])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$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
eng_r(options)38:
34:
43: 22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)block_exec(params)evaluate::evaluate(...)doWithOneRestart(return(expr), restart)
39:
24: 44: 35: eval(expr, envir)call_block(x)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
45: }36: keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestartList(expr, restarts) stop_on_error = if (is.numeric(options$error)) options$error else {
37: withRestarts(with_handlers({process_group(group) if (options$error && options$include)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 0L for (expr in tle$exprs) { if (progress && is.function(pb$interrupt)) pb$interrupt() ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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: else 2L if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)in_dir(input_dir(), expr) if (on_message$silence) { })
47: }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), in_input_dir(evaluate(code, envir = env, new_device = FALSE, invokeRestart("muffleMessage") }
error = function(e) {}, warning = function (cnd) if (progress && is.function(pb$interrupt)) pb$interrupt(){41: 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 (getOption("warn") >= 2 || getOption("warn") < 0) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, return() } if (is_R_CMD_build() || is_R_CMD_check()) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: if (options$error && options$include) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 0L error = function(e) { if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() if (on_warning$capture) { pb$interrupt() else 2L cnd <- sanitize_call(cnd) }, output_handler = knit_handlers(options$render, options))) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt(){ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), 47: 42: eng_r(options)
43: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) block_exec(params) stop = invokeRestart("eval_stop"), error = NULL) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)})
28: eval(call) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 29: error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { }), list(rlang_trace_top_env = knit_global()))eval(call)
30: setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {with_handlers({}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) for (expr in tle$exprs) {
49: 44: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()call_block(x)process_file(text, output)
50: watcher$print_value(ev$value, ev$visible, envir)45: process_group(group)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)46: if (progress && is.function(pb$interrupt))
51: pb$interrupt()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (is_R_CMD_build() || is_R_CMD_check()) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { output_dir = getwd(), ...) if (progress && is.function(pb$interrupt)) pb$interrupt()
error <<- format(e)52: }), list(rlang_trace_top_env = knit_global())), function(loc) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) setwd(wd) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) } TRUE}, handlers)
31: vweave_rmarkdown(...) pb$interrupt() paste0("\nQuitting from ", loc, if (!is.null(error)) doWithOneRestart(return(expr), restart) if (is_R_CMD_build() || is_R_CMD_check()) paste0("\n", rule(), error, "\n", rule())) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)32: withOneRestart(expr, restarts[[1L]]) error <<- format(e)
49:
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) 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(...)
process_file(text, output)39:
}), list(rlang_trace_top_env = knit_global())), function(loc) {50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error))
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, paste0("\n", rule(), error, "\n", rule())) output_dir = getwd(), ...) 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$render, options))
40: in_dir(input_dir(), expr)52:
41: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)53:
54: engine$weave(file, quiet = quiet, encoding = enc)in_input_dir(evaluate(code, envir = env, new_device = FALSE, doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) }
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) keep_message = if (is.numeric(options$message)) TRUE else options$message, 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/RtmpGvV0DV/file8ff146cf84ef.rds") stop_on_error = if (is.numeric(options$error)) options$error else {
54: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
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(...)
if (options$error && options$include)
53: 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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
engine$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: 57:
tryCatch({47: engine$weave(file, quiet = quiet, encoding = enc)tryCatch({ engine$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) }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() setwd(startdir) 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), outputs <- c(outputs, output) error = function(e) {}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 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/RtmpGvV0DV/file8ff146cf84ef.rds")
An irrecoverable exception occurred. R is aborting now ...
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)) 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 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)
fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpGvV0DV/file8ff146cf84ef.rds")
An irrecoverable exception occurred. R is aborting now ...
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/RtmpGvV0DV/file8ff146cf84ef.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