Last updated on 2026-11-08 18:52:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.43 | 223.65 | 227.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.73 | 213.60 | 216.33 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.37 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | OK | ||||
| r-release-linux-x86_64 | 2.0.2 | 3.34 | 211.51 | 214.85 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 51.00 | 53.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 160.00 | 168.00 | 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
2026-11-09 01:38:32.711 R[47991:71561] 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$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
Traceback:
9: 1: tieBreak = FALSE, verbose = verbose)RowCumsum(valid)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 2: ignoreNan = ignoreNan, backend = backend)$predictions)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 6: FUN(X[[i]], ...) tieBreak = FALSE, verbose = verbose)
Traceback:
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
1: 7: 10: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)RowCumsum(valid)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 8: embedded = embedded, validLib = validLib, noTime = noTime, 2: ignoreNan = ignoreNan, backend = backend)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, doTryCatch(return(expr), name, parentenv, handler) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
4: 11: ComputeError(predictions$Observations, predictions$Predictions)tryCatch(expr, error = function(e) { tieBreak = FALSE, verbose = verbose)
call <- conditionCall(e)
9: 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste("Error in", dcall, ": ") 5: 10: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatchList(expr, classes, parentenv, handlers) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)11:
LONG <- 75L 4: tryCatch(expr, error = function(e) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- conditionCall(e) if (!is.null(call)) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")ComputeError(predictions$Observations, predictions$Predictions) if (is.na(w)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], embedded = embedded, validLib = validLib, noTime = noTime, if (identical(call[[1L]], quote(doTryCatch))) ignoreNan = ignoreNan, backend = backend)$predictions) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) 6:
FUN(X[[i]], ...) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste("Error in", dcall, ": ") embedded = embedded, validLib = validLib, noTime = noTime, LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (w > LONG) if (is.na(w)) prefix <- paste0(prefix, "\n ") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") else prefix <- "Error : " if (w > LONG) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste0(prefix, "\n ") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { } ignoreNan = ignoreNan, backend = backend)$predictions) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 6: .Internal(seterrmessage(msg[1L]))FUN(X[[i]], ...) 7: if (!silent && isTRUE(getOption("show.error.messages"))) {
lapply(X = S, FUN = FUN, ...) 7:
cat(msg, file = outFile)lapply(X = S, FUN = FUN, ...) cat(msg, file = outFile) 8: .Internal(printDeferredWarnings()) .Internal(printDeferredWarnings())doTryCatch(return(expr), name, parentenv, handler) }
invisible(structure(msg, class = "try-error", condition = e)) 9: })
tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: 12: doTryCatch(return(expr), name, parentenv, handler)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
10: 9: 13: tryCatchList(expr, classes, parentenv, handlers) }
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatch(expr, error = function(e) {
call <- conditionCall(e) invisible(structure(msg, class = "try-error", condition = e)) if (!is.null(call)) {}) if (identical(call[[1L]], quote(doTryCatch)))
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) call <- sys.call(-4L)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: dcall <- deparse(call, nlines = 1L)lapply(seq_len(cores), inner.do) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L16: sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 17: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], doTryCatch(return(expr), name, parentenv, handler) 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: 18: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 10: tryCatchList(expr, classes, parentenv, handlers)14: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
15:
11: lapply(seq_len(cores), inner.do)20:
16: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatch(expr, error = function(e) { call <- conditionCall(e)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)17: 14: FUN(X[[i]], ...)
mc.preschedule = TRUE), error = function(e) NULL)15:
doTryCatch(return(expr), name, parentenv, handler)21: dcall <- deparse(call, nlines = 1L)
SweepApply(theta, worker, numProcess)lapply(seq_len(cores), inner.do)18:
prefix <- paste("Error in", dcall, ": ")tryCatchOne(expr, names, parentenv, handlers[[1L]])16: LONG <- 75L
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)19:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")17: tryCatchList(expr, classes, parentenv, handlers) if (is.na(w))
doTryCatch(return(expr), name, parentenv, handler)
20: 18: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchList(expr, classes, parentenv, handlers)
mc.preschedule = TRUE), error = function(e) NULL)
type = "b")20: 21: if (w > LONG) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 22: mc.preschedule = TRUE), error = function(e) NULL)SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))unlist(SweepApply(theta, worker, numProcess))
23: 21: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", SweepApply(theta, worker, numProcess) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)
22: 24: unlist(SweepApply(theta, worker, numProcess))
eval(expr, envir)23: 23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 25: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", E = E, showPlot = TRUE) prefix <- paste0(prefix, "\n ") target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
eval(expr, envir) E = E, showPlot = TRUE) }
24: 24: eval(expr, envir)eval(expr, envir)
26: 25: 25: withVisible(eval(expr, envir)) else prefix <- "Error : "
eval(expr, envir)eval(expr, envir) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))26: withVisible(eval(expr, envir)) if (!silent && isTRUE(getOption("show.error.messages"))) {27: cat(msg, file = outFile)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) .Internal(printDeferredWarnings()){ }
invisible(structure(msg, class = "try-error", condition = e)) watcher$capture_plot_and_output()
27: 26: })withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 12: if (on_message$capture) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE){ watcher$push(cnd)withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
if (on_message$capture) { } watcher$push(cnd) if (on_message$silence) {
27: 13: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (on_message$silence) {withCallingHandlers(code, error = function (e) invokeRestart("muffleMessage")rlang::entrace(e), message = function (cnd)
{14: }FUN(X[[i]], ...) watcher$capture_plot_and_output()}, warning = function (cnd)
if (on_message$capture) {15: lapply(seq_len(cores), inner.do){
if (getOption("warn") >= 2 || getOption("warn") < 0) {16: return()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$push(cnd)
}17: if (on_message$silence) {doTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffleMessage") } invokeRestart("muffleMessage")}, warning = function (cnd) } }
watcher$capture_plot_and_output()}, warning = function (cnd) if (on_warning$capture) {18: {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (getOption("warn") >= 2 || getOption("warn") < 0) { cnd <- sanitize_call(cnd) return()
} watcher$capture_plot_and_output() watcher$push(cnd){19: }tryCatchList(expr, classes, parentenv, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_warning$silence) { return() invokeRestart("muffleWarning") } } watcher$capture_plot_and_output()
if (on_warning$capture) { cnd <- sanitize_call(cnd)20: if (on_warning$capture) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }, error = function (cnd) { mc.preschedule = TRUE), error = function(e) NULL) watcher$push(cnd) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd) }21: cnd <- sanitize_call(cnd)SweepApply(theta, worker, numProcess) if (on_warning$silence) { watcher$push(cnd) invokeRestart("muffleWarning") switch(on_error, continue = invokeRestart("eval_continue"), watcher$push(cnd) } } if (on_warning$silence) { stop = invokeRestart("eval_stop"), error = NULL)}, error = function (cnd) invokeRestart("muffleWarning")}) }
}, error = function (cnd) 28: {eval(call) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)
watcher$push(cnd)22: switch(on_error, continue = invokeRestart("eval_continue"), unlist(SweepApply(theta, worker, numProcess)) stop = invokeRestart("eval_stop"), error = NULL)})
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", watcher$capture_plot_and_output() E = E, showPlot = TRUE)
cnd <- sanitize_call(cnd)28: eval(call) watcher$push(cnd)
29: switch(on_error, continue = invokeRestart("eval_continue"), 24: stop = invokeRestart("eval_stop"), error = NULL)eval(expr, envir)eval(call)})
30: with_handlers({29: for (expr in tle$exprs) {28: ev <- withVisible(eval(expr, envir))eval(call) watcher$capture_plot_and_output()
29: watcher$print_value(ev$value, ev$visible, envir)eval(call) }
TRUE}, handlers)
31: 30:
with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {25:
eval(expr, envir) ev <- withVisible(eval(expr, envir))32:
watcher$capture_plot_and_output()26: watcher$print_value(ev$value, ev$visible, envir)withOneRestart(expr, restarts[[1L]])withVisible(eval(expr, envir)) } TRUE
27: eval(call)withCallingHandlers(code, error = function (e) }, handlers)
30: 33: with_handlers({31: rlang::entrace(e), message = function (cnd) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))doWithOneRestart(return(expr), restart)
32: withRestartList(expr, restarts[-nr])withOneRestart(expr, restarts[[1L]]) watcher$capture_plot_and_output()
33: watcher$print_value(ev$value, ev$visible, envir)34: withRestartList(expr, restarts[-nr]) }doWithOneRestart(return(expr), restart)
{ TRUE watcher$capture_plot_and_output()}, handlers)
34: 31: 35: doWithOneRestart(return(expr), restart)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
if (on_message$capture) {
doWithOneRestart(return(expr), restart) watcher$push(cnd)36: }32: withRestartList(expr, restarts)withOneRestart(expr, restarts[[1L]])
37:
withRestarts(with_handlers({35: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output()33:
watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts[-nr]) if (on_message$silence) { }
invokeRestart("muffleMessage")34: 36: doWithOneRestart(return(expr), restart) TRUE }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, warning = function (cnd)
38: evaluate::evaluate(...)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]){withRestartList(expr, restarts)
if (getOption("warn") >= 2 || getOption("warn") < 0) {36: return()withRestartList(expr, restarts) }39: watcher$capture_plot_and_output()
if (on_warning$capture) {37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, cnd <- sanitize_call(cnd) watcher$capture_plot_and_output() watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { } TRUE if (options$error && options$include) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (on_warning$silence) {
0L invokeRestart("muffleWarning") else 2L38: evaluate::evaluate(...) }37: }, error = function (cnd) withRestarts(with_handlers({{
watcher$capture_plot_and_output()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 { }, output_handler = knit_handlers(options$render, options)) if (options$error && options$include)
for (expr in tle$exprs) { 0L ev <- withVisible(eval(expr, envir))40: cnd <- sanitize_call(cnd) else 2Lin_dir(input_dir(), expr) watcher$push(cnd) }, output_handler = knit_handlers(options$render, options))
switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)40: stop = invokeRestart("eval_stop"), error = NULL)in_dir(input_dir(), expr)
})41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 41: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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, 28: stop_on_error = if (is.numeric(options$error)) options$error else {eval(call) if (options$error && options$include) 0L else 2L
}, output_handler = knit_handlers(options$render, options)))29:
0Leval(call)42: }
TRUE30: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
with_handlers({38: else 2L for (expr in tle$exprs) { }, output_handler = knit_handlers(options$render, options)))evaluate::evaluate(...)
42: ev <- withVisible(eval(expr, envir))eng_r(options) watcher$capture_plot_and_output()
eng_r(options)43: 39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 43: keep_message = if (is.numeric(options$message)) TRUE else options$message, block_exec(params) stop_on_error = if (is.numeric(options$error)) options$error else {
watcher$print_value(ev$value, ev$visible, envir)44: block_exec(params) if (options$error && options$include) call_block(x) 0L
44: 45: call_block(x)
process_group(group)45:
process_group(group)46:
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) else 2L error <<- format(e) }, output_handler = knit_handlers(options$render, options)) TRUE })}, handlers)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 47: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()40: if (is_R_CMD_build() || is_R_CMD_check()) in_dir(input_dir(), expr) error <<- format(e)
})
41: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), in_input_dir(evaluate(code, envir = env, new_device = FALSE, error = function(e) {31: 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()))doWithOneRestart(return(expr), restart)
32: 48: withOneRestart(expr, restarts[[1L]])xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error = function(e) { 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) 33: 0LwithRestartList(expr, restarts[-nr]) else 2L
34: 47: doWithOneRestart(return(expr), restart)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { }, output_handler = knit_handlers(options$render, options))) if (progress && is.function(pb$interrupt)) 35: pb$interrupt()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) 36: error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
}), list(rlang_trace_top_env = knit_global())), function(loc) {42: withRestartList(expr, restarts)eng_r(options) setwd(wd)
37: write_utf8(res, output %n% stdout())43: withRestarts(with_handlers({ paste0("\nQuitting from ", loc, if (!is.null(error)) for (expr in tle$exprs) { paste0("\n", rule(), error, "\n", rule())) ev <- withVisible(eval(expr, envir))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)block_exec(params)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
44: 49: watcher$capture_plot_and_output() error = function(e) {process_file(text, output)call_block(x)
50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)45: watcher$print_value(ev$value, ev$visible, envir)process_group(group) }
TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (progress && is.function(pb$interrupt))
pb$interrupt()38: 46: evaluate::evaluate(...) if (is_R_CMD_build() || is_R_CMD_check())
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e)39: error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }), list(rlang_trace_top_env = knit_global())), function(loc) { keep_message = if (is.numeric(options$message)) TRUE else options$message, if (progress && is.function(pb$interrupt)) stop_on_error = if (is.numeric(options$error)) options$error else { setwd(wd) pb$interrupt() if (options$error && options$include) write_utf8(res, output %n% stdout()) if (is_R_CMD_build() || is_R_CMD_check()) paste0("\nQuitting from ", loc, if (!is.null(error))
0L paste0("\n", rule(), error, "\n", rule())) else 2L}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)51: }, output_handler = knit_handlers(options$render, options))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: 40: vweave_rmarkdown(...)in_dir(input_dir(), expr)
53: 41: engine$weave(file, quiet = quiet, encoding = enc)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 54: keep_message = if (is.numeric(options$message)) TRUE else options$message, doTryCatch(return(expr), name, parentenv, handler) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 55: 0LtryCatchOne(expr, names, parentenv, handlers[[1L]]) else 2L
}, output_handler = knit_handlers(options$render, options)))56: tryCatchList(expr, classes, parentenv, handlers)
error <<- format(e)
42: })eng_r(options)57:
tryCatch({47: engine$weave(file, quiet = quiet, encoding = enc)43: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), setwd(startdir)
block_exec(params) output <- find_vignette_product(name, by = "weave", engine = engine)49:
error = function(e) {process_file(text, output)44: if (progress && is.function(pb$interrupt))
pb$interrupt()call_block(x)50: if (is_R_CMD_build() || is_R_CMD_check()) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
error <<- format(e)45: }), list(rlang_trace_top_env = knit_global()))process_group(group)
if (!have.makefile && vignette_is_tex(output)) {48: texi2pdf(file = output, clean = FALSE, quiet = quiet)51: output <- find_vignette_product(name, by = "texi2pdf",
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), engine = engine)46: output_dir = getwd(), ...)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 52: error = function(e) { } if (progress && is.function(pb$interrupt)) pb$interrupt() outputs <- c(outputs, output)vweave_rmarkdown(...)}, error = function(e) {
thisOK <<- FALSE53: fails <<- c(fails, file)engine$weave(file, quiet = quiet, encoding = enc)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {54: if (progress && is.function(pb$interrupt)) doTryCatch(return(expr), name, parentenv, handler) pb$interrupt() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (is_R_CMD_build() || is_R_CMD_check())
file, conditionMessage(e))) error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) })})55: error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatchOne(expr, names, parentenv, handlers[[1L]])58: setwd(wd)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", write_utf8(res, output %n% stdout()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1b1eAz/file8c7f76df90d4.rds") paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))An irrecoverable exception occurred. R is aborting now ...
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt()
56: tryCatchList(expr, classes, parentenv, handlers) if (is_R_CMD_build() || is_R_CMD_check())
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) error <<- format(e)57:
}), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatch({49: engine$weave(file, quiet = quiet, encoding = enc) setwd(wd) setwd(startdir) write_utf8(res, output %n% stdout()) output <- find_vignette_product(name, by = "weave", engine = engine) paste0("\nQuitting from ", loc, if (!is.null(error)) if (!have.makefile && vignette_is_tex(output)) { paste0("\n", rule(), error, "\n", rule())) texi2pdf(file = output, clean = FALSE, quiet = quiet)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)49: }process_file(text, output) outputs <- c(outputs, output)}, error = function(e) {
50: thisOK <<- FALSEknitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) fails <<- c(fails, file)
process_file(text, output)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 50: file, conditionMessage(e)))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)})
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 51: output_dir = getwd(), ...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)52:
52: vweave_rmarkdown(...)vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)53:
engine$weave(file, quiet = quiet, encoding = enc)58:
54: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1b1eAz/file8c7f76df90d4.rds")
An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 54: doTryCatch(return(expr), name, parentenv, handler)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1b1eAz/file8c7f76df90d4.rds")55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])An irrecoverable exception occurred. R is aborting now ...
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/Rtmp1b1eAz/file8c7f76df90d4.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