Last updated on 2026-08-20 09:51:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.57 | 226.51 | 230.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.28 | 224.50 | 226.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 181.30 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 260.00 | 265.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.27 | 210.37 | 213.64 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 0.00 | 6.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 24.00 | 25.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 7.00 | 160.00 | 167.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-20 15:41:38.773 R[51864:75994] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6:
Traceback:
1: RowCumsum(valid)
2: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
4: 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")ComputeError(predictions$Observations, predictions$Predictions)
if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)lapply(X = S, FUN = FUN, ...)
.Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14:
FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 10: tryCatchList(expr, classes, parentenv, handlers)
ignoreNan = ignoreNan, backend = backend)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") 4: LONG <- 75LComputeError(predictions$Observations, predictions$Predictions) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
20: 6: FUN(X[[i]], ...)
7: type = "b")tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")lapply(X = S, FUN = FUN, ...)
mc.preschedule = TRUE), error = function(e) NULL)
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {21: cat(msg, file = outFile)SweepApply(theta, worker, numProcess) 8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))10:
tryCatchList(expr, classes, parentenv, handlers)})
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
Traceback:
22: 1: RowCumsum(valid)
2: unlist(SweepApply(theta, worker, numProcess)) call <- sys.call(-4L)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, dcall <- deparse(call, nlines = 1L) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, prefix <- paste("Error in", dcall, ": ") verbose = verbose)12:
LONG <- 75L
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", .Internal(printDeferredWarnings()) }
13: invisible(structure(msg, class = "try-error", condition = e))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
tau = tau, theta = th, exclusionRadius = exclusionRadius, })14: embedded = embedded, validLib = validLib, noTime = noTime, FUN(X[[i]], ...)
E = E, showPlot = TRUE)15: ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
lapply(seq_len(cores), inner.do)
24: eval(expr, envir)
25: 5:
16: eval(expr, envir)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
12: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage")parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
}17: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
embedded = embedded, validLib = validLib, noTime = noTime, }, warning = function (cnd) ignoreNan = ignoreNan, backend = backend)$predictions){
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: 19: tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)
if (getOption("warn") >= 2 || getOption("warn") < 0) {
20: return() } 7: watcher$capture_plot_and_output()lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (on_warning$capture) {17: doTryCatch(return(expr), name, parentenv, handler)
18: mc.preschedule = TRUE), error = function(e) NULL) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
cnd <- sanitize_call(cnd)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
watcher$push(cnd)11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 23: call <- sys.call(-4L) } if (on_warning$silence) { dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ") LONG <- 75L
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
19: tryCatchList(expr, classes, parentenv, handlers)24: invokeRestart("muffleWarning") sm <- strsplit(conditionMessage(e), "\n")[[1L]]eval(expr, envir)
25:
} 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 ")eval(expr, envir) }}, error = function (cnd) { else prefix <- "Error : " watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) }20: watcher$push(cnd) if (on_message$silence) { msg <- paste0(prefix, conditionMessage(e), "\n") invokeRestart("muffleMessage") }}, warning = function (cnd) .Internal(seterrmessage(msg[1L])){ switch(on_error, continue = invokeRestart("eval_continue"), if (getOption("warn") >= 2 || getOption("warn") < 0) { stop = invokeRestart("eval_stop"), error = NULL)}) return()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: if (!silent && isTRUE(getOption("show.error.messages"))) { watcher$capture_plot_and_output()28: eval(call)eval(expr, envir)
if (on_warning$capture) { cnd <- sanitize_call(cnd)29: watcher$push(cnd)
} cat(msg, file = outFile)25: .Internal(printDeferredWarnings()) if (on_warning$silence) {eval(expr, envir) invokeRestart("muffleWarning") }
26: withVisible(eval(expr, envir))
invisible(structure(msg, class = "try-error", condition = e))27: eval(call)})
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)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
}}, error = function (cnd) 17: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20:
{30: with_handlers({tryCatch(parallel::mclapply(values, worker, mc.cores = cores, { watcher$capture_plot_and_output() for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE watcher$capture_plot_and_output()}, handlers) if (on_message$capture) { watcher$push(cnd) cnd <- sanitize_call(cnd) mc.preschedule = TRUE), error = function(e) NULL) watcher$push(cnd)
}21: if (on_message$silence) { switch(on_error, continue = invokeRestart("eval_continue"), invokeRestart("muffleMessage")
stop = invokeRestart("eval_stop"), error = NULL) }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {31: })doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)SweepApply(theta, worker, numProcess)
return()22: }35: 28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])eval(call) watcher$capture_plot_and_output()
unlist(SweepApply(theta, worker, numProcess))
29: 36: withRestartList(expr, restarts)
if (on_warning$capture) {23:
eval(call) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning")
30: with_handlers({ for (expr in tle$exprs) {37: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
withRestarts(with_handlers({ }31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", withRestartList(expr, restarts[-nr]) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) for (expr in tle$exprs) {
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: }, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)withRestarts(with_handlers({
for (expr in tle$exprs) {24: eval(expr, envir) ev <- withVisible(eval(expr, envir))
29: 25: eval(call) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)eval(expr, envir) }30: TRUE watcher$print_value(ev$value, ev$visible, envir)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
with_handlers({38: for (expr in tle$exprs) {evaluate::evaluate(...) ev <- withVisible(eval(expr, envir))
39: 26: }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withVisible(eval(expr, envir)) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
watcher$capture_plot_and_output()39:
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$warning, if (on_message$silence) { watcher$print_value(ev$value, ev$visible, envir) } invokeRestart("muffleMessage") keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$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)) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
stop_on_error = if (is.numeric(options$error)) options$error else {}, warning = function (cnd)
{40: if (options$error && options$include) 0L else 2L32: }, output_handler = knit_handlers(options$render, options))withOneRestart(expr, restarts[[1L]])in_dir(input_dir(), expr)
33:
withRestartList(expr, restarts[-nr])
if (getOption("warn") >= 2 || getOption("warn") < 0) {34: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, return()doWithOneRestart(return(expr), restart)
35: 40: stop_on_error = if (is.numeric(options$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)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
in_dir(input_dir(), expr) }44: call_block(x)
45: watcher$capture_plot_and_output()36: if (on_warning$capture) { cnd <- sanitize_call(cnd)withRestartList(expr, restarts)
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)41: })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) watcher$push(cnd)37: }withRestarts(with_handlers({ for (expr in tle$exprs) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (on_warning$silence) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 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)
invokeRestart("muffleWarning") pb$interrupt() }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) if (is_R_CMD_build() || is_R_CMD_check()) 38: watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { switch(on_error, continue = invokeRestart("eval_continue"), if (options$error && options$include) 0L else 2Levaluate::evaluate(...)
39: error <<- format(e) }), list(rlang_trace_top_env = knit_global())) }, output_handler = knit_handlers(options$render, options))) stop = invokeRestart("eval_stop"), error = NULL)
})
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)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) {28: setwd(wd) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { write_utf8(res, output %n% stdout())42: 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)
eng_r(options) if (options$error && options$include) 50: eval(call)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: block_exec(params)
0L else 2L44: call_block(x)
51: 45: process_group(group) }, output_handler = knit_handlers(options$render, options))
29: 46:
eval(call)
40: in_dir(input_dir(), expr)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
41: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()54: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {doTryCatch(return(expr), name, parentenv, handler)in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$print_value(ev$value, ev$visible, envir) } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, TRUE}, handlers)
keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L if (progress && is.function(pb$interrupt))
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
else 2L56: }, output_handler = knit_handlers(options$render, options)))tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() setwd(startdir)
31: 42: doWithOneRestart(return(expr), restart) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)32: })withOneRestart(expr, restarts[[1L]])eng_r(options)
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
47: 33: texi2pdf(file = output, clean = FALSE, quiet = quiet)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "texi2pdf", withRestartList(expr, restarts[-nr])
engine = engine)43: block_exec(params)34:
doWithOneRestart(return(expr), restart) pb$interrupt()
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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) if (is_R_CMD_build() || is_R_CMD_check())
} outputs <- c(outputs, output)38: 44: call_block(x) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))}, 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", 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpIdq4fM/file7ff17283c47a.rds")
45: process_group(group)
evaluate::evaluate(...) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
39: }), list(rlang_trace_top_env = knit_global())), function(loc) {46: 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, An irrecoverable exception occurred. R is aborting now ...
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: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), process_file(text, output) stop_on_error = if (is.numeric(options$error)) options$error else {
50: error = function(e) { if (options$error && options$include) 0L if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: error = function(e) { else 2Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
}, output_handler = knit_handlers(options$render, options))55: error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: }), list(rlang_trace_top_env = knit_global()))tryCatchList(expr, classes, parentenv, handlers)
57:
tryCatch({40:
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()in_dir(input_dir(), expr) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) 41: error <<- format(e)in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) stop_on_error = if (is.numeric(options$error)) options$error else { paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 49: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpIdq4fM/file7ff17283c47a.rds")process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51:
if (options$error && options$include) An irrecoverable exception occurred. R is aborting now ...
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) 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)) {
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: 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)))})
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 58: error = function(e) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpIdq4fM/file7ff17283c47a.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpIdq4fM/file7ff17283c47a.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