Last updated on 2026-09-02 12:50:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.45 | 222.09 | 225.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.49 | 218.27 | 220.76 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 183.45 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 186.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 6.00 | 138.00 | 144.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 3.38 | 211.41 | 214.79 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.39 | 203.63 | 207.02 | 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 | 137.00 | 144.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 30.00 | 31.00 | 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 | 164.00 | 172.00 | 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
2026-09-02 19:05:20.501 R[45859:68720] 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)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
Traceback:
1:
Traceback:
1: RowCumsum(valid)
RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: 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, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 22: unlist(SweepApply(theta, worker, numProcess)) tau = tau, theta = th, exclusionRadius = exclusionRadius,
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
Traceback:
1: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
E = E, showPlot = TRUE) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: RowCumsum(valid)
7: ComputeError(predictions$Observations, predictions$Predictions)
24: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, eval(expr, envir) 5: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(X = S, FUN = FUN, ...)
tieBreak = FALSE, verbose = verbose)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
25:
8: doTryCatch(return(expr), name, parentenv, handler)
3: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 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: embedded = embedded, validLib = validLib, noTime = noTime, 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 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)$predictions)
eval(expr, envir)tryCatch(expr, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions) call <- conditionCall(e)
26: 6: if (!is.null(call)) { 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)FUN(X[[i]], ...) prefix <- paste("Error in", dcall, ": ") if (identical(call[[1L]], quote(doTryCatch))) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: lapply(X = S, FUN = FUN, ...)
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) 8: prefix <- paste0(prefix, "\n ")12: withVisible(eval(expr, envir))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
}doTryCatch(return(expr), name, parentenv, handler) else prefix <- "Error : "
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: msg <- paste0(prefix, conditionMessage(e), "\n")13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
27: cat(msg, file = outFile)14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)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") }}, warning = function (cnd) .Internal(printDeferredWarnings())
}16: invisible(structure(msg, class = "try-error", condition = e))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)})
12: {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: 11: watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) call <- sys.call(-4L)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) dcall <- deparse(call, nlines = 1L) }17: doTryCatch(return(expr), name, parentenv, handler) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) 19: prefix <- paste0(prefix, "\n ")17: tryCatchList(expr, classes, parentenv, handlers)
}20: else prefix <- "Error : "doTryCatch(return(expr), name, parentenv, handler)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (on_warning$silence) {
msg <- paste0(prefix, conditionMessage(e), "\n") invokeRestart("muffleWarning") mc.preschedule = TRUE), error = function(e) NULL)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(seterrmessage(msg[1L]))21:
19: tryCatchList(expr, classes, parentenv, handlers)
}20: SweepApply(theta, worker, numProcess)}, error = function (cnd) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
{
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)21: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: 22: eval(call)unlist(SweepApply(theta, worker, numProcess)) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: SweepApply(theta, worker, numProcess)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)23: 29:
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", eval(call)FUN(X[[i]], ...)
15:
lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
22: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
17: 24: 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)30: eval(expr, envir)
doTryCatch(return(expr), name, parentenv, handler)26: withVisible(eval(expr, envir))
18: 27: withCallingHandlers(code, error = function (e) tryCatchOne(expr, names, parentenv, handlers[[1L]])
rlang::entrace(e), message = function (cnd) 25: with_handlers({19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL){ for (expr in tle$exprs) { watcher$capture_plot_and_output()
eval(expr, envir) if (on_message$capture) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }
watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$print_value(ev$value, ev$visible, envir)21: } watcher$push(cnd)26: withVisible(eval(expr, envir)) TRUESweepApply(theta, worker, numProcess)}, handlers)
22: unlist(SweepApply(theta, worker, numProcess))
23:
}31: 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) if (on_warning$silence) {27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) invokeRestart("muffleWarning"){ }doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output()}, error = function (cnd) if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) {
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
26: if (getOption("warn") >= 2 || getOption("warn") < 0) {{34: return()withVisible(eval(expr, envir))doWithOneRestart(return(expr), restart) } watcher$capture_plot_and_output() 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)
35: })
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29:
28: eval(call)
eval(call){36: 29:
eval(call)30: withRestartList(expr, restarts)
watcher$capture_plot_and_output()37: withRestarts(with_handlers({
with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (on_message$capture) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() }30: watcher$push(cnd)with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() TRUE } watcher$print_value(ev$value, ev$visible, envir) watcher$print_value(ev$value, ev$visible, envir)}, handlers) if (on_message$silence) { } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]) invokeRestart("muffleMessage")
} TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)34:
doWithOneRestart(return(expr), restart)31:
doWithOneRestart(return(expr), restart)
38: }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {evaluate::evaluate(...) return() }35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])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 { watcher$capture_plot_and_output() if (on_warning$capture) {
32:
if (options$error && options$include) withOneRestart(expr, restarts[[1L]]) cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }
36: 33: withRestartList(expr, restarts)}, error = function (cnd) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
{ watcher$capture_plot_and_output()41: cnd <- sanitize_call(cnd) watcher$push(cnd)in_input_dir(evaluate(code, envir = env, new_device = FALSE, switch(on_error, continue = invokeRestart("eval_continue"), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: withRestarts(with_handlers({ stop = invokeRestart("eval_stop"), error = NULL) for (expr in tle$exprs) { 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) ev <- withVisible(eval(expr, envir))withRestartList(expr, restarts[-nr]) 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$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$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) {
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)34: 0L
32: withOneRestart(expr, restarts[[1L]])
33: doWithOneRestart(return(expr), restart) if (progress && is.function(pb$interrupt)) pb$interrupt()
else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
if (is_R_CMD_build() || is_R_CMD_check()) withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 43: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: block_exec(params) error = function(e) { if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({35:
44: call_block(x)
45: process_group(group)
46: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { pb$interrupt() ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEwithCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) error = function(e) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: 38: if (progress && is.function(pb$interrupt)) evaluate::evaluate(...)
39: pb$interrupt()48: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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()) keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...) setwd(wd) }) if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 39: write_utf8(res, output %n% stdout())evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 47: paste0("\nQuitting from ", loc, if (!is.null(error)) keep_warning = if (is.numeric(options$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$error else { stop_on_error = if (is.numeric(options$error)) options$error else {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (options$error && options$include) 0L else 2L if (options$error && options$include) paste0("\n", rule(), error, "\n", rule())) error = function(e) { 0L if (progress && is.function(pb$interrupt)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
}, output_handler = knit_handlers(options$render, options)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) else 2L
51: 40: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
if (options$error && options$include) 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)53: 0L else 2Lengine$weave(file, quiet = quiet, encoding = enc) }, output_handler = knit_handlers(options$render, options)))
49: 42: 54: process_file(text, output)doTryCatch(return(expr), name, parentenv, handler)
55:
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
eng_r(options)tryCatchOne(expr, names, parentenv, handlers[[1L]])
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()) 51:
}, output_handler = knit_handlers(options$render, options)))56:
tryCatchList(expr, classes, parentenv, handlers)
57: 42: eng_r(options)
43: block_exec(params)
44: call_block(x) error <<- format(e) })
47: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
tryCatch({ output_dir = getwd(), ...) engine$weave(file, quiet = quiet, encoding = enc)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
45: setwd(startdir) error = function(e) {54: output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { if (progress && is.function(pb$interrupt)) texi2pdf(file = output, clean = FALSE, quiet = quiet)process_group(group) pb$interrupt() output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) doTryCatch(return(expr), name, parentenv, handler) error <<- format(e)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)
}), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 46: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) error = function(e) { } file, conditionMessage(e))) if (progress && is.function(pb$interrupt)) })
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyGMJ8D/file82e4aad268e.rds")
An irrecoverable exception occurred. R is aborting now ...
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), outputs <- c(outputs, output) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e)}, error = function(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)) thisOK <<- FALSE }), 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$weave(file, quiet = quiet, encoding = enc)
54: fails <<- c(fails, file)doTryCatch(return(expr), name, parentenv, handler) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))
})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyGMJ8D/file82e4aad268e.rds")
49: 55: An irrecoverable exception occurred. R is aborting now ...
process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tryCatchOne(expr, names, parentenv, handlers[[1L]])
output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$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: 56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { 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)))})
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }58: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyGMJ8D/file82e4aad268e.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpyGMJ8D/file82e4aad268e.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