Last updated on 2026-08-12 20:52:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | OK | |||||
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.33 | 221.60 | 223.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 4.00 | 257.00 | 261.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 3.74 | 206.25 | 209.99 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.45 | 205.25 | 208.70 | 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 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 26.00 | 27.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 8.00 | 165.00 | 173.00 | 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
2026-08-13 04:17:05.933 R[49666:72801] 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$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
Traceback:
tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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: 1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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) { prefix <- paste("Error in", dcall, ": ") LONG <- 75L call <- conditionCall(e) if (!is.null(call)) { 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))})
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)) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
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))
Traceback:
15: 1: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)RowCumsum(valid)
2: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])})
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
12: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 19: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) verbose = verbose)
Traceback:
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
tryCatchList(expr, classes, parentenv, handlers) 1:
3: RowCumsum(valid)20:
2: 14: FUN(X[[i]], ...)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)15: lapply(seq_len(cores), inner.do)
21: tau = tau, theta = th, exclusionRadius = exclusionRadius, SweepApply(theta, worker, numProcess)
3: embedded = embedded, validLib = validLib, noTime = noTime, 22: 16: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) ignoreNan = ignoreNan, backend = backend) tau = tau, theta = th, exclusionRadius = exclusionRadius, unlist(SweepApply(theta, worker, numProcess))
embedded = embedded, validLib = validLib, noTime = noTime, 4: ignoreNan = ignoreNan, backend = backend)
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", ComputeError(predictions$Observations, predictions$Predictions) E = E, showPlot = TRUE)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
24: eval(expr, envir) 4:
ComputeError(predictions$Observations, predictions$Predictions)
17: 5: 25: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, eval(expr, envir)
26: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) doTryCatch(return(expr), name, parentenv, handler)rlang::entrace(e), message = function (cnd)
embedded = embedded, validLib = validLib, noTime = noTime, { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)18: ignoreNan = ignoreNan, backend = backend)$predictions)
embedded = embedded, validLib = validLib, noTime = noTime, 6: ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
}tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
9: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11:
lapply(X = S, FUN = FUN, ...)19:
if (on_message$silence) { 8: invokeRestart("muffleMessage") }tryCatchList(expr, classes, parentenv, handlers)}, warning = function (cnd) tryCatch(expr, error = function(e) {{
call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (getOption("warn") >= 2 || getOption("warn") < 0) { mc.preschedule = TRUE), error = function(e) NULL)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: return() } watcher$capture_plot_and_output()
tryCatch(expr, error = function(e) { call <- conditionCall(e)21: if (!is.null(call)) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (on_warning$capture) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) cnd <- sanitize_call(cnd)SweepApply(theta, worker, numProcess)
22: dcall <- deparse(call, nlines = 1L)unlist(SweepApply(theta, worker, numProcess)) prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L)
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)
26: withVisible(eval(expr, envir)) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L LONG <- 75L watcher$push(cnd) }
if (on_warning$silence) { 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], invokeRestart("muffleWarning") } sm <- strsplit(conditionMessage(e), "\n")[[1L]]}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (is.na(w)) watcher$push(cnd) if (w > LONG) switch(on_error, continue = invokeRestart("eval_continue"), prefix <- paste0(prefix, "\n ") stop = invokeRestart("eval_stop"), error = NULL)27: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], withCallingHandlers(code, error = function (e) }rlang::entrace(e), message = function (cnd) }){ type = "b")
28: else prefix <- "Error : " 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: watcher$capture_plot_and_output()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (on_message$capture) {
watcher$push(cnd)14: FUN(X[[i]], ...)
msg <- paste0(prefix, conditionMessage(e), "\n") }eval(call)
if (on_message$silence) { .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {15: cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})29: invokeRestart("muffleMessage") }eval(call)}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }
lapply(seq_len(cores), inner.do)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
30: 16: watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) {with_handlers({ invokeRestart("muffleWarning") } for (expr in tle$exprs) {}, error = function (cnd) ev <- withVisible(eval(expr, envir))14: FUN(X[[i]], ...)
watcher$capture_plot_and_output()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)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$print_value(ev$value, ev$visible, envir) }
17: {doTryCatch(return(expr), name, parentenv, handler)
18: 18: TRUE watcher$capture_plot_and_output()}, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]]) cnd <- sanitize_call(cnd) watcher$push(cnd)
31: doWithOneRestart(return(expr), restart)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 19: 32: tryCatchList(expr, classes, parentenv, handlers) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)tryCatchList(expr, classes, parentenv, handlers)})
withOneRestart(expr, restarts[[1L]])
20: 33: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 20: mc.preschedule = TRUE), error = function(e) NULL)
withRestartList(expr, restarts[-nr])tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
34: 21: mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
28: eval(call)doWithOneRestart(return(expr), restart)
22: 29: eval(call)SweepApply(theta, worker, numProcess)
35: unlist(SweepApply(theta, worker, numProcess))
30:
with_handlers({22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])23: unlist(SweepApply(theta, worker, numProcess))
36: withRestartList(expr, restarts) for (expr in tle$exprs) {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", ev <- withVisible(eval(expr, envir)) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", watcher$capture_plot_and_output() E = E, showPlot = TRUE)
37: withRestarts(with_handlers({ for (expr in tle$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)24:
watcher$print_value(ev$value, ev$visible, envir)38: 23: evaluate::evaluate(...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir) }
25: eval(expr, envir) TRUE}, handlers)
31:
eval(expr, envir)
26: doWithOneRestart(return(expr), restart)withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) 39: rlang::entrace(e), message = function (cnd) 32: withOneRestart(expr, restarts[[1L]])25: {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$capture_plot_and_output()
33: withRestartList(expr, restarts[-nr])
if (on_message$capture) { keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {34: eval(expr, envir)doWithOneRestart(return(expr), restart)
26: withVisible(eval(expr, envir)) if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage")35: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_message$capture) { }}, warning = function (cnd)
40: in_dir(input_dir(), expr)
watcher$push(cnd){ if (getOption("warn") >= 2 || getOption("warn") < 0) { }
36: return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) withRestartList(expr, restarts)41:
}{}, error = function (cnd) { watcher$capture_plot_and_output()37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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) { return() cnd <- sanitize_call(cnd) watcher$push(cnd) } watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...) watcher$push(cnd) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()39: switch(on_error, continue = invokeRestart("eval_continue"), evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { } if (on_warning$silence) { if (options$error && options$include) if (is_R_CMD_build() || is_R_CMD_check()) 0L error <<- format(e) stop = invokeRestart("eval_stop"), error = NULL)})
28: else 2L }), list(rlang_trace_top_env = knit_global()))
eval(call)48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
29: eval(call)
30: }, output_handler = knit_handlers(options$render, options)) invokeRestart("muffleWarning") error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)}, error = function (cnd) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
{ watcher$capture_plot_and_output() write_utf8(res, output %n% stdout()) cnd <- sanitize_call(cnd) watcher$push(cnd)40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L paste0("\nQuitting from ", loc, if (!is.null(error)) switch(on_error, continue = invokeRestart("eval_continue"), with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() paste0("\n", rule(), error, "\n", rule())) stop = invokeRestart("eval_stop"), error = NULL)})
28: watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)eval(call) else 2L
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51:
31: 29: }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: doWithOneRestart(return(expr), restart)block_exec(params)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
output_dir = getwd(), ...)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr]) watcher$print_value(ev$value, ev$visible, envir)44: call_block(x)
34:
}doWithOneRestart(return(expr), restart)
TRUE52: 45: vweave_rmarkdown(...)process_group(group)35:
}, handlers)53:
engine$weave(file, quiet = quiet, encoding = enc)46: 31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()doWithOneRestart(return(expr), restart)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)36: })
54:
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)withRestartList(expr, restarts)32: }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 37: doTryCatch(return(expr), name, parentenv, handler)withOneRestart(expr, restarts[[1L]])
error = function(e) {33: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr])
pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e)34: withRestarts(with_handlers({ for (expr in tle$exprs) {doWithOneRestart(return(expr), restart) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)
setwd(startdir) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()38: write_utf8(res, output %n% stdout()) watcher$print_value(ev$value, ev$visible, envir) paste0("\nQuitting from ", loc, if (!is.null(error)) } TRUE output <- find_vignette_product(name, by = "weave", engine = engine) paste0("\n", rule(), error, "\n", rule())) if (!have.makefile && vignette_is_tex(output)) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, 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: texi2pdf(file = output, clean = FALSE, quiet = quiet)engine$weave(file, quiet = quiet, encoding = enc)
38: evaluate::evaluate(...) output <- find_vignette_product(name, by = "texi2pdf", 54: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, engine = engine)39: }doTryCatch(return(expr), name, parentenv, handler) outputs <- c(outputs, output) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L
}, output_handler = knit_handlers(options$render, options))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 55: keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) }, 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/RtmpO3uriV/file7d51bbe895d.rds")40: in_dir(input_dir(), expr) 0L else 2L
An irrecoverable exception occurred. R is aborting now ...
}, output_handler = knit_handlers(options$render, options))tryCatchList(expr, classes, parentenv, handlers)
41: 40:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, in_dir(input_dir(), expr)
41: 57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) keep_message = if (is.numeric(options$message)) TRUE else options$message, in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (!have.makefile && vignette_is_tex(output)) { 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) stop_on_error = if (is.numeric(options$error)) options$error else { 0L texi2pdf(file = output, clean = FALSE, quiet = quiet) else 2L if (options$error && options$include) }, output_handler = knit_handlers(options$render, options))) output <- find_vignette_product(name, by = "texi2pdf",
0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
engine = engine)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: 42: eng_r(options)
43: block_exec(params)
44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call_block(x) } 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: error = function(e) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 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),
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpO3uriV/file7d51bbe895d.rds") error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 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()) error <<- format(e) 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) })
47: An irrecoverable exception occurred. R is aborting now ...
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: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54:
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpO3uriV/file7d51bbe895d.rds")
An irrecoverable exception occurred. R is aborting now ...
57: tryCatch({ engine$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/RtmpO3uriV/file7d51bbe895d.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