Last updated on 2026-10-15 09:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.38 | 227.64 | 231.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.42 | 237.85 | 240.27 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 141.00 | 147.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.18 | 212.69 | 215.87 | 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 | 5.00 | 137.00 | 142.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 36.00 | 38.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 5.00 | 159.00 | 164.00 | 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
2026-10-15 15:11:31.245 R[47709:70931] XType: Using static font registry.
*** 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)
*** caught segfault ***
dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")address 0x110, cause 'invalid permissions'
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)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
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") }}, 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$push(cnd) } if (on_warning$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)})
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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
*** caught segfault ***
32: address 0x110, cause 'invalid permissions'
withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
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) { 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), 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(), ...)
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",
Traceback:
1: engine = engine) }RowCumsum(valid) outputs <- c(outputs, output)
2: }, error = function(e) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, thisOK <<- FALSE fails <<- c(fails, file) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tieBreak = FALSE, verbose = verbose) file, conditionMessage(e)))
})
3: 58: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppL0RIq/file84c6174e54f2.rds")
4: ComputeError(predictions$Observations, predictions$Predictions)An irrecoverable exception occurred. R is aborting now ...
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$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)
Traceback:
1: RowCumsum(valid)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 14: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, FUN(X[[i]], ...) tieBreak = FALSE, verbose = verbose)
15: 3: lapply(seq_len(cores), inner.do)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
16: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
4: 17: ComputeError(predictions$Observations, predictions$Predictions)
doTryCatch(return(expr), name, parentenv, handler) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 18: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])
embedded = embedded, validLib = validLib, noTime = noTime, 19: ignoreNan = ignoreNan, backend = backend)$predictions)tryCatchList(expr, classes, parentenv, handlers)
6: 20: FUN(X[[i]], ...)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 7: mc.preschedule = TRUE), error = function(e) NULL)lapply(X = S, FUN = FUN, ...)
21:
SweepApply(theta, worker, numProcess) 8:
doTryCatch(return(expr), name, parentenv, handler)22:
unlist(SweepApply(theta, worker, numProcess)) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])23:
10: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", tryCatchList(expr, classes, parentenv, handlers) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)11:
tryCatch(expr, error = function(e) {24: call <- conditionCall(e)eval(expr, envir) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 25: call <- sys.call(-4L)eval(expr, envir) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")26: LONG <- 75LwithVisible(eval(expr, envir))
sm <- strsplit(conditionMessage(e), "\n")[[1L]]27: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withCallingHandlers(code, error = function (e) if (is.na(w)) rlang::entrace(e), message = function (cnd) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b"){ if (w > LONG) watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") } if (on_message$capture) { else prefix <- "Error : " watcher$push(cnd) msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) if (on_message$silence) { if (!silent && isTRUE(getOption("show.error.messages"))) { invokeRestart("muffleMessage") cat(msg, file = outFile) }}, warning = function (cnd) .Internal(printDeferredWarnings()) }{ if (getOption("warn") >= 2 || getOption("warn") < 0) { invisible(structure(msg, class = "try-error", condition = e)) return() } watcher$capture_plot_and_output()})
12: if (on_warning$capture) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
cnd <- sanitize_call(cnd) watcher$push(cnd) }13: if (on_warning$silence) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
invokeRestart("muffleWarning")14: }FUN(X[[i]], ...)}, error = function (cnd)
{15: lapply(seq_len(cores), inner.do) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)16: watcher$push(cnd)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)
})
17: doTryCatch(return(expr), name, parentenv, handler)28:
eval(call)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
eval(call)
19: 30: tryCatchList(expr, classes, parentenv, handlers)with_handlers({
for (expr in tle$exprs) {20: ev <- withVisible(eval(expr, envir))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
watcher$capture_plot_and_output()21: watcher$print_value(ev$value, ev$visible, envir) }SweepApply(theta, worker, numProcess)
TRUE22: }, handlers)
unlist(SweepApply(theta, worker, numProcess))31:
doWithOneRestart(return(expr), restart)23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 32: withOneRestart(expr, restarts[[1L]]) E = E, showPlot = TRUE)
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24: 36: eval(expr, envir)withRestartList(expr, restarts)
25: eval(expr, envir)37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
Traceback:
watcher$capture_plot_and_output() 1:
watcher$print_value(ev$value, ev$visible, envir)RowCumsum(valid) }
TRUE26: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 2: withVisible(eval(expr, envir))FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
38: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 27: evaluate::evaluate(...) tieBreak = FALSE, verbose = verbose)
withCallingHandlers(code, error = function (e)
39: rlang::entrace(e), message = function (cnd) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, { 3: keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output()SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, stop_on_error = if (is.numeric(options$error)) options$error else { tau = tau, theta = th, exclusionRadius = exclusionRadius, if (on_message$capture) { if (options$error && options$include) 0L embedded = embedded, validLib = validLib, noTime = noTime, watcher$push(cnd) } else 2L if (on_message$silence) { ignoreNan = ignoreNan, backend = backend) invokeRestart("muffleMessage") } }, output_handler = knit_handlers(options$render, options))}, warning = function (cnd)
{ 4: if (getOption("warn") >= 2 || getOption("warn") < 0) {ComputeError(predictions$Observations, predictions$Predictions)
5: 40: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, return() knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, in_dir(input_dir(), expr) ignoreNan = ignoreNan, backend = backend)$predictions) }
watcher$capture_plot_and_output() if (on_warning$capture) { 6: cnd <- sanitize_call(cnd)FUN(X[[i]], ...)
watcher$push(cnd)41:
}in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (on_warning$silence) { 7: invokeRestart("muffleWarning") keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(X = S, FUN = FUN, ...)
} 8: keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function (cnd) doTryCatch(return(expr), name, parentenv, handler){ stop_on_error = if (is.numeric(options$error)) options$error else { watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), if (options$error && options$include) 9: 0LtryCatchOne(expr, names, parentenv, handlers[[1L]]) stop = invokeRestart("eval_stop"), error = NULL)
else 2L10: })tryCatchList(expr, classes, parentenv, handlers) }, output_handler = knit_handlers(options$render, options)))
28:
42: eval(call)eng_r(options)11:
tryCatch(expr, error = function(e) {43: 29: call <- conditionCall(e)block_exec(params)eval(call) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
44: call <- sys.call(-4L)30: call_block(x) dcall <- deparse(call, nlines = 1L)with_handlers({
prefix <- paste("Error in", dcall, ": ") for (expr in tle$exprs) { LONG <- 75L45: process_group(group) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() sm <- strsplit(conditionMessage(e), "\n")[[1L]]46: watcher$print_value(ev$value, ev$visible, envir)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { TRUE w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (progress && is.function(pb$interrupt)) pb$interrupt()}, handlers) if (is_R_CMD_build() || is_R_CMD_check()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") error <<- format(e)31: })doWithOneRestart(return(expr), restart) if (w > LONG)
prefix <- paste0(prefix, "\n ")47: }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { else prefix <- "Error : " if (progress && is.function(pb$interrupt)) pb$interrupt()32: if (is_R_CMD_build() || is_R_CMD_check()) msg <- paste0(prefix, conditionMessage(e), "\n")withOneRestart(expr, restarts[[1L]]) error <<- format(e)
.Internal(seterrmessage(msg[1L])) }), list(rlang_trace_top_env = knit_global()))33: if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)withRestartList(expr, restarts[-nr]) .Internal(printDeferredWarnings()) }
invisible(structure(msg, class = "try-error", condition = e))34: })doWithOneRestart(return(expr), restart)
48:
12: 35: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) error = function(e) {13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
36: withRestartList(expr, restarts)14: if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 37: FUN(X[[i]], ...)withRestarts(with_handlers({
for (expr in tle$exprs) { error <<- format(e) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()15: watcher$print_value(ev$value, ev$visible, envir)lapply(seq_len(cores), inner.do) } }), list(rlang_trace_top_env = knit_global())), function(loc) { TRUE
setwd(wd)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) write_utf8(res, output %n% stdout())16:
paste0("\nQuitting from ", loc, if (!is.null(error)) 38: paste0("\n", rule(), error, "\n", rule()))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)evaluate::evaluate(...)17: doTryCatch(return(expr), name, parentenv, handler)
39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 49: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {18: if (options$error && options$include) process_file(text, output) 0LtryCatchOne(expr, names, parentenv, handlers[[1L]])
else 2L }, output_handler = knit_handlers(options$render, options))50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)40: in_dir(input_dir(), expr)
19:
51: 41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tryCatchList(expr, classes, parentenv, handlers)in_input_dir(evaluate(code, envir = env, new_device = FALSE, output_dir = getwd(), ...) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 52: stop_on_error = if (is.numeric(options$error)) options$error else {vweave_rmarkdown(...) if (options$error && options$include)
0L53: 20: else 2Lengine$weave(file, quiet = quiet, encoding = enc)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }, output_handler = knit_handlers(options$render, options)))
mc.preschedule = TRUE), error = function(e) NULL)54:
doTryCatch(return(expr), name, parentenv, handler)
42: 21:
eng_r(options)55:
SweepApply(theta, worker, numProcess)tryCatchOne(expr, names, parentenv, handlers[[1L]])43:
block_exec(params)56: 22:
unlist(SweepApply(theta, worker, numProcess))44: tryCatchList(expr, classes, parentenv, handlers)
call_block(x)23:
57: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", tryCatch({45: engine$weave(file, quiet = quiet, encoding = enc) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", setwd(startdir)process_group(group) E = E, showPlot = TRUE) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {46: 24: texi2pdf(file = output, clean = FALSE, quiet = quiet)eval(expr, envir)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
output <- find_vignette_product(name, by = "texi2pdf", if (progress && is.function(pb$interrupt)) pb$interrupt()25: engine = engine) if (is_R_CMD_build() || is_R_CMD_check()) }eval(expr, envir) outputs <- c(outputs, output) error <<- format(e)}, error = function(e) { }) thisOK <<- FALSE
fails <<- c(fails, file)26: withVisible(eval(expr, envir))47: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
file, conditionMessage(e)))}) error = function(e) {27: if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 58: error <<- format(e)withCallingHandlers(code, error = function (e) }), list(rlang_trace_top_env = knit_global()))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
48: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppL0RIq/file84c6174e54f2.rds")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), rlang::entrace(e), message = function (cnd) error = function(e) {
{An irrecoverable exception occurred. R is aborting now ...
if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() if (on_message$capture) { watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) } }), list(rlang_trace_top_env = knit_global())), function(loc) { if (on_message$silence) { setwd(wd) invokeRestart("muffleMessage") write_utf8(res, output %n% stdout()) } paste0("\nQuitting from ", loc, if (!is.null(error)) }, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { paste0("\n", rule(), error, "\n", rule())) return()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }
watcher$capture_plot_and_output() if (on_warning$capture) {49: process_file(text, output) cnd <- sanitize_call(cnd)
watcher$push(cnd)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
}51: if (on_warning$silence) { invokeRestart("muffleWarning")rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } output_dir = getwd(), ...)
}, error = function (cnd) 52: {vweave_rmarkdown(...) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
watcher$push(cnd)53: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
engine$weave(file, quiet = quiet, encoding = enc)28: eval(call)
29: eval(call)
54: 30: with_handlers({ for (expr in tle$exprs) {doTryCatch(return(expr), name, parentenv, handler)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
}56: TRUE}, handlers)tryCatchList(expr, classes, parentenv, handlers)
31: doWithOneRestart(return(expr), restart)57:
32: tryCatch({withOneRestart(expr, restarts[[1L]])
engine$weave(file, quiet = quiet, encoding = enc)33: withRestartList(expr, restarts[-nr]) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {34: texi2pdf(file = output, clean = FALSE, quiet = quiet)doWithOneRestart(return(expr), restart) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)35: }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) outputs <- c(outputs, output)
}, error = function(e) {36: withRestartList(expr, restarts) thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))37: withRestarts(with_handlers({}) for (expr in tle$exprs) {
58: ev <- withVisible(eval(expr, envir))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmppL0RIq/file84c6174e54f2.rds") watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)An irrecoverable exception occurred. R is aborting now ...
} 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) { 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), 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(), ...)
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/RtmppL0RIq/file84c6174e54f2.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