Last updated on 2026-10-10 20:50:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.49 | 219.56 | 223.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.96 | 231.23 | 234.19 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.60 | 213.69 | 217.29 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 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 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 35.00 | 37.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 163.00 | 170.00 | 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
2026-10-11 01:46:07.545 R[40561:62533] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
*** caught segfault ***
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)address 0x110, cause 'invalid permissions'
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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")
*** caught segfault ***
.Internal(seterrmessage(msg[1L]))address 0x110, cause 'invalid permissions'
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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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:
*** caught segfault ***
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), address 0x110, cause 'invalid permissions'
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/RtmprsRkqr/file885c53dc7015.rds")
An irrecoverable exception occurred. R is aborting now ...
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))})
Traceback:
1: 12: RowCumsum(valid)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
2: 13: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
14: FUN(X[[i]], ...) tieBreak = FALSE, verbose = verbose)
3: 15: lapply(seq_len(cores), inner.do)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 16: embedded = embedded, validLib = validLib, noTime = noTime, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) ignoreNan = ignoreNan, backend = backend)
17:
doTryCatch(return(expr), name, parentenv, handler)
4: 18: ComputeError(predictions$Observations, predictions$Predictions)tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: 19: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatchList(expr, classes, parentenv, handlers) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
20: 6: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, FUN(X[[i]], ...) mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess) 7:
22: lapply(X = S, FUN = FUN, ...)unlist(SweepApply(theta, worker, numProcess))
8: 23: doTryCatch(return(expr), name, parentenv, handler)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 9: E = E, showPlot = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: eval(expr, envir)
10: 25: tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
11: tryCatch(expr, error = function(e) {26: call <- conditionCall(e)withVisible(eval(expr, envir)) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 27: withCallingHandlers(code, error = function (e) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)rlang::entrace(e), message = function (cnd) prefix <- paste("Error in", dcall, ": "){ LONG <- 75L watcher$capture_plot_and_output() if (on_message$capture) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$push(cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) if (on_message$silence) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invokeRestart("muffleMessage") type = "b") } if (w > LONG) prefix <- paste0(prefix, "\n ")}, warning = function (cnd) }{ else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") if (getOption("warn") >= 2 || getOption("warn") < 0) { .Internal(seterrmessage(msg[1L])) return() if (!silent && isTRUE(getOption("show.error.messages"))) { } watcher$capture_plot_and_output() cat(msg, file = outFile) if (on_warning$capture) { .Internal(printDeferredWarnings()) cnd <- sanitize_call(cnd) watcher$push(cnd) } } invisible(structure(msg, class = "try-error", condition = e)) if (on_warning$silence) {}) invokeRestart("muffleWarning")
}}, error = function (cnd) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE){ watcher$capture_plot_and_output()
13: cnd <- sanitize_call(cnd)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 14: stop = invokeRestart("eval_stop"), error = NULL)FUN(X[[i]], ...)
15: })lapply(seq_len(cores), inner.do)
28: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)eval(call)
17: 29: doTryCatch(return(expr), name, parentenv, handler)eval(call)
18: 30: tryCatchOne(expr, names, parentenv, handlers[[1L]])with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))19: tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)20: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
TRUE}, handlers)21:
SweepApply(theta, worker, numProcess)31:
doWithOneRestart(return(expr), restart)22: unlist(SweepApply(theta, worker, numProcess))
32: 23: withOneRestart(expr, restarts[[1L]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 33: E = E, showPlot = TRUE)withRestartList(expr, restarts[-nr])
24: 34: eval(expr, envir)doWithOneRestart(return(expr), restart)
25: 35: eval(expr, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26:
withVisible(eval(expr, envir))36:
withRestartList(expr, restarts)27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 37: {withRestarts(with_handlers({ watcher$capture_plot_and_output() for (expr in tle$exprs) { if (on_message$capture) { ev <- withVisible(eval(expr, envir)) watcher$push(cnd) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) } if (on_message$silence) { TRUE invokeRestart("muffleMessage")}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
}, warning = function (cnd) 38: {evaluate::evaluate(...) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }
watcher$capture_plot_and_output()39: if (on_warning$capture) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, cnd <- sanitize_call(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) } if (on_warning$silence) { 0L invokeRestart("muffleWarning") else 2L }}, error = function (cnd) }, output_handler = knit_handlers(options$render, options)){ watcher$capture_plot_and_output()
40: in_dir(input_dir(), expr)
cnd <- sanitize_call(cnd)41: 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$warning, stop = invokeRestart("eval_stop"), error = NULL) keep_message = if (is.numeric(options$message)) TRUE else options$message,
Traceback:
}) 1:
stop_on_error = if (is.numeric(options$error)) options$error else {RowCumsum(valid)28: if (options$error && options$include) 0Leval(call) else 2L
29: }, output_handler = knit_handlers(options$render, options))) 2:
eval(call)42:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, eng_r(options)30: validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)with_handlers({43: for (expr in tle$exprs) {
block_exec(params) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
3: watcher$print_value(ev$value, ev$visible, envir)44: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, call_block(x) }
tau = tau, theta = th, exclusionRadius = exclusionRadius, TRUE45: embedded = embedded, validLib = validLib, noTime = noTime, }, handlers) ignoreNan = ignoreNan, backend = backend)
process_group(group)31:
doWithOneRestart(return(expr), restart)
4: 32: 46: ComputeError(predictions$Observations, predictions$Predictions)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withOneRestart(expr, restarts[[1L]])
error = function(e) {
if (progress && is.function(pb$interrupt)) 5: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 33: error <<- format(e) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, withRestartList(expr, restarts[-nr]) embedded = embedded, validLib = validLib, noTime = noTime, })
ignoreNan = ignoreNan, backend = backend)$predictions)
34: 6: doWithOneRestart(return(expr), restart)47: FUN(X[[i]], ...)
35: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 7: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])lapply(X = S, FUN = FUN, ...)
error = function(e) {36: withRestartList(expr, restarts)
if (progress && is.function(pb$interrupt)) 8: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)doTryCatch(return(expr), name, parentenv, handler) }), list(rlang_trace_top_env = knit_global()))37:
48: withRestarts(with_handlers({ 9: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) { ev <- withVisible(eval(expr, envir))
if (progress && is.function(pb$interrupt)) 10: watcher$capture_plot_and_output() pb$interrupt()tryCatchList(expr, classes, parentenv, handlers) watcher$print_value(ev$value, ev$visible, envir)
if (is_R_CMD_build() || is_R_CMD_check()) 11: } TRUE error <<- format(e)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)tryCatch(expr, error = function(e) {
}), list(rlang_trace_top_env = knit_global())), function(loc) { call <- conditionCall(e) setwd(wd) if (!is.null(call)) {38: write_utf8(res, output %n% stdout()) if (identical(call[[1L]], quote(doTryCatch))) paste0("\nQuitting from ", loc, if (!is.null(error)) evaluate::evaluate(...) call <- sys.call(-4L) paste0("\n", rule(), error, "\n", rule()))
dcall <- deparse(call, nlines = 1L)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L49: 39: sm <- strsplit(conditionMessage(e), "\n")[[1L]]process_file(text, output)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is.na(w)) 50: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], stop_on_error = if (is.numeric(options$error)) options$error else { type = "b")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (options$error && options$include) if (w > LONG)
51: prefix <- paste0(prefix, "\n ") 0Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), else 2L output_dir = getwd(), ...) }
}, output_handler = knit_handlers(options$render, options)) else prefix <- "Error : "52:
msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))40: vweave_rmarkdown(...)in_dir(input_dir(), expr) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)53: 41: engine$weave(file, quiet = quiet, encoding = enc) .Internal(printDeferredWarnings())in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }54: keep_message = if (is.numeric(options$message)) TRUE else options$message, doTryCatch(return(expr), name, parentenv, handler) invisible(structure(msg, class = "try-error", condition = e)) stop_on_error = if (is.numeric(options$error)) options$error else {}) if (options$error && options$include)
0L12: else 2L55: }, output_handler = knit_handlers(options$render, options)))tryCatchOne(expr, names, parentenv, handlers[[1L]])
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)42:
eng_r(options)13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
56:
43: 14: tryCatchList(expr, classes, parentenv, handlers)block_exec(params)FUN(X[[i]], ...)
44: 15: 57: call_block(x)lapply(seq_len(cores), inner.do)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)45: 16: setwd(startdir)process_group(group)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) output <- find_vignette_product(name, by = "weave", engine = engine)
46: if (!have.makefile && vignette_is_tex(output)) {17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), doTryCatch(return(expr), name, parentenv, handler) texi2pdf(file = output, clean = FALSE, quiet = quiet) error = function(e) { output <- find_vignette_product(name, by = "texi2pdf",
if (progress && is.function(pb$interrupt)) engine = engine)18: pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]]) } if (is_R_CMD_build() || is_R_CMD_check()) outputs <- c(outputs, output)
error <<- format(e)19: }, error = function(e) { })tryCatchList(expr, classes, parentenv, handlers) thisOK <<- FALSE
20: 47: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 21: file, conditionMessage(e)))SweepApply(theta, worker, numProcess) error = function(e) {})
if (progress && is.function(pb$interrupt)) 22: 58: unlist(SweepApply(theta, worker, numProcess))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt()
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmprsRkqr/file885c53dc7015.rds") if (is_R_CMD_build() || is_R_CMD_check()) 23:
error <<- format(e)An irrecoverable exception occurred. R is aborting now ...
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), E = E, showPlot = TRUE) error = function(e) {
if (progress && is.function(pb$interrupt)) 24: pb$interrupt()eval(expr, envir)
if (is_R_CMD_build() || is_R_CMD_check()) 25: error <<- format(e)eval(expr, envir) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)26: write_utf8(res, output %n% stdout())withVisible(eval(expr, envir)) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))27: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
{49: watcher$capture_plot_and_output()process_file(text, output) if (on_message$capture) {
watcher$push(cnd)50: }knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (on_message$silence) {
invokeRestart("muffleMessage")51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } output_dir = getwd(), ...)}, warning = function (cnd)
52: {vweave_rmarkdown(...) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()53: engine$weave(file, quiet = quiet, encoding = enc) }
watcher$capture_plot_and_output()54: if (on_warning$capture) {doTryCatch(return(expr), name, parentenv, handler) cnd <- sanitize_call(cnd)
watcher$push(cnd)55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
56: if (on_warning$silence) {tryCatchList(expr, classes, parentenv, handlers)
invokeRestart("muffleWarning")57: }tryCatch({}, error = function (cnd) engine$weave(file, quiet = quiet, encoding = enc){ setwd(startdir) watcher$capture_plot_and_output() output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { cnd <- sanitize_call(cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet) watcher$push(cnd) output <- find_vignette_product(name, by = "texi2pdf", switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) engine = engine) }}) outputs <- c(outputs, output)}, error = function(e) {
thisOK <<- FALSE fails <<- c(fails, file)28: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", eval(call) file, conditionMessage(e)))
})29:
eval(call)
58: 30: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", with_handlers({ skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmprsRkqr/file885c53dc7015.rds")
for (expr in tle$exprs) {An irrecoverable exception occurred. R is aborting now ...
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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", 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/RtmprsRkqr/file885c53dc7015.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