Last updated on 2026-10-01 05:54:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.83 | 223.64 | 227.47 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.59 | 218.37 | 220.96 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.12 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.10 | 210.00 | 214.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.56 | 209.84 | 213.40 | 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 | 1.00 | 40.00 | 41.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 158.00 | 166.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-30 14:51:31.057 R[43319:64587] 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, 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")
*** caught segfault ***
.Internal(seterrmessage(msg[1L]))address 0x110, cause 'invalid permissions'
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())
*** caught segfault ***
}address 0x110, cause 'invalid permissions'
invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
*** caught segfault ***
13: address 0x110, cause 'invalid permissions'
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: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
Traceback:
1: RowCumsum(valid)
52: vweave_rmarkdown(...) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 53: tieBreak = FALSE, verbose = verbose)engine$weave(file, quiet = quiet, encoding = enc)
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, 54: ignoreNan = ignoreNan, backend = backend)doTryCatch(return(expr), name, parentenv, handler)
55: 4: ComputeError(predictions$Observations, predictions$Predictions)tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 56: tryCatchList(expr, classes, parentenv, handlers) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
Traceback:
1: 57: embedded = embedded, validLib = validLib, noTime = noTime, RowCumsum(valid)
tryCatch({ 2: ignoreNan = ignoreNan, backend = backend)$predictions)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, engine$weave(file, quiet = quiet, encoding = enc)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) 6: tieBreak = FALSE, verbose = verbose) if (!have.makefile && vignette_is_tex(output)) {
FUN(X[[i]], ...)
Traceback:
3: texi2pdf(file = output, clean = FALSE, quiet = quiet)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
1: 7: output <- find_vignette_product(name, by = "texi2pdf", tau = tau, theta = th, exclusionRadius = exclusionRadius, engine = engine)lapply(X = S, FUN = FUN, ...)RowCumsum(valid) }
embedded = embedded, validLib = validLib, noTime = noTime, outputs <- c(outputs, output)
ignoreNan = ignoreNan, backend = backend) 8: doTryCatch(return(expr), name, parentenv, handler)
2: }, error = function(e) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
9: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tieBreak = FALSE, verbose = verbose)
10: thisOK <<- FALSEtryCatchList(expr, classes, parentenv, handlers)ComputeError(predictions$Observations, predictions$Predictions) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
3: 5: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, file, conditionMessage(e)))11: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, })
tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch(expr, error = function(e) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- conditionCall(e) embedded = embedded, validLib = validLib, noTime = noTime, if (!is.null(call)) { embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) ignoreNan = ignoreNan, backend = backend) if (identical(call[[1L]], quote(doTryCatch)))
58: 4: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDc4uKo/file81af6d78699a.rds")
6: call <- sys.call(-4L)
ComputeError(predictions$Observations, predictions$Predictions)
dcall <- deparse(call, nlines = 1L) 5: FUN(X[[i]], ...)An irrecoverable exception occurred. R is aborting now ...
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 7: lapply(X = S, FUN = FUN, ...) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) 8: embedded = embedded, validLib = validLib, noTime = noTime, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], doTryCatch(return(expr), name, parentenv, handler) type = "b")
if (w > LONG) ignoreNan = ignoreNan, backend = backend)$predictions) 9:
prefix <- paste0(prefix, "\n ") 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...) } else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 7:
.Internal(seterrmessage(msg[1L]))lapply(X = S, FUN = FUN, ...) if (!silent && isTRUE(getOption("show.error.messages"))) {10:
tryCatchList(expr, classes, parentenv, handlers) 8: cat(msg, file = outFile)
.Internal(printDeferredWarnings())11: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {
9: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
call <- conditionCall(e)}) if (!is.null(call)) {10:
if (identical(call[[1L]], quote(doTryCatch))) tryCatchList(expr, classes, parentenv, handlers) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE) prefix <- paste("Error in", dcall, ": ")
11: LONG <- 75LtryCatch(expr, error = function(e) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- conditionCall(e)13: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!is.null(call)) { if (is.na(w)) if (identical(call[[1L]], quote(doTryCatch))) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) type = "b") call <- sys.call(-4L)
if (w > LONG) dcall <- deparse(call, nlines = 1L)14: prefix <- paste("Error in", dcall, ": ") prefix <- paste0(prefix, "\n ") LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]]FUN(X[[i]], ...) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")15: .Internal(seterrmessage(msg[1L])) if (is.na(w)) lapply(seq_len(cores), inner.do) if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], cat(msg, file = outFile)
.Internal(printDeferredWarnings()) type = "b") } if (w > LONG) invisible(structure(msg, class = "try-error", condition = e))16: prefix <- paste0(prefix, "\n ")parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) }
else prefix <- "Error : "17: })doTryCatch(return(expr), name, parentenv, handler) msg <- paste0(prefix, conditionMessage(e), "\n")
12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)18: .Internal(seterrmessage(msg[1L]))tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())
}19:
tryCatchList(expr, classes, parentenv, handlers)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))20: invisible(structure(msg, class = "try-error", condition = e))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }) mc.preschedule = TRUE), error = function(e) NULL)
12:
21: SweepApply(theta, worker, numProcess)14: FUN(X[[i]], ...)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: 22: unlist(SweepApply(theta, worker, numProcess))
lapply(seq_len(cores), inner.do)23: 13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
17: E = E, showPlot = TRUE)14: FUN(X[[i]], ...)
24: 15: doTryCatch(return(expr), name, parentenv, handler)eval(expr, envir)lapply(seq_len(cores), inner.do)
18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: eval(expr, envir)19: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatchList(expr, classes, parentenv, handlers)
17:
doTryCatch(return(expr), name, parentenv, handler)26:
20: withVisible(eval(expr, envir))
18: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatchOne(expr, names, parentenv, handlers[[1L]])
mc.preschedule = TRUE), error = function(e) NULL)27:
19: withCallingHandlers(code, error = function (e) 21: rlang::entrace(e), message = function (cnd) SweepApply(theta, worker, numProcess)
{22: tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) {unlist(SweepApply(theta, worker, numProcess))
20:
invokeRestart("muffleMessage")23: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }, warning = function (cnd) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", mc.preschedule = TRUE), error = function(e) NULL) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE){ if (getOption("warn") >= 2 || getOption("warn") < 0) {
21: 24: return()eval(expr, envir)SweepApply(theta, worker, numProcess) }
22:
unlist(SweepApply(theta, worker, numProcess))25: watcher$capture_plot_and_output()
if (on_warning$capture) {eval(expr, envir)23: cnd <- sanitize_call(cnd)
watcher$push(cnd)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 26: } target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (on_warning$silence) { E = E, showPlot = TRUE)
invokeRestart("muffleWarning")24: withVisible(eval(expr, envir)) }eval(expr, envir)}, error = function (cnd)
{25: watcher$capture_plot_and_output()27: withCallingHandlers(code, error = function (e) cnd <- sanitize_call(cnd)eval(expr, envir) watcher$push(cnd)
rlang::entrace(e), message = function (cnd) switch(on_error, continue = invokeRestart("eval_continue"), 26: {withVisible(eval(expr, envir)) stop = invokeRestart("eval_stop"), error = NULL)
watcher$capture_plot_and_output()27: if (on_message$capture) {})withCallingHandlers(code, error = function (e)
watcher$push(cnd)rlang::entrace(e), message = function (cnd) 28: }{eval(call) if (on_message$silence) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)
invokeRestart("muffleMessage") }29: }eval(call) if (on_message$silence) {
}, warning = function (cnd) 30: { invokeRestart("muffleMessage")with_handlers({ if (getOption("warn") >= 2 || getOption("warn") < 0) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) } watcher$capture_plot_and_output() return() } watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output()}, warning = function (cnd) } if (on_warning$capture) { TRUE{ cnd <- sanitize_call(cnd)}, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd)
31: } return() } if (on_warning$silence) {doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)
invokeRestart("muffleWarning") watcher$push(cnd)32: } } if (on_warning$silence) { invokeRestart("muffleWarning")}, error = function (cnd) }withOneRestart(expr, restarts[[1L]])}, error = function (cnd) {
33: { watcher$capture_plot_and_output() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) cnd <- sanitize_call(cnd)withRestartList(expr, restarts[-nr]) switch(on_error, continue = invokeRestart("eval_continue"), watcher$push(cnd)
stop = invokeRestart("eval_stop"), error = NULL)34: }) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)})
28: doWithOneRestart(return(expr), restart)eval(call)28:
eval(call)35:
29: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])eval(call)
36: 29: 30: eval(call)with_handlers({withRestartList(expr, restarts) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))37:
withRestarts(with_handlers({ watcher$capture_plot_and_output()30: for (expr in tle$exprs) {with_handlers({ watcher$print_value(ev$value, ev$visible, envir) ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) { watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) ev <- withVisible(eval(expr, envir)) TRUE}, handlers) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir)
TRUE }31: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
doWithOneRestart(return(expr), restart)38: TRUE
evaluate::evaluate(...)32: }, handlers)
39: withOneRestart(expr, restarts[[1L]])
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 33: keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {31: withRestartList(expr, restarts[-nr]) if (options$error && options$include) doWithOneRestart(return(expr), restart) 0L
else 2L32:
withOneRestart(expr, restarts[[1L]]) }, output_handler = knit_handlers(options$render, options))34:
40: 33: in_dir(input_dir(), expr)doWithOneRestart(return(expr), restart)withRestartList(expr, restarts[-nr])
41:
34: doWithOneRestart(return(expr), restart)35: in_input_dir(evaluate(code, envir = env, new_device = FALSE, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: 36: keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestartList(expr, restarts)
withRestartList(expr, restarts)37: stop_on_error = if (is.numeric(options$error)) options$error else {
withRestarts(with_handlers({37: if (options$error && options$include) for (expr in tle$exprs) {withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) ev <- withVisible(eval(expr, envir)) 0L watcher$capture_plot_and_output() else 2L watcher$print_value(ev$value, ev$visible, envir) } }, output_handler = knit_handlers(options$render, options))) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
TRUE }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)42:
TRUEeng_r(options)38: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)evaluate::evaluate(...)
39: 38: 43: evaluate::evaluate(...)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, 39: block_exec(params)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, 44: stop_on_error = if (is.numeric(options$error)) options$error else {call_block(x) if (options$error && options$include) stop_on_error = if (is.numeric(options$error)) options$error else { 0L if (options$error && options$include)
0L45: else 2Lprocess_group(group)
else 2L46: }, output_handler = knit_handlers(options$render, options)) }, output_handler = knit_handlers(options$render, options))
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
40: error = function(e) { if (progress && is.function(pb$interrupt)) 40: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) in_dir(input_dir(), expr) error <<- format(e)
})
41: 47: in_dir(input_dir(), expr)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), in_input_dir(evaluate(code, envir = env, new_device = FALSE, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt))
keep_message = if (is.numeric(options$message)) TRUE else options$message, pb$interrupt()41: if (is_R_CMD_build() || is_R_CMD_check()) in_input_dir(evaluate(code, envir = env, new_device = FALSE, error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { }), list(rlang_trace_top_env = knit_global()))
if (options$error && options$include) 48: 0L else 2Lxfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, output_handler = knit_handlers(options$render, options))) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt() keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {42: if (is_R_CMD_build() || is_R_CMD_check()) if (options$error && options$include) error <<- format(e) 0Leng_r(options) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
else 2L43: write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) block_exec(params) paste0("\n", rule(), error, "\n", rule())) }, output_handler = knit_handlers(options$render, options)))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: eng_r(options)44: call_block(x)49: process_file(text, output)
50: 45: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
process_group(group)51:
43: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 46: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output_dir = getwd(), ...) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()52: if (is_R_CMD_build() || is_R_CMD_check()) vweave_rmarkdown(...)44: call_block(x)
error <<- format(e)45: })53:
process_group(group)engine$weave(file, quiet = quiet, encoding = enc)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {54: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 46: error <<- format(e)doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global()))
55: 48: error = function(e) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt()56: error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)tryCatchList(expr, classes, parentenv, handlers) }), list(rlang_trace_top_env = knit_global())), function(loc) { }) setwd(wd) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))57: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
47: 49: tryCatch({process_file(text, output) engine$weave(file, quiet = quiet, encoding = enc)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), setwd(startdir)
error = function(e) { output <- find_vignette_product(name, by = "weave", engine = engine) if (progress && is.function(pb$interrupt)) if (!have.makefile && vignette_is_tex(output)) { pb$interrupt() texi2pdf(file = output, clean = FALSE, quiet = quiet) if (is_R_CMD_build() || is_R_CMD_check()) output <- find_vignette_product(name, by = "texi2pdf", 50: error <<- format(e) engine = engine) }), list(rlang_trace_top_env = knit_global()))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
}48: outputs <- c(outputs, output)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
}, error = function(e) { thisOK <<- FALSE if (progress && is.function(pb$interrupt)) pb$interrupt()51: if (is_R_CMD_build() || is_R_CMD_check()) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), error <<- format(e) file, conditionMessage(e))) output_dir = getwd(), ...) }), list(rlang_trace_top_env = knit_global())), function(loc) {}) setwd(wd)
write_utf8(res, output %n% stdout())
52: paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))58: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
vweave_rmarkdown(...)49: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
process_file(text, output)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDc4uKo/file81af6d78699a.rds")50:
53: An irrecoverable exception occurred. R is aborting now ...
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
engine$weave(file, quiet = quiet, encoding = enc)
51: 54: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), doTryCatch(return(expr), name, parentenv, handler) output_dir = getwd(), ...)
55: 52: vweave_rmarkdown(...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 53: engine$weave(file, quiet = quiet, encoding = enc)tryCatchList(expr, classes, parentenv, handlers)
54: 57: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatch({tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
56: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchList(expr, classes, parentenv, handlers)
if (!have.makefile && vignette_is_tex(output)) {57: tryCatch({ texi2pdf(file = output, clean = FALSE, quiet = quiet) engine$weave(file, quiet = quiet, encoding = enc) output <- find_vignette_product(name, by = "texi2pdf", setwd(startdir) engine = engine) output <- find_vignette_product(name, by = "weave", engine = engine) } if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) outputs <- c(outputs, output)}, error = function(e) { output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } thisOK <<- FALSE outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 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/RtmpDc4uKo/file81af6d78699a.rds")
58: An irrecoverable exception occurred. R is aborting now ...
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDc4uKo/file81af6d78699a.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