Last updated on 2026-10-26 00:51:54 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.91 | 223.80 | 227.71 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.60 | 237.04 | 239.64 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 191.21 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 139.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.75 | 212.15 | 215.90 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.10 | 211.40 | 214.50 | 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 | 6.00 | 129.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 47.00 | 49.00 | 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 | 161.00 | 169.00 | 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
2026-10-26 08:34:56.587 R[46331:69792] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
Traceback:
1: 33: RowCumsum(valid)
withRestartList(expr, restarts[-nr]) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)34:
doWithOneRestart(return(expr), restart)
3: 35: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)36:
withRestartList(expr, restarts)
4: 37: ComputeError(predictions$Observations, predictions$Predictions)withRestarts(with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) 5: watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, watcher$print_value(ev$value, ev$visible, envir) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } embedded = embedded, validLib = validLib, noTime = noTime, TRUE ignoreNan = ignoreNan, backend = backend)$predictions)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 6: FUN(X[[i]], ...)
38: evaluate::evaluate(...) 7:
39: lapply(X = S, FUN = FUN, ...)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 { 8: if (options$error && options$include) 0LdoTryCatch(return(expr), name, parentenv, handler) else 2L
}, output_handler = knit_handlers(options$render, options)) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: 10: in_dir(input_dir(), expr)tryCatchList(expr, classes, parentenv, handlers)
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 11: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatch(expr, error = function(e) { stop_on_error = if (is.numeric(options$error)) options$error else { call <- conditionCall(e) if (options$error && options$include) if (!is.null(call)) { 0L if (identical(call[[1L]], quote(doTryCatch))) else 2L call <- sys.call(-4L) }, output_handler = knit_handlers(options$render, options))) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")42: LONG <- 75Leng_r(options) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 43: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], block_exec(params) type = "b")
if (w > LONG) 44: prefix <- paste0(prefix, "\n ")call_block(x)
}45: else prefix <- "Error : "process_group(group) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))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) }) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())
}47: invisible(structure(msg, class = "try-error", condition = e))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) {
if (progress && is.function(pb$interrupt)) 12: pb$interrupt()try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)13: }), list(rlang_trace_top_env = knit_global()))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 48: FUN(X[[i]], ...)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
15: error = function(e) {lapply(seq_len(cores), inner.do) if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 16: error <<- format(e)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)17: doTryCatch(return(expr), name, parentenv, handler)
write_utf8(res, output %n% stdout())18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))19: tryCatchList(expr, classes, parentenv, handlers)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 49: mc.preschedule = TRUE), error = function(e) NULL)process_file(text, output)
50: 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
SweepApply(theta, worker, numProcess)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 22: output_dir = getwd(), ...)
unlist(SweepApply(theta, worker, numProcess))52:
23: vweave_rmarkdown(...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
53: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", engine$weave(file, quiet = quiet, encoding = enc) E = E, showPlot = TRUE)
54:
doTryCatch(return(expr), name, parentenv, handler)24:
eval(expr, envir)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])25:
eval(expr, envir)56: tryCatchList(expr, classes, parentenv, handlers)
26:
withVisible(eval(expr, envir))57:
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)27: setwd(startdir)withCallingHandlers(code, error = function (e) output <- find_vignette_product(name, by = "weave", engine = engine)rlang::entrace(e), message = function (cnd) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet){ output <- find_vignette_product(name, by = "texi2pdf", watcher$capture_plot_and_output() engine = engine) if (on_message$capture) { watcher$push(cnd) } } if (on_message$silence) { invokeRestart("muffleMessage") outputs <- c(outputs, output)}, error = function(e) { } thisOK <<- FALSE}, warning = function (cnd) fails <<- c(fails, file){ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (getOption("warn") >= 2 || getOption("warn") < 0) { file, conditionMessage(e))) return()}) }
watcher$capture_plot_and_output()58: if (on_warning$capture) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", cnd <- sanitize_call(cnd) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpuCDpzv/file91336f2c8bf9.rds") watcher$push(cnd)
}An irrecoverable exception occurred. R is aborting now ...
if (on_warning$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(), ...)
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/RtmpuCDpzv/file91336f2c8bf9.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]])
Traceback:
10: 1: RowCumsum(valid)tryCatchList(expr, classes, parentenv, handlers)
2:
11: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatch(expr, error = function(e) { call <- conditionCall(e) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, if (!is.null(call)) { tieBreak = FALSE, verbose = verbose) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, dcall <- deparse(call, nlines = 1L) tau = tau, theta = th, exclusionRadius = exclusionRadius, prefix <- paste("Error in", dcall, ": ") embedded = embedded, validLib = validLib, noTime = noTime, LONG <- 75L ignoreNan = ignoreNan, backend = backend) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 4: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ComputeError(predictions$Observations, predictions$Predictions) type = "b")
5: if (w > LONG) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, prefix <- paste0(prefix, "\n ") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } embedded = embedded, validLib = validLib, noTime = noTime, else prefix <- "Error : " ignoreNan = ignoreNan, backend = backend)$predictions) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
6: if (!silent && isTRUE(getOption("show.error.messages"))) {FUN(X[[i]], ...) cat(msg, file = outFile)
7: .Internal(printDeferredWarnings())lapply(X = S, FUN = FUN, ...)
} 8: invisible(structure(msg, class = "try-error", condition = e))doTryCatch(return(expr), name, parentenv, handler)})
9: 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)10: tryCatchList(expr, classes, parentenv, handlers)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))11: tryCatch(expr, error = function(e) {
call <- conditionCall(e)14: if (!is.null(call)) {FUN(X[[i]], ...) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)15: dcall <- deparse(call, nlines = 1L)lapply(seq_len(cores), inner.do) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L16: sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")17: doTryCatch(return(expr), name, parentenv, handler) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")18: if (w > LONG) tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste0(prefix, "\n ")
}19: else prefix <- "Error : "tryCatchList(expr, classes, parentenv, handlers) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {20: cat(msg, file = outFile) .Internal(printDeferredWarnings())tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } invisible(structure(msg, class = "try-error", condition = e)) mc.preschedule = TRUE), error = function(e) NULL)})
12: 21: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)SweepApply(theta, worker, numProcess)
13: 22: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
unlist(SweepApply(theta, worker, numProcess))14:
FUN(X[[i]], ...)23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: 15: eval(expr, envir)lapply(seq_len(cores), inner.do)
25: 16: eval(expr, envir)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)26:
withVisible(eval(expr, envir))17:
doTryCatch(return(expr), name, parentenv, handler)27:
withCallingHandlers(code, error = function (e) 18: rlang::entrace(e), message = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]]){ watcher$capture_plot_and_output()
if (on_message$capture) {19: watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) }
20: if (on_message$silence) { invokeRestart("muffleMessage")tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } mc.preschedule = TRUE), error = function(e) NULL)}, warning = function (cnd)
21: {SweepApply(theta, worker, numProcess) if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
} watcher$capture_plot_and_output()22: if (on_warning$capture) {unlist(SweepApply(theta, worker, numProcess)) cnd <- sanitize_call(cnd)
watcher$push(cnd)23: }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (on_warning$silence) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", invokeRestart("muffleWarning") E = E, showPlot = TRUE) }
}, error = function (cnd) 24: {eval(expr, envir) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)25: eval(expr, envir) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)26: })withVisible(eval(expr, envir))
28: 27: withCallingHandlers(code, error = function (e) eval(call)
rlang::entrace(e), message = function (cnd) 29: {eval(call) watcher$capture_plot_and_output()
if (on_message$capture) {30: watcher$push(cnd)with_handlers({ } if (on_message$silence) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) invokeRestart("muffleMessage") } watcher$capture_plot_and_output()}, warning = function (cnd) watcher$print_value(ev$value, ev$visible, envir){ } TRUE if (getOption("warn") >= 2 || getOption("warn") < 0) { return()}, handlers) }
watcher$capture_plot_and_output()31: if (on_warning$capture) {doWithOneRestart(return(expr), restart) cnd <- sanitize_call(cnd) watcher$push(cnd)
}32: if (on_warning$silence) {withOneRestart(expr, restarts[[1L]]) invokeRestart("muffleWarning")
33: }withRestartList(expr, restarts[-nr])}, error = function (cnd)
{ watcher$capture_plot_and_output()34: cnd <- sanitize_call(cnd)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$warning, watcher$push(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, switch(on_error, continue = invokeRestart("eval_continue"), stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
stop = invokeRestart("eval_stop"), error = NULL)40: })in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 28: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {eval(call)
29: eval(call)
30: with_handlers({ if (options$error && options$include) for (expr in tle$exprs) { 0L else 2L ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options))) watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)32: withOneRestart(expr, restarts[[1L]]) })
47: 33: withRestartList(expr, restarts[-nr])with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
if (progress && is.function(pb$interrupt)) 34: 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$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)doWithOneRestart(return(expr), restart)
write_utf8(res, output %n% stdout())35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) paste0("\nQuitting from ", loc, if (!is.null(error))
36: paste0("\n", rule(), error, "\n", rule()))withRestartList(expr, restarts)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
37: withRestarts(with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))49: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEprocess_file(text, output)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: 50: evaluate::evaluate(...)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
39: 51: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 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)
0L52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
else 2L56: tryCatchList(expr, classes, parentenv, handlers) }, output_handler = knit_handlers(options$render, options))
57:
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$render, options)))
42: eng_r(options)tryCatch({
43: engine$weave(file, quiet = quiet, encoding = enc)block_exec(params) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)44: call_block(x) if (!have.makefile && vignette_is_tex(output)) {
45: texi2pdf(file = output, clean = FALSE, quiet = quiet)process_group(group) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)46: } outputs <- c(outputs, output)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function(e) { error = function(e) { thisOK <<- FALSE if (progress && is.function(pb$interrupt)) fails <<- c(fails, file) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) error <<- format(e) })})
58: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", error = function(e) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpuCDpzv/file91336f2c8bf9.rds") 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()))An irrecoverable exception occurred. R is aborting now ...
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/RtmpuCDpzv/file91336f2c8bf9.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