Last updated on 2026-10-13 09:50:37 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 | 2.54 | 234.52 | 237.06 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | 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 | 3.18 | 212.69 | 215.87 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 5.00 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 36.00 | 38.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 157.00 | 165.00 | 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
2026-10-13 16:34:52.423 R[46543:69604] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 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)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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
*** caught segfault ***
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)address 0x110, cause 'invalid permissions'
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$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
Traceback:
1: RowCumsum(valid)
56: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchList(expr, classes, parentenv, handlers) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)57:
tryCatch({ 3: engine$weave(file, quiet = quiet, encoding = enc)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, setwd(startdir) tau = tau, theta = th, exclusionRadius = exclusionRadius, output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { embedded = embedded, validLib = validLib, noTime = noTime, texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", ignoreNan = ignoreNan, backend = backend) engine = engine)
} 4: outputs <- c(outputs, output)ComputeError(predictions$Observations, predictions$Predictions)}, error = function(e) {
thisOK <<- FALSE fails <<- c(fails, file) 5: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, file, conditionMessage(e))) embedded = embedded, validLib = validLib, noTime = noTime, })
ignoreNan = ignoreNan, backend = backend)$predictions)58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 6: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWfe6EM/file834a55f9345f.rds")
FUN(X[[i]], ...)An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
26: withVisible(eval(expr, envir)) 1:
RowCumsum(valid)27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 2: { watcher$capture_plot_and_output()FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (on_message$capture) { watcher$push(cnd) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, } tieBreak = FALSE, verbose = verbose) if (on_message$silence) {
invokeRestart("muffleMessage") 3: }}, warning = function (cnd) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, { if (getOption("warn") >= 2 || getOption("warn") < 0) { tau = tau, theta = th, exclusionRadius = exclusionRadius, return() } embedded = embedded, validLib = validLib, noTime = noTime, watcher$capture_plot_and_output() if (on_warning$capture) { ignoreNan = ignoreNan, backend = backend) cnd <- sanitize_call(cnd)
watcher$push(cnd) 4: }ComputeError(predictions$Observations, predictions$Predictions) if (on_warning$silence) {
invokeRestart("muffleWarning") 5: }}, error = function (cnd) { watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, stop = invokeRestart("eval_stop"), error = NULL)})
embedded = embedded, validLib = validLib, noTime = noTime, 28: ignoreNan = ignoreNan, backend = backend)$predictions)eval(call)
6:
FUN(X[[i]], ...)29:
7: eval(call)lapply(X = S, FUN = FUN, ...)
8: 30: with_handlers({doTryCatch(return(expr), name, parentenv, handler) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() 9: watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
TRUE10: }, handlers)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {31: call <- conditionCall(e)doWithOneRestart(return(expr), restart)
if (!is.null(call)) {32: if (identical(call[[1L]], quote(doTryCatch))) withOneRestart(expr, restarts[[1L]]) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")33: LONG <- 75LwithRestartList(expr, restarts[-nr]) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
34: if (is.na(w)) doWithOneRestart(return(expr), restart) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (w > LONG)
prefix <- paste0(prefix, "\n ") }36: else prefix <- "Error : "withRestartList(expr, restarts) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))37: if (!silent && isTRUE(getOption("show.error.messages"))) {withRestarts(with_handlers({ for (expr in tle$exprs) { cat(msg, file = outFile) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) watcher$print_value(ev$value, ev$visible, envir) } } invisible(structure(msg, class = "try-error", condition = e))}) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 38: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: evaluate::evaluate(...)FUN(X[[i]], ...)
39: 15: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(seq_len(cores), inner.do)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 16: stop_on_error = if (is.numeric(options$error)) options$error else {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (options$error && options$include) 0L
else 2L17: }, output_handler = knit_handlers(options$render, options))doTryCatch(return(expr), name, parentenv, handler)
18:
Traceback:
tryCatchOne(expr, names, parentenv, handlers[[1L]])40:
1: in_dir(input_dir(), expr)RowCumsum(valid)
19: 41:
tryCatchList(expr, classes, parentenv, handlers)in_input_dir(evaluate(code, envir = env, new_device = FALSE, 2: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 20: keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, mc.preschedule = TRUE), error = function(e) NULL) stop_on_error = if (is.numeric(options$error)) options$error else {
21: tieBreak = FALSE, verbose = verbose)SweepApply(theta, worker, numProcess) if (options$error && options$include)
0L 3: 22: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, unlist(SweepApply(theta, worker, numProcess)) else 2L
tau = tau, theta = th, exclusionRadius = exclusionRadius, }, output_handler = knit_handlers(options$render, options))) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)23: 42:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 4: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", eng_r(options)ComputeError(predictions$Observations, predictions$Predictions) E = E, showPlot = TRUE)
43:
5: block_exec(params)24:
eval(expr, envir)44:
call_block(x)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 25: embedded = embedded, validLib = validLib, noTime = noTime, 45: ignoreNan = ignoreNan, backend = backend)$predictions)eval(expr, envir)
process_group(group)
6:
FUN(X[[i]], ...)26: 46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withVisible(eval(expr, envir)) 7:
error = function(e) {27: lapply(X = S, FUN = FUN, ...)withCallingHandlers(code, error = function (e) if (progress && is.function(pb$interrupt)) rlang::entrace(e), message = function (cnd)
{ 8: pb$interrupt() watcher$capture_plot_and_output()doTryCatch(return(expr), name, parentenv, handler) if (on_message$capture) { if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) }
if (on_message$silence) { error <<- format(e) invokeRestart("muffleMessage") 9: }) }tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: }, warning = function (cnd)
{with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 10: if (getOption("warn") >= 2 || getOption("warn") < 0) {tryCatchList(expr, classes, parentenv, handlers) error = function(e) {
return() }11: watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) if (on_warning$capture) { pb$interrupt()tryCatch(expr, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) cnd <- sanitize_call(cnd) call <- conditionCall(e) error <<- format(e) watcher$push(cnd) if (!is.null(call)) { }), list(rlang_trace_top_env = knit_global())) } if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
if (on_warning$silence) {48: dcall <- deparse(call, nlines = 1L)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), invokeRestart("muffleWarning") error = function(e) { prefix <- paste("Error in", dcall, ": ") } if (progress && is.function(pb$interrupt)) }, error = function (cnd) { LONG <- 75L watcher$capture_plot_and_output() pb$interrupt() cnd <- sanitize_call(cnd) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) error <<- format(e) switch(on_error, continue = invokeRestart("eval_continue"), w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") stop = invokeRestart("eval_stop"), error = NULL) if (is.na(w)) }) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }), list(rlang_trace_top_env = knit_global())), function(loc) { type = "b") setwd(wd) if (w > LONG)
write_utf8(res, output %n% stdout()) prefix <- paste0(prefix, "\n ") paste0("\nQuitting from ", loc, if (!is.null(error)) 28: } paste0("\n", rule(), error, "\n", rule()))eval(call)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")29: 49: .Internal(seterrmessage(msg[1L]))eval(call)process_file(text, output) if (!silent && isTRUE(getOption("show.error.messages"))) {
30: 50: with_handlers({knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) for (expr in tle$exprs) {
cat(msg, file = outFile) ev <- withVisible(eval(expr, envir))51: .Internal(printDeferredWarnings()) watcher$capture_plot_and_output()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), watcher$print_value(ev$value, ev$visible, envir) } } TRUE output_dir = getwd(), ...)}, handlers)
invisible(structure(msg, class = "try-error", condition = e))31: 52: })doWithOneRestart(return(expr), restart)vweave_rmarkdown(...)
32: 12: withOneRestart(expr, restarts[[1L]])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
53: 33:
engine$weave(file, quiet = quiet, encoding = enc)13: withRestartList(expr, restarts[-nr])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
34:
doWithOneRestart(return(expr), restart)
14: 54: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
55: 36: 15: withRestartList(expr, restarts)
tryCatchOne(expr, names, parentenv, handlers[[1L]])37:
withRestarts(with_handlers({56: lapply(seq_len(cores), inner.do)tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))57: 16: tryCatch({ watcher$capture_plot_and_output()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir) }
TRUE setwd(startdir)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)17:
output <- find_vignette_product(name, by = "weave", engine = engine)38: if (!have.makefile && vignette_is_tex(output)) {doTryCatch(return(expr), name, parentenv, handler)evaluate::evaluate(...)
texi2pdf(file = output, clean = FALSE, quiet = quiet)
18: output <- find_vignette_product(name, by = "texi2pdf", 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, engine = engine)tryCatchOne(expr, names, parentenv, handlers[[1L]]) } keep_message = if (is.numeric(options$message)) TRUE else options$message, outputs <- c(outputs, output) stop_on_error = if (is.numeric(options$error)) options$error else {
}, error = function(e) {19: if (options$error && options$include) thisOK <<- FALSE 0L fails <<- c(fails, file)tryCatchList(expr, classes, parentenv, handlers) else 2L message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))20: }) }, output_handler = knit_handlers(options$render, options))
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 58: 40: mc.preschedule = TRUE), error = function(e) NULL)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
in_dir(input_dir(), expr) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWfe6EM/file834a55f9345f.rds")
21: SweepApply(theta, worker, numProcess)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, An irrecoverable exception occurred. R is aborting now ...
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 22: keep_message = if (is.numeric(options$message)) TRUE else options$message, unlist(SweepApply(theta, worker, numProcess)) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 23: 0LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", else 2L E = E, showPlot = TRUE) }, output_handler = knit_handlers(options$render, options)))
42: 24: eng_r(options)eval(expr, envir)
25: 43: block_exec(params)
eval(expr, envir)44:
call_block(x)26:
withVisible(eval(expr, envir))45:
process_group(group)27:
withCallingHandlers(code, error = function (e) 46: rlang::entrace(e), message = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { watcher$capture_plot_and_output() error = function(e) { if (on_message$capture) { watcher$push(cnd) if (progress && is.function(pb$interrupt)) pb$interrupt() } if (on_message$silence) { if (is_R_CMD_build() || is_R_CMD_check()) invokeRestart("muffleMessage") error <<- format(e) }}, warning = function (cnd) }){
if (getOption("warn") >= 2 || getOption("warn") < 0) {47: return()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) pb$interrupt() if (on_warning$capture) { if (is_R_CMD_build() || is_R_CMD_check()) cnd <- sanitize_call(cnd) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) watcher$push(cnd)
48: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (on_warning$silence) { error = function(e) { invokeRestart("muffleWarning") if (progress && is.function(pb$interrupt)) } pb$interrupt()}, error = function (cnd) if (is_R_CMD_build() || is_R_CMD_check()) { error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) cnd <- sanitize_call(cnd) write_utf8(res, output %n% stdout()) watcher$push(cnd) paste0("\nQuitting from ", loc, if (!is.null(error)) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) paste0("\n", rule(), error, "\n", rule()))})}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
28: 49: eval(call)process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)29:
eval(call)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 30: output_dir = getwd(), ...)with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))52: watcher$capture_plot_and_output()vweave_rmarkdown(...) watcher$print_value(ev$value, ev$visible, envir)
}53: TRUEengine$weave(file, quiet = quiet, encoding = enc)}, handlers)
54: 31: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])32: withOneRestart(expr, restarts[[1L]])
56: 33: withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
34: 57: doWithOneRestart(return(expr), restart)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {36: texi2pdf(file = output, clean = FALSE, quiet = quiet)withRestartList(expr, restarts) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)
} outputs <- c(outputs, output)37: }, error = function(e) {withRestarts(with_handlers({ thisOK <<- FALSE for (expr in tle$exprs) { fails <<- c(fails, file) ev <- withVisible(eval(expr, envir)) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", watcher$capture_plot_and_output() file, conditionMessage(e))) watcher$print_value(ev$value, ev$visible, envir)}) }
TRUE58: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 38: evaluate::evaluate(...) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWfe6EM/file834a55f9345f.rds")
39: An irrecoverable exception occurred. R is aborting now ...
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/RtmpWfe6EM/file834a55f9345f.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