Last updated on 2026-11-15 00:50:19 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.68 | 225.13 | 228.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.66 | 231.27 | 233.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 174.74 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.27 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.32 | 208.12 | 212.44 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.34 | 211.51 | 214.85 | 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 | 4.00 | 131.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 43.00 | 45.00 | 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 | 156.00 | 164.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-15 07:44:56.833 R[43429:66320] 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") .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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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),
*** caught segfault ***
error = function(e) {address 0x110, cause 'invalid permissions'
if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
*** caught segfault ***
47: address 0x110, cause 'invalid permissions'
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/RtmpyUavXy/file90b75a52c6d9.rds")
An irrecoverable exception occurred. R is aborting now ...
*** 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$Predictions)
Traceback:
1: 5: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tieBreak = FALSE, verbose = verbose) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
3: embedded = embedded, validLib = validLib, noTime = noTime, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ignoreNan = ignoreNan, backend = backend)$predictions) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) 6:
FUN(X[[i]], ...) 4:
7: lapply(X = S, FUN = FUN, ...)ComputeError(predictions$Observations, predictions$Predictions)
5: 8: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, doTryCatch(return(expr), name, parentenv, handler) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: FUN(X[[i]], ...)
10: 7: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)
8: 11: doTryCatch(return(expr), name, parentenv, handler)
tryCatch(expr, error = function(e) { 9: call <- conditionCall(e) if (!is.null(call)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)10: tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L)
11: prefix <- paste("Error in", dcall, ": ")tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { LONG <- 75L if (identical(call[[1L]], quote(doTryCatch))) sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") dcall <- deparse(call, nlines = 1L) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste("Error in", dcall, ": ") LONG <- 75L type = "b") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (w > LONG) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste0(prefix, "\n ") if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") type = "b") if (w > LONG) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { prefix <- paste0(prefix, "\n ") cat(msg, file = outFile) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(printDeferredWarnings()) } .Internal(seterrmessage(msg[1L])) invisible(structure(msg, class = "try-error", condition = e)) if (!silent && isTRUE(getOption("show.error.messages"))) {}) cat(msg, file = outFile)
.Internal(printDeferredWarnings())12: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invisible(structure(msg, class = "try-error", condition = e))
})13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14:
12: FUN(X[[i]], ...)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13:
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
lapply(seq_len(cores), inner.do)14:
FUN(X[[i]], ...)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
15: lapply(seq_len(cores), inner.do)
16: 17: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
18: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
19:
19: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) mc.preschedule = TRUE), error = function(e) NULL)
21: 21: SweepApply(theta, worker, numProcess)
SweepApply(theta, worker, numProcess)
22: 22: unlist(SweepApply(theta, worker, numProcess))unlist(SweepApply(theta, worker, numProcess))
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 23: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", E = E, showPlot = TRUE) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)
24: eval(expr, envir)
24: eval(expr, envir)
25: eval(expr, envir)25:
eval(expr, envir)
26: 26: withVisible(eval(expr, envir))
withVisible(eval(expr, envir))
27: 27: withCallingHandlers(code, error = function (e) withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) rlang::entrace(e), message = function (cnd) {{ watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_message$capture) { if (on_message$capture) { watcher$push(cnd) watcher$push(cnd) } } if (on_message$silence) { if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) invokeRestart("muffleMessage"){ } if (getOption("warn") >= 2 || getOption("warn") < 0) {}, warning = function (cnd) return(){ } watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_warning$capture) { cnd <- sanitize_call(cnd) return() watcher$push(cnd) } } watcher$capture_plot_and_output() if (on_warning$silence) { if (on_warning$capture) { invokeRestart("muffleWarning") cnd <- sanitize_call(cnd) }}, error = function (cnd) { watcher$push(cnd) watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd) if (on_warning$silence) { watcher$push(cnd) invokeRestart("muffleWarning") switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) }})}, error = function (cnd) {
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)28: watcher$push(cnd)eval(call) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)29: })eval(call)
30: with_handlers({28: for (expr in tle$exprs) {eval(call) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)29: }eval(call) TRUE
30: }, handlers)with_handlers({
for (expr in tle$exprs) {31: ev <- withVisible(eval(expr, envir))doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)32: } TRUEwithOneRestart(expr, restarts[[1L]])
33: }, handlers)withRestartList(expr, restarts[-nr])
31: doWithOneRestart(return(expr), restart)34: doWithOneRestart(return(expr), restart)
32: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withOneRestart(expr, restarts[[1L]])
33:
withRestartList(expr, restarts[-nr])
36: 34: withRestartList(expr, restarts)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])37:
36: withRestartList(expr, restarts)
withRestarts(with_handlers({37: for (expr in tle$exprs) {withRestarts(with_handlers({ ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) watcher$print_value(ev$value, ev$visible, envir) } } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38:
evaluate::evaluate(...)38:
evaluate::evaluate(...)
39: 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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 { 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) if (options$error && options$include) 0L 0L else 2L }, output_handler = knit_handlers(options$render, options)) else 2L }, output_handler = knit_handlers(options$render, options))
40:
in_dir(input_dir(), expr)40:
in_dir(input_dir(), expr)
41: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
Traceback:
keep_message = if (is.numeric(options$message)) TRUE else options$message, 1: stop_on_error = if (is.numeric(options$error)) options$error else { keep_message = if (is.numeric(options$message)) TRUE else options$message, if (options$error && options$include) RowCumsum(valid) stop_on_error = if (is.numeric(options$error)) options$error else { 0L if (options$error && options$include)
else 2L 2: 0LFindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, }, output_handler = knit_handlers(options$render, options))) else 2L validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose) }, output_handler = knit_handlers(options$render, options)))
42:
42: eng_r(options) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, eng_r(options)
tau = tau, theta = th, exclusionRadius = exclusionRadius, 43: 43: block_exec(params)block_exec(params) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)44: 44:
call_block(x)call_block(x) 4:
ComputeError(predictions$Observations, predictions$Predictions)45:
process_group(group) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 45: embedded = embedded, validLib = validLib, noTime = noTime, error = function(e) {process_group(group) ignoreNan = ignoreNan, backend = backend)$predictions)
if (progress && is.function(pb$interrupt))
46: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) error = function(e) { }) 6:
if (progress && is.function(pb$interrupt)) 47: pb$interrupt()FUN(X[[i]], ...)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) 7: error <<- format(e)lapply(X = S, FUN = FUN, ...) if (progress && is.function(pb$interrupt)) pb$interrupt()
}) if (is_R_CMD_build() || is_R_CMD_check()) 8: error <<- format(e)doTryCatch(return(expr), name, parentenv, handler)
}), list(rlang_trace_top_env = knit_global()))
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 9: 48: error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) 10: pb$interrupt()tryCatchList(expr, classes, parentenv, handlers) error = function(e) { if (is_R_CMD_build() || is_R_CMD_check())
if (progress && is.function(pb$interrupt)) 11: tryCatch(expr, error = function(e) { pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) call <- conditionCall(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) if (!is.null(call)) {
}), list(rlang_trace_top_env = knit_global())), function(loc) {48: if (identical(call[[1L]], quote(doTryCatch))) setwd(wd) call <- sys.call(-4L)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), dcall <- deparse(call, nlines = 1L) write_utf8(res, output %n% stdout()) error = function(e) { prefix <- paste("Error in", dcall, ": ") paste0("\nQuitting from ", loc, if (!is.null(error)) LONG <- 75L paste0("\n", rule(), error, "\n", rule())) if (progress && is.function(pb$interrupt)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] pb$interrupt() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (is_R_CMD_build() || is_R_CMD_check())
if (is.na(w)) error <<- format(e)49: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }), list(rlang_trace_top_env = knit_global())), function(loc) { type = "b") setwd(wd)process_file(text, output) write_utf8(res, output %n% stdout())
if (w > LONG) 50: prefix <- paste0(prefix, "\n ")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) paste0("\nQuitting from ", loc, if (!is.null(error)) } paste0("\n", rule(), error, "\n", rule())) else prefix <- "Error : "
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)51:
msg <- paste0(prefix, conditionMessage(e), "\n")49: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {process_file(text, output) cat(msg, file = outFile) output_dir = getwd(), ...)
.Internal(printDeferredWarnings())
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
invisible(structure(msg, class = "try-error", condition = e))51: })52: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), vweave_rmarkdown(...)
output_dir = getwd(), ...)
12: 53: engine$weave(file, quiet = quiet, encoding = enc)52:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)54: vweave_rmarkdown(...)doTryCatch(return(expr), name, parentenv, handler)
13:
55: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))53: tryCatchOne(expr, names, parentenv, handlers[[1L]])
engine$weave(file, quiet = quiet, encoding = enc)
14: 54: 56: FUN(X[[i]], ...)
tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
15:
57: lapply(seq_len(cores), inner.do)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch({16:
engine$weave(file, quiet = quiet, encoding = enc)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) setwd(startdir)56:
17: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchList(expr, classes, parentenv, handlers) if (!have.makefile && vignette_is_tex(output)) {
doTryCatch(return(expr), name, parentenv, handler)57: tryCatch({
texi2pdf(file = output, clean = FALSE, quiet = quiet) engine$weave(file, quiet = quiet, encoding = enc)18: output <- find_vignette_product(name, by = "texi2pdf", tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine = engine) setwd(startdir) } output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { outputs <- c(outputs, output)19: }, error = function(e) { thisOK <<- FALSEtryCatchList(expr, classes, parentenv, handlers) texi2pdf(file = output, clean = FALSE, quiet = quiet)
fails <<- c(fails, file) output <- find_vignette_product(name, by = "texi2pdf", message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 20: file, conditionMessage(e)))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, engine = engine)}) } mc.preschedule = TRUE), error = function(e) NULL)
outputs <- c(outputs, output)21: 58: SweepApply(theta, worker, numProcess)}, error = function(e) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
thisOK <<- FALSE fails <<- c(fails, file)22: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyUavXy/file90b75a52c6d9.rds")unlist(SweepApply(theta, worker, numProcess)) file, conditionMessage(e)))
})An irrecoverable exception occurred. R is aborting now ...
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 58: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", E = E, showPlot = TRUE)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpyUavXy/file90b75a52c6d9.rds")24:
eval(expr, envir)An irrecoverable exception occurred. R is aborting now ...
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(), ...)
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/RtmpyUavXy/file90b75a52c6d9.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