Last updated on 2026-09-27 01:53:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.19 | 226.61 | 229.80 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.48 | 233.13 | 235.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.47 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.72 | 205.17 | 208.89 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.82 | 212.42 | 215.24 | 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 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 37.00 | 39.00 | 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 | 162.00 | 170.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-27 03:45:12.747 R[43679:66643] 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), 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/RtmpHuOoLi/file9db036928909.rds")
An irrecoverable exception occurred. R is aborting now ...
*** 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) {
Traceback:
1: RowCumsum(valid) return()
} 2: watcher$capture_plot_and_output()FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (on_warning$capture) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, cnd <- sanitize_call(cnd) watcher$push(cnd) tieBreak = FALSE, verbose = verbose) }
if (on_warning$silence) { 3: invokeRestart("muffleWarning") }}, error = function (cnd) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call) tau = tau, theta = th, exclusionRadius = exclusionRadius,
29: embedded = embedded, validLib = validLib, noTime = noTime, eval(call) ignoreNan = ignoreNan, backend = backend)
30: 4: with_handlers({ComputeError(predictions$Observations, predictions$Predictions) for (expr in tle$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}, handlers) ignoreNan = ignoreNan, backend = backend)$predictions)
6: 31: FUN(X[[i]], ...)
doWithOneRestart(return(expr), restart) 7:
Traceback:
lapply(X = S, FUN = FUN, ...) 1:
RowCumsum(valid)32:
withOneRestart(expr, restarts[[1L]]) 8:
2: doTryCatch(return(expr), name, parentenv, handler)33:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 9: withRestartList(expr, restarts[-nr]) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tryCatchOne(expr, names, parentenv, handlers[[1L]]) tieBreak = FALSE, verbose = verbose)34:
doWithOneRestart(return(expr), restart)
10: 3: 35: tryCatchList(expr, classes, parentenv, handlers)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, 11:
ignoreNan = ignoreNan, backend = backend)36: tryCatch(expr, error = function(e) {
call <- conditionCall(e)withRestartList(expr, restarts) 4:
if (!is.null(call)) {37: ComputeError(predictions$Observations, predictions$Predictions) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)withRestarts(with_handlers({ dcall <- deparse(call, nlines = 1L) 5: for (expr in tle$exprs) { prefix <- paste("Error in", dcall, ": ")SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, LONG <- 75L ev <- withVisible(eval(expr, envir)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, watcher$capture_plot_and_output() embedded = embedded, validLib = validLib, noTime = noTime, watcher$print_value(ev$value, ev$visible, envir) ignoreNan = ignoreNan, backend = backend)$predictions) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
} 6: TRUE if (is.na(w)) FUN(X[[i]], ...) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) type = "b")
38: if (w > LONG) evaluate::evaluate(...) 7: prefix <- paste0(prefix, "\n ")
lapply(X = S, FUN = FUN, ...) }39:
else prefix <- "Error : " 8: doTryCatch(return(expr), name, parentenv, handler)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
msg <- paste0(prefix, conditionMessage(e), "\n") keep_message = if (is.numeric(options$message)) TRUE else options$message, .Internal(seterrmessage(msg[1L])) 9: if (!silent && isTRUE(getOption("show.error.messages"))) { stop_on_error = if (is.numeric(options$error)) options$error else { cat(msg, file = outFile)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (options$error && options$include) .Internal(printDeferredWarnings()) 0L }
else 2L10: invisible(structure(msg, class = "try-error", condition = e))tryCatchList(expr, classes, parentenv, handlers)}) }, output_handler = knit_handlers(options$render, options))
12:
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(expr, error = function(e) {
call <- conditionCall(e)13: if (!is.null(call)) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))40:
if (identical(call[[1L]], quote(doTryCatch))) in_dir(input_dir(), expr)14:
call <- sys.call(-4L)FUN(X[[i]], ...)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 15: dcall <- deparse(call, nlines = 1L)lapply(seq_len(cores), inner.do) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, prefix <- paste("Error in", dcall, ": ") stop_on_error = if (is.numeric(options$error)) options$error else {16: if (options$error && options$include) LONG <- 75L 0L sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") else 2L if (is.na(w)) }, output_handler = knit_handlers(options$render, options))) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
17: type = "b")doTryCatch(return(expr), name, parentenv, handler) if (w > LONG) 42:
prefix <- paste0(prefix, "\n ") }eng_r(options)18: else prefix <- "Error : "
tryCatchOne(expr, names, parentenv, handlers[[1L]]) msg <- paste0(prefix, conditionMessage(e), "\n")43:
.Internal(seterrmessage(msg[1L]))block_exec(params)19: tryCatchList(expr, classes, parentenv, handlers)
if (!silent && isTRUE(getOption("show.error.messages"))) {44: cat(msg, file = outFile)20: call_block(x)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, .Internal(printDeferredWarnings())
mc.preschedule = TRUE), error = function(e) NULL)45:
}process_group(group)21:
SweepApply(theta, worker, numProcess) invisible(structure(msg, class = "try-error", condition = e))
})46: 22: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {unlist(SweepApply(theta, worker, numProcess))12: if (progress && is.function(pb$interrupt))
pb$interrupt()23: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (is_R_CMD_build() || is_R_CMD_check())
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", error <<- format(e) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", })13: E = E, showPlot = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 24: 47: FUN(X[[i]], ...)eval(expr, envir)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {15: 25: if (progress && is.function(pb$interrupt)) lapply(seq_len(cores), inner.do)eval(expr, envir) pb$interrupt()
16: 26: if (is_R_CMD_build() || is_R_CMD_check()) withVisible(eval(expr, envir)) error <<- format(e)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
}), list(rlang_trace_top_env = knit_global()))27: 17:
doTryCatch(return(expr), name, parentenv, handler)48: withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 18: { error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()
if (on_message$capture) {19: watcher$push(cnd) if (progress && is.function(pb$interrupt)) tryCatchList(expr, classes, parentenv, handlers) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 20: error <<- format(e)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }), list(rlang_trace_top_env = knit_global())), function(loc) { } mc.preschedule = TRUE), error = function(e) NULL) setwd(wd)
write_utf8(res, output %n% stdout())21: paste0("\nQuitting from ", loc, if (!is.null(error)) SweepApply(theta, worker, numProcess) if (on_message$silence) { paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)22: invokeRestart("muffleMessage")
unlist(SweepApply(theta, worker, numProcess))49:
}process_file(text, output)23: }, warning = function (cnd) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", {50: if (getOption("warn") >= 2 || getOption("warn") < 0) { E = E, showPlot = TRUE) return()
}knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)24:
watcher$capture_plot_and_output()eval(expr, envir)51:
if (on_warning$capture) {25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), eval(expr, envir) cnd <- sanitize_call(cnd) output_dir = getwd(), ...)
watcher$push(cnd)52: vweave_rmarkdown(...)26:
}53: withVisible(eval(expr, envir))engine$weave(file, quiet = quiet, encoding = enc)
if (on_warning$silence) {27: invokeRestart("muffleWarning")
withCallingHandlers(code, error = function (e) 54: }doTryCatch(return(expr), name, parentenv, handler)rlang::entrace(e), message = function (cnd)
{}, error = function (cnd) 55: { watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output() if (on_message$capture) {
cnd <- sanitize_call(cnd) watcher$push(cnd)56: watcher$push(cnd) }tryCatchList(expr, classes, parentenv, handlers) switch(on_error, continue = invokeRestart("eval_continue"),
if (on_message$silence) { stop = invokeRestart("eval_stop"), error = NULL)57: invokeRestart("muffleMessage")}) }tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)}, warning = function (cnd) 28: { if (getOption("warn") >= 2 || getOption("warn") < 0) { setwd(startdir)eval(call) return() output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { }29: texi2pdf(file = output, clean = FALSE, quiet = quiet) watcher$capture_plot_and_output()eval(call) output <- find_vignette_product(name, by = "texi2pdf", if (on_warning$capture) {
cnd <- sanitize_call(cnd) engine = engine)30: }with_handlers({ watcher$push(cnd) for (expr in tle$exprs) { outputs <- c(outputs, output) ev <- withVisible(eval(expr, envir))}, error = function(e) { } thisOK <<- FALSE watcher$capture_plot_and_output() fails <<- c(fails, file) watcher$print_value(ev$value, ev$visible, envir) if (on_warning$silence) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", invokeRestart("muffleWarning") file, conditionMessage(e))) } } TRUE})}, error = function (cnd)
{58: watcher$capture_plot_and_output()}, handlers) cnd <- sanitize_call(cnd)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", watcher$push(cnd) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpHuOoLi/file9db036928909.rds")
switch(on_error, continue = invokeRestart("eval_continue"), 31:
stop = invokeRestart("eval_stop"), error = NULL)doWithOneRestart(return(expr), restart)})
An irrecoverable exception occurred. R is aborting now ...
28: 32: eval(call)withOneRestart(expr, restarts[[1L]])
29: 33: eval(call)withRestartList(expr, restarts[-nr])
30: with_handlers({34: for (expr in tle$exprs) {doWithOneRestart(return(expr), restart)
ev <- withVisible(eval(expr, envir))35: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$print_value(ev$value, ev$visible, envir)
}36: TRUE}, handlers)withRestartList(expr, restarts)
31: 37: doWithOneRestart(return(expr), restart)withRestarts(with_handlers({
32: withOneRestart(expr, restarts[[1L]]) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))33: watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr]) watcher$print_value(ev$value, ev$visible, envir)
} TRUE34: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)doWithOneRestart(return(expr), restart)
38: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])evaluate::evaluate(...)
36: 39: withRestartList(expr, restarts)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 37: stop_on_error = if (is.numeric(options$error)) options$error else {withRestarts(with_handlers({ if (options$error && options$include) for (expr in tle$exprs) { 0L ev <- withVisible(eval(expr, envir)) else 2L watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options)) watcher$print_value(ev$value, ev$visible, envir) }
TRUE40: in_dir(input_dir(), expr)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
41: 38: in_input_dir(evaluate(code, envir = env, new_device = FALSE, evaluate::evaluate(...) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 39: stop_on_error = if (is.numeric(options$error)) options$error else {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L stop_on_error = if (is.numeric(options$error)) options$error else { else 2L if (options$error && options$include) }, output_handler = knit_handlers(options$render, options))) 0L
else 2L42: }, output_handler = knit_handlers(options$render, options))eng_r(options)
43: 40: in_dir(input_dir(), expr)block_exec(params)
41: 44: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, call_block(x) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {45: if (options$error && options$include) process_group(group) 0L
else 2L46: }, output_handler = knit_handlers(options$render, options)))withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {42: if (progress && is.function(pb$interrupt)) eng_r(options) pb$interrupt()
43: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)block_exec(params) })
44: 47: call_block(x)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
if (progress && is.function(pb$interrupt)) 45: pb$interrupt()process_group(group) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)46: }), list(rlang_trace_top_env = knit_global()))
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 48: error = function(e) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) }) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {47: setwd(wd)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) error = function(e) { paste0("\n", rule(), error, "\n", rule())) if (progress && is.function(pb$interrupt)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 49: error <<- format(e)process_file(text, output) }), list(rlang_trace_top_env = knit_global()))
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 51: error = function(e) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (progress && is.function(pb$interrupt)) output_dir = getwd(), ...) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {52: setwd(wd)vweave_rmarkdown(...) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))53: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
engine$weave(file, quiet = quiet, encoding = enc)49:
process_file(text, output)54:
50: doTryCatch(return(expr), name, parentenv, handler)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
55: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tryCatchOne(expr, names, parentenv, handlers[[1L]]) output_dir = getwd(), ...)
56: tryCatchList(expr, classes, parentenv, handlers)52: vweave_rmarkdown(...)
57: 53: tryCatch({engine$weave(file, quiet = quiet, encoding = enc)
54: engine$weave(file, quiet = quiet, encoding = enc)doTryCatch(return(expr), name, parentenv, handler) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {55: texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine = engine)
}56: outputs <- c(outputs, output)}, error = function(e) {tryCatchList(expr, classes, parentenv, handlers) thisOK <<- FALSE
fails <<- c(fails, file)57: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tryCatch({ file, conditionMessage(e))) engine$weave(file, quiet = quiet, encoding = enc)})
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)58: if (!have.makefile && vignette_is_tex(output)) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", texi2pdf(file = output, clean = FALSE, quiet = quiet) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpHuOoLi/file9db036928909.rds") output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)An irrecoverable exception occurred. R is aborting now ...
} 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/RtmpHuOoLi/file9db036928909.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