Last updated on 2026-10-13 12:53:00 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 | 35.00 | 37.00 | 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 22:03:26.494 R[47792:70826] 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)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
Traceback:
1: 16: RowCumsum(valid)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
17: 3: doTryCatch(return(expr), name, parentenv, handler)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 18: embedded = embedded, validLib = validLib, noTime = noTime, tryCatchOne(expr, names, parentenv, handlers[[1L]]) ignoreNan = ignoreNan, backend = backend)
19: 4: tryCatchList(expr, classes, parentenv, handlers)
ComputeError(predictions$Observations, predictions$Predictions)20:
5: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, mc.preschedule = TRUE), error = function(e) NULL) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 21: ignoreNan = ignoreNan, backend = backend)$predictions)SweepApply(theta, worker, numProcess)
6: 22: FUN(X[[i]], ...)
unlist(SweepApply(theta, worker, numProcess))
7: 23: lapply(X = S, FUN = FUN, ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 8: doTryCatch(return(expr), name, parentenv, handler) E = E, showPlot = TRUE)
24: 9: eval(expr, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: 10: eval(expr, envir)tryCatchList(expr, classes, parentenv, handlers)
26:
*** caught segfault ***
11: address 0x110, cause 'invalid permissions'
withVisible(eval(expr, envir))tryCatch(expr, error = function(e) {
call <- conditionCall(e)27: if (!is.null(call)) {withCallingHandlers(code, error = function (e) if (identical(call[[1L]], quote(doTryCatch))) rlang::entrace(e), message = function (cnd) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L){ prefix <- paste("Error in", dcall, ": ") watcher$capture_plot_and_output() LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_message$capture) { watcher$push(cnd) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (on_message$silence) { type = "b") if (w > LONG) invokeRestart("muffleMessage") prefix <- paste0(prefix, "\n ") } }}, warning = function (cnd) else prefix <- "Error : "{ msg <- paste0(prefix, conditionMessage(e), "\n") if (getOption("warn") >= 2 || getOption("warn") < 0) { .Internal(seterrmessage(msg[1L])) return() if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) if (on_warning$capture) { } cnd <- sanitize_call(cnd) invisible(structure(msg, class = "try-error", condition = e)) watcher$push(cnd)})
12: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (on_warning$silence) {
13: invokeRestart("muffleWarning")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}14: }, error = function (cnd) FUN(X[[i]], ...)
{ watcher$capture_plot_and_output()15: lapply(seq_len(cores), inner.do) cnd <- sanitize_call(cnd)
watcher$push(cnd)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) switch(on_error, continue = invokeRestart("eval_continue"),
17: stop = invokeRestart("eval_stop"), error = NULL)doTryCatch(return(expr), name, parentenv, handler)})
18: 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)
19: 29: tryCatchList(expr, classes, parentenv, handlers)eval(call)
20: 30: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, with_handlers({ mc.preschedule = TRUE), error = function(e) NULL) for (expr in tle$exprs) {
21: SweepApply(theta, worker, numProcess) ev <- withVisible(eval(expr, envir))
22: watcher$capture_plot_and_output()unlist(SweepApply(theta, worker, numProcess))
23: watcher$print_value(ev$value, ev$visible, envir) }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", TRUE target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)}, handlers)
24:
eval(expr, envir)31:
doWithOneRestart(return(expr), restart)25: eval(expr, envir)
26:
32: withVisible(eval(expr, envir))
27: withOneRestart(expr, restarts[[1L]])withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) {33: withRestartList(expr, restarts[-nr]) watcher$capture_plot_and_output() if (on_message$capture) {
34: watcher$push(cnd) } if (on_message$silence) {doWithOneRestart(return(expr), restart) invokeRestart("muffleMessage")
}35: }, warning = function (cnd) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return() }36: watcher$capture_plot_and_output()withRestartList(expr, restarts) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)
} if (on_warning$silence) {37: withRestarts(with_handlers({ invokeRestart("muffleWarning") for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() }}, error = function (cnd) watcher$print_value(ev$value, ev$visible, envir) }{ TRUE watcher$capture_plot_and_output()}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
cnd <- sanitize_call(cnd)38: watcher$push(cnd)evaluate::evaluate(...) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)
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, 28: stop_on_error = if (is.numeric(options$error)) options$error else {eval(call) if (options$error && options$include) 0L
else 2L }, output_handler = knit_handlers(options$render, options))29:
eval(call)40:
in_dir(input_dir(), expr)30:
with_handlers({ for (expr in tle$exprs) {41: ev <- withVisible(eval(expr, envir))in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$capture_plot_and_output() keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$print_value(ev$value, ev$visible, envir) } stop_on_error = if (is.numeric(options$error)) options$error else { TRUE if (options$error && options$include) }, handlers) 0L
else 2L31: doWithOneRestart(return(expr), restart) }, output_handler = knit_handlers(options$render, options)))
32:
42:
*** caught segfault ***
withOneRestart(expr, restarts[[1L]])address 0x110, cause 'invalid permissions'
eng_r(options)33: withRestartList(expr, restarts[-nr])
43: block_exec(params)34:
doWithOneRestart(return(expr), restart)44:
call_block(x)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 36: error = function(e) {withRestartList(expr, restarts) if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)37: })withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)47: }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
error = function(e) { if (progress && is.function(pb$interrupt)) 38: evaluate::evaluate(...) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
39: error <<- format(e)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }), list(rlang_trace_top_env = knit_global())) 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) 48: 0Lxfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), else 2L error = function(e) { }, output_handler = knit_handlers(options$render, options)) if (progress && is.function(pb$interrupt))
40: pb$interrupt()in_dir(input_dir(), expr) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)41: write_utf8(res, output %n% stdout())in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, paste0("\nQuitting from ", loc, if (!is.null(error)) keep_message = if (is.numeric(options$message)) TRUE else options$message, paste0("\n", rule(), error, "\n", rule())) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 0L
else 2L49: }, output_handler = knit_handlers(options$render, options)))process_file(text, output)
50: 42: eng_r(options)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: 51: block_exec(params)
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)44:
call_block(x)52:
vweave_rmarkdown(...)45:
53: process_group(group)engine$weave(file, quiet = quiet, encoding = enc)
54: 46: doTryCatch(return(expr), name, parentenv, handler)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {55: if (progress && is.function(pb$interrupt)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
pb$interrupt()56: tryCatchList(expr, classes, parentenv, handlers) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)57: })tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)
47: 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)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { output <- find_vignette_product(name, by = "texi2pdf", if (progress && is.function(pb$interrupt)) engine = engine) pb$interrupt() } outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) { thisOK <<- FALSE error <<- format(e) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }), list(rlang_trace_top_env = knit_global())) file, conditionMessage(e)))
})48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {58: if (progress && is.function(pb$interrupt)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBxzJDK/file84f6735c7e71.rds")
pb$interrupt()An irrecoverable exception occurred. R is aborting now ...
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)))
Traceback:
}) 1:
58: RowCumsum(valid)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBxzJDK/file84f6735c7e71.rds")
An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
} 1: TRUERowCumsum(valid)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 2:
38: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, evaluate::evaluate(...) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 3: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2LSMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, }, output_handler = knit_handlers(options$render, options))
tau = tau, theta = th, exclusionRadius = exclusionRadius, 40: embedded = embedded, validLib = validLib, noTime = noTime, in_dir(input_dir(), expr) ignoreNan = ignoreNan, backend = backend)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 4: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, ComputeError(predictions$Observations, predictions$Predictions) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (options$error && options$include) embedded = embedded, validLib = validLib, noTime = noTime, 0L else 2L ignoreNan = ignoreNan, backend = backend)$predictions)
}, output_handler = knit_handlers(options$render, options))) 6:
FUN(X[[i]], ...)
42: 7: eng_r(options)lapply(X = S, FUN = FUN, ...)
43: 8: block_exec(params)doTryCatch(return(expr), name, parentenv, handler)
44: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])call_block(x)
10:
45: tryCatchList(expr, classes, parentenv, handlers)
process_group(group)11: tryCatch(expr, error = function(e) {
call <- conditionCall(e)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (!is.null(call)) { error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) if (progress && is.function(pb$interrupt)) dcall <- deparse(call, nlines = 1L) pb$interrupt() prefix <- paste("Error in", dcall, ": ") if (is_R_CMD_build() || is_R_CMD_check()) LONG <- 75L error <<- format(e) sm <- strsplit(conditionMessage(e), "\n")[[1L]] }) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 47: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), type = "b") error = function(e) { if (w > LONG) if (progress && is.function(pb$interrupt)) pb$interrupt() prefix <- paste0(prefix, "\n ") if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) else prefix <- "Error : " }), list(rlang_trace_top_env = knit_global())) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))48: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), .Internal(printDeferredWarnings()) } error = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (is_R_CMD_build() || is_R_CMD_check())
13: error <<- format(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd) write_utf8(res, output %n% stdout())14: paste0("\nQuitting from ", loc, if (!is.null(error)) FUN(X[[i]], ...) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
15: 49: lapply(seq_len(cores), inner.do)process_file(text, output)
50: 16: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 51: doTryCatch(return(expr), name, parentenv, handler)
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 18: output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: 19: vweave_rmarkdown(...)tryCatchList(expr, classes, parentenv, handlers)
53: 20: engine$weave(file, quiet = quiet, encoding = enc)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)54: doTryCatch(return(expr), name, parentenv, handler)
55: 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))56:
23: tryCatchList(expr, classes, parentenv, handlers)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 57: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tryCatch({ E = E, showPlot = TRUE) engine$weave(file, quiet = quiet, encoding = enc)
24: setwd(startdir)eval(expr, envir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {25: texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", eval(expr, envir) engine = engine)
}26: outputs <- c(outputs, output)withVisible(eval(expr, envir))}, error = function(e) {
thisOK <<- FALSE27: fails <<- c(fails, file)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", { watcher$capture_plot_and_output() file, conditionMessage(e))) if (on_message$capture) { watcher$push(cnd)}) }
if (on_message$silence) {58: invokeRestart("muffleMessage")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBxzJDK/file84f6735c7e71.rds")}, warning = function (cnd)
{ if (getOption("warn") >= 2 || getOption("warn") < 0) {An irrecoverable exception occurred. R is aborting now ...
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/RtmpBxzJDK/file84f6735c7e71.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