Last updated on 2026-10-15 19:57:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.38 | 227.64 | 231.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.42 | 237.85 | 240.27 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 141.00 | 147.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | 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 | 137.00 | 142.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 36.00 | 38.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 158.00 | 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
2026-10-16 05:03:02.909 R[46801:69598] 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]])
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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 ") }
Traceback:
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") 1: .Internal(seterrmessage(msg[1L]))RowCumsum(valid) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
})
2: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
14: tieBreak = FALSE, verbose = verbose)FUN(X[[i]], ...)
15:
lapply(seq_len(cores), inner.do)
3: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 17: doTryCatch(return(expr), name, parentenv, handler) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: 19: ComputeError(predictions$Observations, predictions$Predictions)tryCatchList(expr, classes, parentenv, handlers)
5: 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, mc.preschedule = TRUE), error = function(e) NULL) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
21: embedded = embedded, validLib = validLib, noTime = noTime, SweepApply(theta, worker, numProcess) ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)22:
unlist(SweepApply(theta, worker, numProcess)) 7:
lapply(X = S, FUN = FUN, ...)
23: 8: doTryCatch(return(expr), name, parentenv, handler)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
9: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tryCatchOne(expr, names, parentenv, handlers[[1L]]) E = E, showPlot = TRUE)
10: 24: tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
25: 11: eval(expr, envir)tryCatch(expr, error = function(e) {
26: call <- conditionCall(e) if (!is.null(call)) {withVisible(eval(expr, envir)) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)27: dcall <- deparse(call, nlines = 1L)withCallingHandlers(code, error = function (e) prefix <- paste("Error in", dcall, ": ")rlang::entrace(e), message = function (cnd) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]{ watcher$capture_plot_and_output() if (on_message$capture) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") watcher$push(cnd) } if (on_message$silence) { if (is.na(w)) invokeRestart("muffleMessage") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b")}, warning = function (cnd) if (w > LONG) { prefix <- paste0(prefix, "\n ") if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") watcher$capture_plot_and_output() .Internal(seterrmessage(msg[1L])) if (on_warning$capture) { if (!silent && isTRUE(getOption("show.error.messages"))) { cnd <- sanitize_call(cnd) cat(msg, file = outFile) watcher$push(cnd) .Internal(printDeferredWarnings()) } } if (on_warning$silence) { invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffleWarning")}) }
}, error = function (cnd) 12: {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)13: watcher$push(cnd)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)14: })FUN(X[[i]], ...)
15: 28: lapply(seq_len(cores), inner.do)eval(call)
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)29:
eval(call)17:
doTryCatch(return(expr), name, parentenv, handler)30:
with_handlers({18: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
} TRUE19: }, handlers)tryCatchList(expr, classes, parentenv, handlers)
31: 20: doWithOneRestart(return(expr), restart)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21:
SweepApply(theta, worker, numProcess)32:
withOneRestart(expr, restarts[[1L]])
22: 33: unlist(SweepApply(theta, worker, numProcess))withRestartList(expr, restarts[-nr])
23: 34: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", doWithOneRestart(return(expr), restart) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) E = E, showPlot = TRUE)
36: withRestartList(expr, restarts)24: eval(expr, envir)
37: 25: eval(expr, envir)withRestarts(with_handlers({
for (expr in tle$exprs) {26: ev <- withVisible(eval(expr, envir))withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
} TRUE27: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) {38: watcher$capture_plot_and_output()evaluate::evaluate(...) if (on_message$capture) { watcher$push(cnd)
}39: if (on_message$silence) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleMessage") keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else {}, warning = function (cnd) { if (options$error && options$include) if (getOption("warn") >= 2 || getOption("warn") < 0) {
*** caught segfault ***
0L return() else 2L } }, output_handler = knit_handlers(options$render, options)) watcher$capture_plot_and_output()address 0x110, cause 'invalid permissions'
40: if (on_warning$capture) { cnd <- sanitize_call(cnd)in_dir(input_dir(), expr) watcher$push(cnd)
41: }in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (on_warning$silence) { invokeRestart("muffleWarning") keep_warning = if (is.numeric(options$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$error else {}, error = function (cnd) if (options$error && options$include) 0L{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) else 2L }, output_handler = knit_handlers(options$render, options))) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 42: stop = invokeRestart("eval_stop"), error = NULL)eng_r(options)})
43: 28: block_exec(params)eval(call)
44: call_block(x)
29: 45: process_group(group)eval(call)
46: 30: with_handlers({withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), for (expr in tle$exprs) { error = function(e) { ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() watcher$print_value(ev$value, ev$visible, envir) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) })
47: TRUEwith_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {}, handlers)
if (progress && is.function(pb$interrupt)) pb$interrupt()31: if (is_R_CMD_build() || is_R_CMD_check()) doWithOneRestart(return(expr), restart) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))32:
withOneRestart(expr, restarts[[1L]])48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {33: if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr]) pb$interrupt()
34: if (is_R_CMD_build() || is_R_CMD_check()) doWithOneRestart(return(expr), restart) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)35: write_utf8(res, output %n% stdout())withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
paste0("\nQuitting from ", loc, if (!is.null(error)) 36: paste0("\n", rule(), error, "\n", rule()))withRestartList(expr, restarts)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
37: withRestarts(with_handlers({
49: for (expr in tle$exprs) {process_file(text, output) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()50: watcher$print_value(ev$value, ev$visible, envir)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 38: output_dir = getwd(), ...)
evaluate::evaluate(...)
39: 52: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, vweave_rmarkdown(...) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
53: if (options$error && options$include) engine$weave(file, quiet = quiet, encoding = enc)
0L else 2L54: }, output_handler = knit_handlers(options$render, options))doTryCatch(return(expr), name, parentenv, handler)
40: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])in_dir(input_dir(), expr)
56: 41: tryCatchList(expr, classes, parentenv, handlers)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 57: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {tryCatch({ if (options$error && options$include) engine$weave(file, quiet = quiet, encoding = enc) 0L else 2L setwd(startdir) }, output_handler = knit_handlers(options$render, options))) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)42: output <- find_vignette_product(name, by = "texi2pdf", eng_r(options) engine = engine)
}43: outputs <- c(outputs, output)}, error = function(e) {block_exec(params) thisOK <<- FALSE
fails <<- c(fails, file)44: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))call_block(x)})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 45: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYPCKVY/file84b16fa507c1.rds")process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), An irrecoverable exception occurred. R is aborting now ...
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(), ...)
Traceback:
1: 52: vweave_rmarkdown(...)RowCumsum(valid)
53: engine$weave(file, quiet = quiet, encoding = enc)
2: 54: doTryCatch(return(expr), name, parentenv, handler)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
55: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatchOne(expr, names, parentenv, handlers[[1L]]) tieBreak = FALSE, verbose = verbose)
56: 3: tryCatchList(expr, classes, parentenv, handlers)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
57: tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch({ embedded = embedded, validLib = validLib, noTime = noTime, engine$weave(file, quiet = quiet, encoding = enc) ignoreNan = ignoreNan, backend = backend) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { 4: texi2pdf(file = output, clean = FALSE, quiet = quiet)ComputeError(predictions$Observations, predictions$Predictions) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine) 5: }SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, outputs <- c(outputs, output) embedded = embedded, validLib = validLib, noTime = noTime, }, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions) thisOK <<- FALSE
fails <<- c(fails, file) 6: FUN(X[[i]], ...) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
7: lapply(X = S, FUN = FUN, ...) file, conditionMessage(e)))
8: })doTryCatch(return(expr), name, parentenv, handler)
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 9: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYPCKVY/file84b16fa507c1.rds")tryCatchOne(expr, names, parentenv, handlers[[1L]])
An irrecoverable exception occurred. R is aborting now ...
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 {
Traceback:
if (options$error && options$include) 1: RowCumsum(valid) 0L
else 2L 2: }, output_handler = knit_handlers(options$render, options))FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: 40: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, in_dir(input_dir(), expr) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
41: 4: in_input_dir(evaluate(code, envir = env, new_device = FALSE, ComputeError(predictions$Observations, predictions$Predictions) 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) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 0L else 2L knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options) 6:
FUN(X[[i]], ...)43: block_exec(params)
7: lapply(X = S, FUN = FUN, ...)44:
call_block(x)
45: 8: process_group(group)doTryCatch(return(expr), name, parentenv, handler)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { 9: if (progress && is.function(pb$interrupt)) tryCatchOne(expr, names, parentenv, handlers[[1L]]) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)10: })tryCatchList(expr, classes, parentenv, handlers)
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {11: if (progress && is.function(pb$interrupt)) pb$interrupt()tryCatch(expr, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: call <- conditionCall(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (!is.null(call)) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (identical(call[[1L]], quote(doTryCatch))) error <<- format(e) call <- sys.call(-4L) }), list(rlang_trace_top_env = knit_global())), function(loc) { dcall <- deparse(call, nlines = 1L) setwd(wd) write_utf8(res, output %n% stdout()) prefix <- paste("Error in", dcall, ": ") LONG <- 75L paste0("\nQuitting from ", loc, if (!is.null(error)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") paste0("\n", rule(), error, "\n", rule())) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (w > LONG)
prefix <- paste0(prefix, "\n ")49: }process_file(text, output) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))50: if (!silent && isTRUE(getOption("show.error.messages"))) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) cat(msg, file = outFile)
.Internal(printDeferredWarnings())51: }rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), invisible(structure(msg, class = "try-error", condition = e))})
output_dir = getwd(), ...)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)52:
vweave_rmarkdown(...)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
53: 14: engine$weave(file, quiet = quiet, encoding = enc)FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)54:
doTryCatch(return(expr), name, parentenv, handler)
16: 55: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 17: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({18: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)19: tryCatchList(expr, classes, parentenv, handlers)
output <- find_vignette_product(name, by = "texi2pdf", 20: engine = engine) }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, outputs <- c(outputs, output) mc.preschedule = TRUE), error = function(e) NULL)}, error = function(e) { thisOK <<- FALSE
21: fails <<- c(fails, file)SweepApply(theta, worker, numProcess) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))22: unlist(SweepApply(theta, worker, numProcess))})
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYPCKVY/file84b16fa507c1.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpYPCKVY/file84b16fa507c1.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