Last updated on 2026-10-09 09:55:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 2.91 | 225.24 | 228.15 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.42 | 229.06 | 231.48 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | 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 | 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 | 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 | 163.00 | 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
2026-10-09 17:34:20.527 R[46029:68991] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
Traceback:
1: 1: RowCumsum(valid)RowCumsum(valid)
2: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 3: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ignoreNan = ignoreNan, backend = backend) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 4: ignoreNan = ignoreNan, backend = backend)ComputeError(predictions$Observations, predictions$Predictions)
5: 4: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, ComputeError(predictions$Observations, predictions$Predictions) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 5: ignoreNan = ignoreNan, backend = backend)$predictions)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 6: embedded = embedded, validLib = validLib, noTime = noTime, FUN(X[[i]], ...) ignoreNan = ignoreNan, backend = backend)$predictions)
6:
FUN(X[[i]], ...)
7: 7: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
8: 8: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
9: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
*** caught segfault ***
tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: address 0x110, cause 'invalid permissions'
tryCatchList(expr, classes, parentenv, handlers)10:
tryCatchList(expr, classes, parentenv, handlers)11:
tryCatch(expr, error = function(e) { call <- conditionCall(e)11: if (!is.null(call)) {tryCatch(expr, error = function(e) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) call <- conditionCall(e) dcall <- deparse(call, nlines = 1L) if (!is.null(call)) { prefix <- paste("Error in", dcall, ": ") if (identical(call[[1L]], quote(doTryCatch))) LONG <- 75L call <- sys.call(-4L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] dcall <- deparse(call, nlines = 1L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste("Error in", dcall, ": ") if (is.na(w)) LONG <- 75L w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (w > LONG) prefix <- paste0(prefix, "\n ") if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], else prefix <- "Error : " type = "b") msg <- paste0(prefix, conditionMessage(e), "\n") if (w > LONG) .Internal(seterrmessage(msg[1L])) prefix <- paste0(prefix, "\n ") if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) .Internal(printDeferredWarnings()) else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") invisible(structure(msg, class = "try-error", condition = e)) .Internal(seterrmessage(msg[1L]))}) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) .Internal(printDeferredWarnings())12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
invisible(structure(msg, class = "try-error", condition = e))13: })sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: 14: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)FUN(X[[i]], ...)
13: 15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))lapply(seq_len(cores), inner.do)
16: 14: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)FUN(X[[i]], ...)
17:
doTryCatch(return(expr), name, parentenv, handler)15:
lapply(seq_len(cores), inner.do)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
19: 17: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
20: 18: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatchOne(expr, names, parentenv, handlers[[1L]])
mc.preschedule = TRUE), error = function(e) NULL)19:
tryCatchList(expr, classes, parentenv, handlers)21:
SweepApply(theta, worker, numProcess)20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 22: mc.preschedule = TRUE), error = function(e) NULL)unlist(SweepApply(theta, worker, numProcess))
23: 21: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", SweepApply(theta, worker, numProcess) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)22:
unlist(SweepApply(theta, worker, numProcess))
24: 23: eval(expr, envir)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)25:
eval(expr, envir)24:
eval(expr, envir)26:
25: withVisible(eval(expr, envir))eval(expr, envir)
27: 26: withCallingHandlers(code, error = function (e) withVisible(eval(expr, envir))rlang::entrace(e), message = function (cnd)
27: {withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) watcher$capture_plot_and_output(){ if (on_message$capture) { watcher$capture_plot_and_output() watcher$push(cnd) if (on_message$capture) { } watcher$push(cnd) if (on_message$silence) { } invokeRestart("muffleMessage") if (on_message$silence) { } invokeRestart("muffleMessage")}, warning = function (cnd) }{}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() return() } } watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) if (on_warning$capture) { watcher$push(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) } } if (on_warning$silence) { if (on_warning$silence) { invokeRestart("muffleWarning") invokeRestart("muffleWarning") } }}, error = function (cnd) }, error = function (cnd) {{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$capture_plot_and_output() switch(on_error, continue = invokeRestart("eval_continue"), cnd <- sanitize_call(cnd) stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd)}) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)28: })eval(call)
28: 29: eval(call)eval(call)
29: 30: eval(call)with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))30: watcher$capture_plot_and_output()with_handlers({ watcher$print_value(ev$value, ev$visible, envir) for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir)) TRUE}, handlers) watcher$capture_plot_and_output()
31: watcher$print_value(ev$value, ev$visible, envir)doWithOneRestart(return(expr), restart) }
TRUE32: }, handlers)withOneRestart(expr, restarts[[1L]])
31: 33: doWithOneRestart(return(expr), restart)withRestartList(expr, restarts[-nr])
32: 34: doWithOneRestart(return(expr), restart)withOneRestart(expr, restarts[[1L]])
35: 33: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withRestartList(expr, restarts[-nr])
36: 34: withRestartList(expr, restarts)doWithOneRestart(return(expr), restart)
37: 35: withRestarts(with_handlers({withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))36: watcher$capture_plot_and_output()withRestartList(expr, restarts) watcher$print_value(ev$value, ev$visible, envir)
}37: TRUEwithRestarts(with_handlers({}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))38: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)evaluate::evaluate(...)
}39: TRUEevaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {38: if (options$error && options$include) evaluate::evaluate(...) 0L
else 2L39: }, output_handler = knit_handlers(options$render, options))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 40: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) in_dir(input_dir(), expr) 0L
else 2L41: }, output_handler = knit_handlers(options$render, options))in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 40: keep_message = if (is.numeric(options$message)) TRUE else options$message, in_dir(input_dir(), expr) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 41: 0Lin_input_dir(evaluate(code, envir = env, new_device = FALSE, else 2L keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, output_handler = knit_handlers(options$render, options))) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 42: 0Leng_r(options) else 2L
}, output_handler = knit_handlers(options$render, options)))43:
block_exec(params)
42: 44: call_block(x)
eng_r(options)45:
process_group(group)43:
block_exec(params)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 44: error = function(e) { if (progress && is.function(pb$interrupt)) call_block(x) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 45: error <<- format(e)process_group(group) })
46: 47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) })
48: 47: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { 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()) }), list(rlang_trace_top_env = knit_global())), function(loc) { error <<- format(e) setwd(wd) }), list(rlang_trace_top_env = knit_global())) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))48: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {49: if (progress && is.function(pb$interrupt)) process_file(text, output) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 50: error <<- format(e)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
}), list(rlang_trace_top_env = knit_global())), function(loc) {51: setwd(wd)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) write_utf8(res, output %n% stdout())
52: paste0("\nQuitting from ", loc, if (!is.null(error)) vweave_rmarkdown(...) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)53:
engine$weave(file, quiet = quiet, encoding = enc)49:
process_file(text, output)54:
doTryCatch(return(expr), name, parentenv, handler)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
56: 52: tryCatchList(expr, classes, parentenv, handlers)vweave_rmarkdown(...)
57: 53: tryCatch({engine$weave(file, quiet = quiet, encoding = enc) engine$weave(file, quiet = quiet, encoding = enc)
*** caught segfault ***
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)address 0x110, cause 'invalid permissions'
if (!have.makefile && vignette_is_tex(output)) {54: texi2pdf(file = output, clean = FALSE, quiet = quiet)doTryCatch(return(expr), name, parentenv, handler) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)
}55: outputs <- c(outputs, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function(e) {
thisOK <<- FALSE56: fails <<- c(fails, file)tryCatchList(expr, classes, parentenv, handlers) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))57: })
tryCatch({58: engine$weave(file, quiet = quiet, encoding = enc)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", setwd(startdir) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpaG9LlZ/file8bd3179bb08d.rds") output <- find_vignette_product(name, by = "weave", engine = engine)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpaG9LlZ/file8bd3179bb08d.rds")
An irrecoverable exception occurred. R is aborting now ...
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) }
Traceback:
1: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)RowCumsum(valid)
2: 38: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, evaluate::evaluate(...) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)39:
3: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, keep_message = if (is.numeric(options$message)) TRUE else options$message, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend)
4: if (options$error && options$include) ComputeError(predictions$Observations, predictions$Predictions) 0L else 2L
}, output_handler = knit_handlers(options$render, options)) 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)$predictions)
6: 40: FUN(X[[i]], ...)in_dir(input_dir(), expr)
7:
lapply(X = S, FUN = FUN, ...)
41: 8: in_input_dir(evaluate(code, envir = env, new_device = FALSE, doTryCatch(return(expr), name, parentenv, handler) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 9: stop_on_error = if (is.numeric(options$error)) options$error else {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (options$error && options$include) 0L
else 2L10: }, output_handler = knit_handlers(options$render, options)))tryCatchList(expr, classes, parentenv, handlers)
42: 11: eng_r(options)tryCatch(expr, error = function(e) {
call <- conditionCall(e)43: block_exec(params) if (!is.null(call)) {
44: if (identical(call[[1L]], quote(doTryCatch))) call_block(x) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)45: prefix <- paste("Error in", dcall, ": ") LONG <- 75Lprocess_group(group) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")46: if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), type = "b") error = function(e) { if (w > LONG) if (progress && is.function(pb$interrupt)) prefix <- paste0(prefix, "\n ") } pb$interrupt() else prefix <- "Error : " if (is_R_CMD_build() || is_R_CMD_check()) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) error <<- format(e) if (!silent && isTRUE(getOption("show.error.messages"))) { }) cat(msg, file = outFile)
.Internal(printDeferredWarnings())47: }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), invisible(structure(msg, class = "try-error", condition = e)) error = function(e) {}) if (progress && is.function(pb$interrupt))
pb$interrupt()12: if (is_R_CMD_build() || is_R_CMD_check()) try(lapply(X = S, FUN = FUN, ...), silent = TRUE) error <<- format(e)
13: }), list(rlang_trace_top_env = knit_global()))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
48: 14: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), FUN(X[[i]], ...) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()15: if (is_R_CMD_build() || is_R_CMD_check()) lapply(seq_len(cores), inner.do) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)16: write_utf8(res, output %n% stdout())parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))17: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)doTryCatch(return(expr), name, parentenv, handler)
49: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])process_file(text, output)
19: 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)tryCatchList(expr, classes, parentenv, handlers)
51: 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tryCatch(parallel::mclapply(values, worker, mc.cores = cores, output_dir = getwd(), ...) mc.preschedule = TRUE), error = function(e) NULL)
52:
21: vweave_rmarkdown(...)SweepApply(theta, worker, numProcess)
53: engine$weave(file, quiet = quiet, encoding = enc)22:
54: unlist(SweepApply(theta, worker, numProcess))doTryCatch(return(expr), name, parentenv, handler)
23: 55: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", tryCatchOne(expr, names, parentenv, handlers[[1L]]) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)56:
tryCatchList(expr, classes, parentenv, handlers)24:
eval(expr, envir)57:
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)25: if (!have.makefile && vignette_is_tex(output)) {eval(expr, envir) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", engine = engine)26: }withVisible(eval(expr, envir)) outputs <- c(outputs, output)
}, error = function(e) {27: thisOK <<- FALSEwithCallingHandlers(code, error = function (e) fails <<- c(fails, file)rlang::entrace(e), message = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", { file, conditionMessage(e)))})
watcher$capture_plot_and_output()58: if (on_message$capture) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", watcher$push(cnd) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpaG9LlZ/file8bd3179bb08d.rds") }
if (on_message$silence) {An irrecoverable exception occurred. R is aborting now ...
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/RtmpaG9LlZ/file8bd3179bb08d.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