Last updated on 2026-11-12 02:55:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.76 | 227.38 | 231.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.84 | 227.62 | 230.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.27 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | OK | ||||
| r-release-linux-x86_64 | 2.0.2 | 3.34 | 211.51 | 214.85 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 5.00 | 130.00 | 135.00 | 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 | 154.00 | 161.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-12 08:09:11.810 R[47596:71222] 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:
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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")
*** caught segfault ***
}address 0x110, cause 'invalid permissions'
}, 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/RtmpNwCgKD/file91703e034032.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)
Traceback:
20: 1: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, RowCumsum(valid) mc.preschedule = TRUE), error = function(e) NULL)
21:
SweepApply(theta, worker, numProcess) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 22: tieBreak = FALSE, verbose = verbose)
unlist(SweepApply(theta, worker, numProcess))
3: 23: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tau = tau, theta = th, exclusionRadius = exclusionRadius, E = E, showPlot = TRUE) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)24: eval(expr, envir)
4:
ComputeError(predictions$Observations, predictions$Predictions)25: eval(expr, envir)
26: 5: withVisible(eval(expr, envir))
27: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
withCallingHandlers(code, error = function (e) 7: rlang::entrace(e), message = function (cnd) lapply(X = S, FUN = FUN, ...){
watcher$capture_plot_and_output() if (on_message$capture) { 8: watcher$push(cnd)doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { } call <- conditionCall(e) if (on_message$silence) { if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) invokeRestart("muffleMessage") } call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)}, warning = function (cnd) prefix <- paste("Error in", dcall, ": "){ LONG <- 75L if (getOption("warn") >= 2 || getOption("warn") < 0) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] return() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (on_warning$capture) { type = "b") cnd <- sanitize_call(cnd) if (w > LONG) watcher$push(cnd) prefix <- paste0(prefix, "\n ") } } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") if (on_warning$silence) { .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { invokeRestart("muffleWarning") } cat(msg, file = outFile)}, error = function (cnd) .Internal(printDeferredWarnings()){ } watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) invisible(structure(msg, class = "try-error", condition = e)) watcher$push(cnd)})
switch(on_error, continue = invokeRestart("eval_continue"), 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) stop = invokeRestart("eval_stop"), error = NULL)})
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
28: 14: FUN(X[[i]], ...)eval(call)
15: 29: eval(call)lapply(seq_len(cores), inner.do)
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 30: doTryCatch(return(expr), name, parentenv, handler)with_handlers({
18: for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir))
19: watcher$capture_plot_and_output()tryCatchList(expr, classes, parentenv, handlers)
watcher$print_value(ev$value, ev$visible, envir)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } TRUE mc.preschedule = TRUE), error = function(e) NULL)}, handlers)
21: SweepApply(theta, worker, numProcess)
22: 31: unlist(SweepApply(theta, worker, numProcess))doWithOneRestart(return(expr), restart)
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 32: E = E, showPlot = TRUE)
withOneRestart(expr, restarts[[1L]])24:
eval(expr, envir)33: withRestartList(expr, restarts[-nr])
25: 34:
Traceback:
eval(expr, envir) 1: doWithOneRestart(return(expr), restart)
26:
RowCumsum(valid)
withVisible(eval(expr, envir)) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 35: tieBreak = FALSE, verbose = verbose)27:
3: withCallingHandlers(code, error = function (e) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, rlang::entrace(e), message = function (cnd) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, { ignoreNan = ignoreNan, backend = backend)
4: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output() if (on_message$capture) {ComputeError(predictions$Observations, predictions$Predictions) watcher$push(cnd)
} 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (on_message$silence) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
invokeRestart("muffleMessage") embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
} 6: }, warning = function (cnd) 36: FUN(X[[i]], ...){ if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()withRestartList(expr, restarts) 7: }lapply(X = S, FUN = FUN, ...)
watcher$capture_plot_and_output()
37: if (on_warning$capture) { 8: cnd <- sanitize_call(cnd)doTryCatch(return(expr), name, parentenv, handler) watcher$push(cnd)
} 9: withRestarts(with_handlers({ if (on_warning$silence) { invokeRestart("muffleWarning")tryCatchOne(expr, names, parentenv, handlers[[1L]]) for (expr in tle$exprs) {
}10: }, error = function (cnd) tryCatchList(expr, classes, parentenv, handlers) ev <- withVisible(eval(expr, envir))
{ watcher$capture_plot_and_output() watcher$capture_plot_and_output()11: tryCatch(expr, error = function(e) { watcher$print_value(ev$value, ev$visible, envir) cnd <- sanitize_call(cnd) call <- conditionCall(e) } watcher$push(cnd) if (!is.null(call)) { TRUE if (identical(call[[1L]], quote(doTryCatch))) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) switch(on_error, continue = invokeRestart("eval_continue"),
38: call <- sys.call(-4L)evaluate::evaluate(...) stop = invokeRestart("eval_stop"), error = NULL) dcall <- deparse(call, nlines = 1L)
39: prefix <- paste("Error in", dcall, ": ")evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, LONG <- 75L keep_message = if (is.numeric(options$message)) TRUE else options$message, sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") stop_on_error = if (is.numeric(options$error)) options$error else { if (is.na(w)) if (options$error && options$include) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 0L type = "b") else 2L }, output_handler = knit_handlers(options$render, options))
})40: if (w > LONG)
prefix <- paste0(prefix, "\n ")in_dir(input_dir(), expr)
}28: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, else prefix <- "Error : " keep_message = if (is.numeric(options$message)) TRUE else options$message,
msg <- paste0(prefix, conditionMessage(e), "\n") stop_on_error = if (is.numeric(options$error)) options$error else { .Internal(seterrmessage(msg[1L])) if (options$error && options$include) 29: eval(call)
0L if (!silent && isTRUE(getOption("show.error.messages"))) {30: else 2L }, output_handler = knit_handlers(options$render, options))) cat(msg, file = outFile)with_handlers({ for (expr in tle$exprs) { .Internal(printDeferredWarnings())
ev <- withVisible(eval(expr, envir)) } watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) invisible(structure(msg, class = "try-error", condition = e))})42:
} TRUEeng_r(options)}, handlers)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)31:
doWithOneRestart(return(expr), restart)43: 13:
block_exec(params)32:
withOneRestart(expr, restarts[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
44: 14: call_block(x)33:
withRestartList(expr, restarts[-nr])
FUN(X[[i]], ...)34: 45: doWithOneRestart(return(expr), restart)
process_group(group)15: 35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])lapply(seq_len(cores), inner.do)
46: 36:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 16: withRestartList(expr, restarts) error = function(e) {
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (progress && is.function(pb$interrupt))
pb$interrupt()37: 17: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)doTryCatch(return(expr), name, parentenv, handler) })withRestarts(with_handlers({
18: for (expr in tle$exprs) {47: tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
watcher$capture_plot_and_output() error = function(e) { watcher$print_value(ev$value, ev$visible, envir)19: } if (progress && is.function(pb$interrupt)) tryCatchList(expr, classes, parentenv, handlers)
pb$interrupt()20: if (is_R_CMD_build() || is_R_CMD_check()) TRUEtryCatch(parallel::mclapply(values, worker, mc.cores = cores, error <<- format(e)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }), list(rlang_trace_top_env = knit_global())) mc.preschedule = TRUE), error = function(e) NULL)
38: 21: 48: evaluate::evaluate(...)SweepApply(theta, worker, numProcess)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) 22: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)39: unlist(SweepApply(theta, worker, numProcess)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 23: setwd(wd) keep_message = if (is.numeric(options$message)) TRUE else options$message, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) stop_on_error = if (is.numeric(options$error)) options$error else { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", paste0("\n", rule(), error, "\n", rule())) E = E, showPlot = TRUE) if (options$error && options$include) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
0L49: else 2Lprocess_file(text, output)24: }, output_handler = knit_handlers(options$render, options))
eval(expr, envir)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)40:
25: in_dir(input_dir(), expr)51: eval(expr, envir)
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
26: 41: withVisible(eval(expr, envir)) output_dir = getwd(), ...)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
27: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 52: withCallingHandlers(code, error = function (e) keep_message = if (is.numeric(options$message)) TRUE else options$message, vweave_rmarkdown(...) stop_on_error = if (is.numeric(options$error)) options$error else {rlang::entrace(e), message = function (cnd) if (options$error && options$include)
53: 0Lengine$weave(file, quiet = quiet, encoding = enc) else 2L{
}, output_handler = knit_handlers(options$render, options)))54: watcher$capture_plot_and_output()
doTryCatch(return(expr), name, parentenv, handler) if (on_message$capture) {
watcher$push(cnd)55: 42: tryCatchOne(expr, names, parentenv, handlers[[1L]])eng_r(options)
}
43: if (on_message$silence) {block_exec(params)56:
invokeRestart("muffleMessage") }}, warning = function (cnd) tryCatchList(expr, classes, parentenv, handlers){44: if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
}call_block(x)57: tryCatch({
watcher$capture_plot_and_output() if (on_warning$capture) { engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) cnd <- sanitize_call(cnd) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {45: process_group(group) watcher$push(cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet) }
output <- find_vignette_product(name, by = "texi2pdf", 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine = engine) if (on_warning$silence) { error = function(e) { if (progress && is.function(pb$interrupt)) invokeRestart("muffleWarning") } pb$interrupt() } outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) }, error = function (cnd) }, error = function(e) {{ error <<- format(e) thisOK <<- FALSE }) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
fails <<- c(fails, file) watcher$push(cnd)47: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", switch(on_error, continue = invokeRestart("eval_continue"), with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), file, conditionMessage(e))) error = function(e) {}) stop = invokeRestart("eval_stop"), error = NULL) if (progress && is.function(pb$interrupt)) })
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpNwCgKD/file91703e034032.rds") error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))
28: 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()) eval(call) error <<- format(e)
An irrecoverable exception occurred. R is aborting now ...
29: eval(call) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
write_utf8(res, output %n% stdout())30: with_handlers({ paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
for (expr in tle$exprs) {49: process_file(text, output)
ev <- withVisible(eval(expr, envir))50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
watcher$capture_plot_and_output()51: watcher$print_value(ev$value, ev$visible, envir)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } output_dir = getwd(), ...)
TRUE52: }, handlers)vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)31: doWithOneRestart(return(expr), restart)
54:
doTryCatch(return(expr), name, parentenv, handler)32:
withOneRestart(expr, restarts[[1L]])55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: 56: withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
34:
57: tryCatch({doWithOneRestart(return(expr), restart) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)35: if (!have.makefile && vignette_is_tex(output)) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
texi2pdf(file = output, clean = FALSE, quiet = quiet)36: output <- find_vignette_product(name, by = "texi2pdf", withRestartList(expr, restarts) engine = engine) } outputs <- c(outputs, output)
}, error = function(e) {37: withRestarts(with_handlers({ for (expr in tle$exprs) { thisOK <<- FALSE ev <- withVisible(eval(expr, envir)) fails <<- c(fails, file) watcher$capture_plot_and_output() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", watcher$print_value(ev$value, ev$visible, envir) } file, conditionMessage(e))) TRUE})
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)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/RtmpNwCgKD/file91703e034032.rds")
38: An irrecoverable exception occurred. R is aborting now ...
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/RtmpNwCgKD/file91703e034032.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