Last updated on 2026-10-23 06:54:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.62 | 226.38 | 230.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.48 | 245.41 | 247.89 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 191.21 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 139.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.75 | 212.15 | 215.90 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.20 | 209.21 | 212.41 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 6.00 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 37.00 | 39.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 164.00 | 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
2026-10-23 13:50:41.245 R[42492:69179] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { 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) {
Traceback:
1: ev <- withVisible(eval(expr, envir))RowCumsum(valid) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) 2: }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, TRUE validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
3: 38: evaluate::evaluate(...)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 39: ignoreNan = ignoreNan, backend = backend)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 4: keep_message = if (is.numeric(options$message)) TRUE else options$message, ComputeError(predictions$Observations, predictions$Predictions)
stop_on_error = if (is.numeric(options$error)) options$error else { 5: if (options$error && options$include) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 0L knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, else 2L embedded = embedded, validLib = validLib, noTime = noTime, }, output_handler = knit_handlers(options$render, options)) ignoreNan = ignoreNan, backend = backend)$predictions)
40: 6: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, FUN(X[[i]], ...)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 7: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {lapply(X = S, FUN = FUN, ...) if (options$error && options$include)
0L else 2L 8: }, output_handler = knit_handlers(options$render, options)))doTryCatch(return(expr), name, parentenv, handler)
42: 9: eng_r(options)tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: 10: block_exec(params)tryCatchList(expr, classes, parentenv, handlers)
44: 11: call_block(x)tryCatch(expr, error = function(e) {
call <- conditionCall(e)45: if (!is.null(call)) {process_group(group) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)46: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), LONG <- 75L error = function(e) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (progress && is.function(pb$interrupt)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") pb$interrupt() if (is.na(w)) if (is_R_CMD_build() || is_R_CMD_check()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], error <<- format(e) type = "b") })
if (w > LONG) 47: prefix <- paste0(prefix, "\n ") }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), else prefix <- "Error : " error = function(e) { msg <- paste0(prefix, conditionMessage(e), "\n") if (progress && is.function(pb$interrupt)) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) cat(msg, file = outFile) }), list(rlang_trace_top_env = knit_global())) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))48: })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
if (progress && is.function(pb$interrupt)) 12: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
error <<- format(e)13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)14: write_utf8(res, output %n% stdout())FUN(X[[i]], ...) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)15:
lapply(seq_len(cores), inner.do)49:
16: process_file(text, output)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)17: doTryCatch(return(expr), name, parentenv, handler)
51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) output_dir = getwd(), ...)
19: 52: tryCatchList(expr, classes, parentenv, handlers)vweave_rmarkdown(...)
20: 53: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, engine$weave(file, quiet = quiet, encoding = enc) mc.preschedule = TRUE), error = function(e) NULL)
54: 21: doTryCatch(return(expr), name, parentenv, handler)
55: SweepApply(theta, worker, numProcess)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 22: tryCatchList(expr, classes, parentenv, handlers)unlist(SweepApply(theta, worker, numProcess))
57: 23: tryCatch({PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", engine$weave(file, quiet = quiet, encoding = enc) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", setwd(startdir) E = E, showPlot = TRUE) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)24: output <- find_vignette_product(name, by = "texi2pdf", eval(expr, envir) engine = engine)
}25: outputs <- c(outputs, output)eval(expr, envir)}, error = function(e) {
26: thisOK <<- FALSEwithVisible(eval(expr, envir))
fails <<- c(fails, file)27: withCallingHandlers(code, error = function (e) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", rlang::entrace(e), message = function (cnd) file, conditionMessage(e))){}) watcher$capture_plot_and_output()
if (on_message$capture) {58: watcher$push(cnd)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", } if (on_message$silence) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBCBQY5/file897d7844b3fc.rds") invokeRestart("muffleMessage") }
An irrecoverable exception occurred. R is aborting now ...
}, 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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 36: withRestartList(expr, restarts) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)37:
withRestarts(with_handlers({ 4: ComputeError(predictions$Observations, predictions$Predictions) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) 5: watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, watcher$print_value(ev$value, ev$visible, envir) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } TRUE embedded = embedded, validLib = validLib, noTime = noTime, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) ignoreNan = ignoreNan, backend = backend)$predictions)
38: 6: evaluate::evaluate(...)FUN(X[[i]], ...)
39: 7: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(X = S, FUN = FUN, ...) 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 8: else 2LdoTryCatch(return(expr), name, parentenv, handler) }, output_handler = knit_handlers(options$render, options))
9: 40: tryCatchOne(expr, names, parentenv, handlers[[1L]])in_dir(input_dir(), expr)
10:
tryCatchList(expr, classes, parentenv, handlers)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 11: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch(expr, error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, call <- conditionCall(e) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) }, output_handler = knit_handlers(options$render, options))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]42: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eng_r(options) if (is.na(w))
43: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], block_exec(params) type = "b")
if (w > LONG) 44: prefix <- paste0(prefix, "\n ")call_block(x) }
else prefix <- "Error : "45: msg <- paste0(prefix, conditionMessage(e), "\n")process_group(group) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)46: .Internal(printDeferredWarnings())withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 12: error <<- format(e)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) })
13: 47: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
14: error = function(e) {FUN(X[[i]], ...) if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 15: error <<- format(e)lapply(seq_len(cores), inner.do) }), list(rlang_trace_top_env = knit_global()))
48: 16: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) error = function(e) {
if (progress && is.function(pb$interrupt)) 17: pb$interrupt()doTryCatch(return(expr), name, parentenv, handler) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)19: write_utf8(res, output %n% stdout())tryCatchList(expr, classes, parentenv, handlers) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)20:
Traceback:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
1: 49: mc.preschedule = TRUE), error = function(e) NULL)process_file(text, output)RowCumsum(valid)
50: 2: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)21:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 51: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
SweepApply(theta, worker, numProcess) output_dir = getwd(), ...) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 22: 52: tau = tau, theta = th, exclusionRadius = exclusionRadius, vweave_rmarkdown(...) embedded = embedded, validLib = validLib, noTime = noTime, unlist(SweepApply(theta, worker, numProcess)) ignoreNan = ignoreNan, backend = backend)
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 53: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 4: engine$weave(file, quiet = quiet, encoding = enc) E = E, showPlot = TRUE)ComputeError(predictions$Observations, predictions$Predictions)
54:
5: 24: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, eval(expr, envir)doTryCatch(return(expr), name, parentenv, handler) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 55: ignoreNan = ignoreNan, backend = backend)$predictions)tryCatchOne(expr, names, parentenv, handlers[[1L]])
25:
eval(expr, envir)56: 6:
tryCatchList(expr, classes, parentenv, handlers)FUN(X[[i]], ...)26:
withVisible(eval(expr, envir))57:
tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)27: setwd(startdir) 7: output <- find_vignette_product(name, by = "weave", engine = engine)withCallingHandlers(code, error = function (e) if (!have.makefile && vignette_is_tex(output)) {rlang::entrace(e), message = function (cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet){ output <- find_vignette_product(name, by = "texi2pdf", watcher$capture_plot_and_output()lapply(X = S, FUN = FUN, ...) engine = engine)
} if (on_message$capture) { outputs <- c(outputs, output) watcher$push(cnd)}, error = function(e) { thisOK <<- FALSE } fails <<- c(fails, file) 8: if (on_message$silence) {doTryCatch(return(expr), name, parentenv, handler) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", invokeRestart("muffleMessage")
} file, conditionMessage(e))) 9: }, warning = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]])})
{
10: 58: if (getOption("warn") >= 2 || getOption("warn") < 0) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", return()tryCatchList(expr, classes, parentenv, handlers) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBCBQY5/file897d7844b3fc.rds") }
11: watcher$capture_plot_and_output()An irrecoverable exception occurred. R is aborting now ...
if (on_warning$capture) {tryCatch(expr, error = function(e) { cnd <- sanitize_call(cnd) call <- conditionCall(e) if (!is.null(call)) { watcher$push(cnd) if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) if (on_warning$silence) { invokeRestart("muffleWarning") dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ")}, error = function (cnd) LONG <- 75L{ sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cnd <- sanitize_call(cnd) if (is.na(w)) watcher$push(cnd) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") switch(on_error, continue = invokeRestart("eval_continue"), if (w > LONG) stop = invokeRestart("eval_stop"), error = NULL)}) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : "28: msg <- paste0(prefix, conditionMessage(e), "\n")eval(call) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)29: .Internal(printDeferredWarnings())eval(call) } invisible(structure(msg, class = "try-error", condition = e))})
30:
with_handlers({12: for (expr in tle$exprs) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()13: watcher$print_value(ev$value, ev$visible, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
14: TRUEFUN(X[[i]], ...)}, handlers)
15: 31: lapply(seq_len(cores), inner.do)doWithOneRestart(return(expr), restart)
16: 32: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withOneRestart(expr, restarts[[1L]])
17: 33: doTryCatch(return(expr), name, parentenv, handler)withRestartList(expr, restarts[-nr])
18: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])19:
tryCatchList(expr, classes, parentenv, handlers)36:
withRestartList(expr, restarts)
20: 37: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, withRestarts(with_handlers({ mc.preschedule = TRUE), error = function(e) NULL) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()21: watcher$print_value(ev$value, ev$visible, envir)SweepApply(theta, worker, numProcess) } TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)22:
unlist(SweepApply(theta, worker, numProcess))38:
23: evaluate::evaluate(...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
39: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, E = E, showPlot = TRUE)
24: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {eval(expr, envir) if (options$error && options$include)
0L25: else 2Leval(expr, envir) }, output_handler = knit_handlers(options$render, options))
26: 40: withVisible(eval(expr, envir))
in_dir(input_dir(), expr)27:
41: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { if (on_message$capture) { if (options$error && options$include) watcher$push(cnd) 0L } else 2L if (on_message$silence) { }, output_handler = knit_handlers(options$render, options))) invokeRestart("muffleMessage")
}}, warning = function (cnd) 42: {eng_r(options) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()43: block_exec(params) }
watcher$capture_plot_and_output()44: if (on_warning$capture) {call_block(x) cnd <- sanitize_call(cnd) watcher$push(cnd)
45: }process_group(group)
if (on_warning$silence) {46: invokeRestart("muffleWarning") }withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function (cnd) error = function(e) {{ if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() cnd <- sanitize_call(cnd) if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) error <<- format(e) switch(on_error, continue = invokeRestart("eval_continue"), }) stop = invokeRestart("eval_stop"), error = NULL)
})47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 28: error = function(e) {eval(call) if (progress && is.function(pb$interrupt))
pb$interrupt()29: if (is_R_CMD_build() || is_R_CMD_check()) eval(call)
error <<- format(e) }), list(rlang_trace_top_env = knit_global()))30:
with_handlers({48: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() error = function(e) { watcher$print_value(ev$value, ev$visible, envir) if (progress && is.function(pb$interrupt)) } pb$interrupt() TRUE}, handlers) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)31: }), list(rlang_trace_top_env = knit_global())), function(loc) {doWithOneRestart(return(expr), restart) setwd(wd)
write_utf8(res, output %n% stdout())32: paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))withOneRestart(expr, restarts[[1L]])}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49:
process_file(text, output)33:
50: withRestartList(expr, restarts[-nr])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: 51: doWithOneRestart(return(expr), restart)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)35:
52: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])vweave_rmarkdown(...)
36: 53: withRestartList(expr, restarts)engine$weave(file, quiet = quiet, encoding = enc)
37: withRestarts(with_handlers({
for (expr in tle$exprs) {54: ev <- withVisible(eval(expr, envir))doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
55: watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) } TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)56:
tryCatchList(expr, classes, parentenv, handlers)38:
evaluate::evaluate(...)57: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, setwd(startdir) 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) output <- find_vignette_product(name, by = "weave", engine = engine) 0L if (!have.makefile && vignette_is_tex(output)) { else 2L texi2pdf(file = output, clean = FALSE, quiet = quiet) }, output_handler = knit_handlers(options$render, options)) output <- find_vignette_product(name, by = "texi2pdf",
40: engine = engine)in_dir(input_dir(), expr) }
outputs <- c(outputs, output)41: }, error = function(e) { thisOK <<- FALSEin_input_dir(evaluate(code, envir = env, new_device = FALSE, fails <<- c(fails, file) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { file, conditionMessage(e))) if (options$error && options$include) }) 0L
else 2L58: }, output_handler = knit_handlers(options$render, options)))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpBCBQY5/file897d7844b3fc.rds")42: eng_r(options)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpBCBQY5/file897d7844b3fc.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