Last updated on 2026-10-25 13:51:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.91 | 223.80 | 227.71 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.50 | 225.82 | 228.32 | 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 | 3.10 | 211.40 | 214.50 | 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 | 129.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 46.00 | 48.00 | 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
2026-10-25 18:39:31.852 R[42334:63964] 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)
Traceback:
6: 1: FUN(X[[i]], ...)RowCumsum(valid)
2: 7: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(X = S, FUN = FUN, ...) tieBreak = FALSE, verbose = verbose)
3: 8: doTryCatch(return(expr), name, parentenv, handler)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 9: embedded = embedded, validLib = validLib, noTime = noTime, tryCatchOne(expr, names, parentenv, handlers[[1L]]) ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
10: 5: tryCatchList(expr, classes, parentenv, handlers)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 11: embedded = embedded, validLib = validLib, noTime = noTime, tryCatch(expr, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions) call <- conditionCall(e)
6: if (!is.null(call)) {FUN(X[[i]], ...)
if (identical(call[[1L]], quote(doTryCatch))) 7: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")lapply(X = S, FUN = FUN, ...) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 8: doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 9: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchOne(expr, names, parentenv, handlers[[1L]]) type = "b")
if (w > LONG) 10: tryCatchList(expr, classes, parentenv, handlers) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : "11: msg <- paste0(prefix, conditionMessage(e), "\n")tryCatch(expr, error = function(e) { call <- conditionCall(e) .Internal(seterrmessage(msg[1L])) if (!is.null(call)) { if (!silent && isTRUE(getOption("show.error.messages"))) { 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)) cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(printDeferredWarnings()) type = "b") } invisible(structure(msg, class = "try-error", condition = e)) if (w > LONG) prefix <- paste0(prefix, "\n ") }}) else prefix <- "Error : "
12: msg <- paste0(prefix, conditionMessage(e), "\n")try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
14: FUN(X[[i]], ...) invisible(structure(msg, class = "try-error", condition = e))
})15:
12: lapply(seq_len(cores), inner.do)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)14:
FUN(X[[i]], ...)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])15:
lapply(seq_len(cores), inner.do)19:
tryCatchList(expr, classes, parentenv, handlers)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
17: 21: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
18: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)19:
24: tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 25: mc.preschedule = TRUE), error = function(e) NULL)eval(expr, envir)
21:
SweepApply(theta, worker, numProcess)26:
withVisible(eval(expr, envir))22:
unlist(SweepApply(theta, worker, numProcess))27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
{ watcher$capture_plot_and_output()23: if (on_message$capture) {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$push(cnd) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", } E = E, showPlot = TRUE) if (on_message$silence) {
invokeRestart("muffleMessage")24: }}, warning = function (cnd) eval(expr, envir)
{ if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)25: watcher$push(cnd)eval(expr, envir) }
if (on_warning$silence) {26: invokeRestart("muffleWarning")withVisible(eval(expr, envir))
}}, error = function (cnd) 27: {withCallingHandlers(code, error = function (e) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)rlang::entrace(e), message = function (cnd) watcher$push(cnd){ switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL) if (on_message$capture) { watcher$push(cnd)})
28: eval(call) }
if (on_message$silence) {29: invokeRestart("muffleMessage")eval(call) }}, warning = function (cnd)
30: {with_handlers({ for (expr in tle$exprs) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() } if (on_warning$capture) { TRUE}, handlers) cnd <- sanitize_call(cnd)
watcher$push(cnd)31: }doWithOneRestart(return(expr), restart) if (on_warning$silence) { invokeRestart("muffleWarning")
32: withOneRestart(expr, restarts[[1L]]) }
}, error = function (cnd) {33: watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr]) cnd <- sanitize_call(cnd)
34: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})doWithOneRestart(return(expr), restart)
28:
eval(call)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
Traceback:
29: 1: eval(call)
RowCumsum(valid)
30: 36: 2: with_handlers({withRestartList(expr, restarts) for (expr in tle$exprs) {
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 37: ev <- withVisible(eval(expr, envir)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)withRestarts(with_handlers({
Traceback:
} tieBreak = FALSE, verbose = verbose) for (expr in tle$exprs) { TRUE
1: }, handlers)RowCumsum(valid) ev <- withVisible(eval(expr, envir))
3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, watcher$capture_plot_and_output() tau = tau, theta = th, exclusionRadius = exclusionRadius, 31: watcher$print_value(ev$value, ev$visible, envir) embedded = embedded, validLib = validLib, noTime = noTime, doWithOneRestart(return(expr), restart) ignoreNan = ignoreNan, backend = backend)
2: }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
4: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ComputeError(predictions$Observations, predictions$Predictions) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)32: tieBreak = FALSE, verbose = verbose)
withOneRestart(expr, restarts[[1L]]) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 38:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, evaluate::evaluate(...) 3: 33: ignoreNan = ignoreNan, backend = backend)$predictions)
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 39: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
6: 4: withRestartList(expr, restarts[-nr])FUN(X[[i]], ...)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, ComputeError(predictions$Observations, predictions$Predictions)
7:
34: stop_on_error = if (is.numeric(options$error)) options$error else { 5: lapply(X = S, FUN = FUN, ...)doWithOneRestart(return(expr), restart)
8:
if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 35: 0L knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) ignoreNan = ignoreNan, backend = backend)$predictions) 9:
else 2L 6: 36: withRestartList(expr, restarts)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }, output_handler = knit_handlers(options$render, options))FUN(X[[i]], ...)
40: 7: 37: lapply(X = S, FUN = FUN, ...)withRestarts(with_handlers({in_dir(input_dir(), expr)
10: 8:
tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, for (expr in tle$exprs) {11: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch(expr, error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, 9: ev <- withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- conditionCall(e) stop_on_error = if (is.numeric(options$error)) options$error else { watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) if (options$error && options$include) if (!is.null(call)) { 0L }10: if (identical(call[[1L]], quote(doTryCatch))) TRUE else 2L call <- sys.call(-4L)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }, output_handler = knit_handlers(options$render, options))) dcall <- deparse(call, nlines = 1L)
tryCatchList(expr, classes, parentenv, handlers)38: prefix <- paste("Error in", dcall, ": ")
evaluate::evaluate(...)11: LONG <- 75L
42: 39: sm <- strsplit(conditionMessage(e), "\n")[[1L]]eng_r(options) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")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, tryCatch(expr, error = function(e) {43: if (is.na(w)) block_exec(params) call <- conditionCall(e) if (!is.null(call)) { stop_on_error = if (is.numeric(options$error)) options$error else { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
if (options$error && options$include) if (identical(call[[1L]], quote(doTryCatch))) 44: 0L type = "b")call_block(x) call <- sys.call(-4L) if (w > LONG) else 2L prefix <- paste0(prefix, "\n ") dcall <- deparse(call, nlines = 1L) } }, output_handler = knit_handlers(options$render, options))
else prefix <- "Error : "
prefix <- paste("Error in", dcall, ": ")45: msg <- paste0(prefix, conditionMessage(e), "\n")process_group(group)40: .Internal(seterrmessage(msg[1L])) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]in_dir(input_dir(), expr) if (!silent && isTRUE(getOption("show.error.messages"))) {46:
cat(msg, file = outFile)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error = function(e) { if (is.na(w)) .Internal(printDeferredWarnings()) if (progress && is.function(pb$interrupt)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], pb$interrupt()41: if (is_R_CMD_build() || is_R_CMD_check()) }in_input_dir(evaluate(code, envir = env, new_device = FALSE, invisible(structure(msg, class = "try-error", condition = e)) error <<- format(e) keep_warning = if (is.numeric(options$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$error else { }) type = "b") if (options$error && options$include) }) 0L
else 2L
if (w > LONG) }, output_handler = knit_handlers(options$render, options)))12:
prefix <- paste0(prefix, "\n ")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }47:
42: 13: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eng_r(options) else prefix <- "Error : "sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
error = function(e) { msg <- paste0(prefix, conditionMessage(e), "\n")43: 14: if (progress && is.function(pb$interrupt)) block_exec(params)FUN(X[[i]], ...) .Internal(seterrmessage(msg[1L]))
pb$interrupt()15:
lapply(seq_len(cores), inner.do)
16: if (is_R_CMD_build() || is_R_CMD_check()) 44: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)call_block(x) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())) if (!silent && isTRUE(getOption("show.error.messages"))) {45: 17:
doTryCatch(return(expr), name, parentenv, handler)48:
cat(msg, file = outFile)process_group(group)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), .Internal(printDeferredWarnings())18: } error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (progress && is.function(pb$interrupt))
invisible(structure(msg, class = "try-error", condition = e))46: 19: pb$interrupt()})withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) 12: tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
pb$interrupt()13: error <<- format(e)
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }), list(rlang_trace_top_env = knit_global())), function(loc) { })
14: 20: FUN(X[[i]], ...) setwd(wd)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, write_utf8(res, output %n% stdout()) mc.preschedule = TRUE), error = function(e) NULL)
paste0("\nQuitting from ", loc, if (!is.null(error))
15: paste0("\n", rule(), error, "\n", rule()))47: 21: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)lapply(seq_len(cores), inner.do)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
SweepApply(theta, worker, numProcess)
error = function(e) {16: 49: 22: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
if (progress && is.function(pb$interrupt)) process_file(text, output) pb$interrupt()17:
if (is_R_CMD_build() || is_R_CMD_check()) unlist(SweepApply(theta, worker, numProcess))doTryCatch(return(expr), name, parentenv, handler) error <<- format(e)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
}), list(rlang_trace_top_env = knit_global()))18: 23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 51: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tryCatchOne(expr, names, parentenv, handlers[[1L]])rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), E = E, showPlot = TRUE)48: output_dir = getwd(), ...)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {19: if (progress && is.function(pb$interrupt))
tryCatchList(expr, classes, parentenv, handlers) pb$interrupt()
52: 24: 20: vweave_rmarkdown(...)
if (is_R_CMD_build() || is_R_CMD_check()) eval(expr, envir)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 53:
mc.preschedule = TRUE), error = function(e) NULL)25:
engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e)21: eval(expr, envir)SweepApply(theta, worker, numProcess)
22:
}), list(rlang_trace_top_env = knit_global())), function(loc) {unlist(SweepApply(theta, worker, numProcess))26: setwd(wd)withVisible(eval(expr, envir)) write_utf8(res, output %n% stdout())
54: paste0("\nQuitting from ", loc, if (!is.null(error)) 27: paste0("\n", rule(), error, "\n", rule()))doTryCatch(return(expr), name, parentenv, handler)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withCallingHandlers(code, error = function (e) 23:
rlang::entrace(e), message = function (cnd)
{55: watcher$capture_plot_and_output()49: tryCatchOne(expr, names, parentenv, handlers[[1L]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (on_message$capture) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
56: E = E, showPlot = TRUE) watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers)
24: }eval(expr, envir)
57: if (on_message$silence) {
25: invokeRestart("muffleMessage") }tryCatch({}, warning = function (cnd) eval(expr, envir){ engine$weave(file, quiet = quiet, encoding = enc) if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) }26: if (!have.makefile && vignette_is_tex(output)) { watcher$capture_plot_and_output()withVisible(eval(expr, envir)) texi2pdf(file = output, clean = FALSE, quiet = quiet) if (on_warning$capture) {
cnd <- sanitize_call(cnd) watcher$push(cnd) }27: withCallingHandlers(code, error = function (e) output <- find_vignette_product(name, by = "texi2pdf", rlang::entrace(e), message = function (cnd) { if (on_warning$silence) { watcher$capture_plot_and_output() engine = engine) invokeRestart("muffleWarning") if (on_message$capture) { } } watcher$push(cnd)}, error = function (cnd) } if (on_message$silence) {{ invokeRestart("muffleMessage") watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) } watcher$push(cnd)process_file(text, output) outputs <- c(outputs, output)}, error = function(e) {
switch(on_error, continue = invokeRestart("eval_continue"), thisOK <<- FALSE stop = invokeRestart("eval_stop"), error = NULL) fails <<- c(fails, file)}, warning = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", { file, conditionMessage(e))) if (getOption("warn") >= 2 || getOption("warn") < 0) { return()}) }50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)58: watcher$capture_plot_and_output()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
if (on_warning$capture) {})51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), cnd <- sanitize_call(cnd)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2QhGZL/file8fa54689046c.rds") output_dir = getwd(), ...)28:
eval(call)52: watcher$push(cnd)
}vweave_rmarkdown(...)
29:
eval(call)53: An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc)30: with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))54: watcher$capture_plot_and_output()doTryCatch(return(expr), name, parentenv, handler)
55: if (on_warning$silence) { invokeRestart("muffleWarning")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
56: tryCatchList(expr, classes, parentenv, handlers)}, error = function (cnd)
{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)57: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), tryCatch({ watcher$print_value(ev$value, ev$visible, envir) } TRUE stop = invokeRestart("eval_stop"), error = NULL) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)}, handlers)})
output <- find_vignette_product(name, by = "weave", engine = engine)
31: doWithOneRestart(return(expr), restart) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)
28: output <- find_vignette_product(name, by = "texi2pdf", 32: withOneRestart(expr, restarts[[1L]]) engine = engine)eval(call)
} outputs <- c(outputs, output)29: eval(call)}, error = function(e) {
thisOK <<- FALSE30: fails <<- c(fails, file)33: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", withRestartList(expr, restarts[-nr])with_handlers({ for (expr in tle$exprs) { file, conditionMessage(e))) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()34: }) watcher$print_value(ev$value, ev$visible, envir)
doWithOneRestart(return(expr), restart)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/Rtmp2QhGZL/file8fa54689046c.rds") TRUE
}, handlers)An irrecoverable exception occurred. R is aborting now ...
31: doWithOneRestart(return(expr), restart)
35: 32: withOneRestart(expr, restarts[[1L]])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33:
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]])
36: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEwithRestartList(expr, restarts)
37: withRestarts(with_handlers({}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) for (expr in tle$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(...)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 {39: if (options$error && options$include) 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 0L else 2L }, output_handler = knit_handlers(options$render, options))
else 2L40: in_dir(input_dir(), expr) }, output_handler = knit_handlers(options$render, options))
40: 41: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 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) keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
stop_on_error = if (is.numeric(options$error)) options$error else {44: if (options$error && options$include) 0Lcall_block(x) else 2L
}, output_handler = knit_handlers(options$render, options)))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(), ...)
42: 52: eng_r(options)
vweave_rmarkdown(...)43:
block_exec(params)
44: 53: call_block(x)engine$weave(file, quiet = quiet, encoding = enc)
45: 54: process_group(group)doTryCatch(return(expr), name, parentenv, handler)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
55: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: if (is_R_CMD_build() || is_R_CMD_check()) tryCatchList(expr, classes, parentenv, handlers) error <<- format(e)
57: tryCatch({ }) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {47: texi2pdf(file = output, clean = FALSE, quiet = quiet)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) output <- find_vignette_product(name, by = "texi2pdf", write_utf8(res, output %n% stdout()) engine = engine) paste0("\nQuitting from ", loc, if (!is.null(error)) } paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) outputs <- c(outputs, output)
}, error = function(e) {49: thisOK <<- FALSEprocess_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", fails <<- c(fails, file) file, conditionMessage(e))) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})})
58: 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/Rtmp2QhGZL/file8fa54689046c.rds")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2QhGZL/file8fa54689046c.rds")
An irrecoverable exception occurred. R is aborting now ...
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