Last updated on 2026-10-28 01:58:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.97 | 226.48 | 230.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.87 | 219.11 | 221.98 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | 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 | 8.00 | 132.00 | 140.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 48.00 | 50.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 161.00 | 169.00 | 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
2026-10-27 21:45:00.512 R[41137:62723] 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:
Traceback:
RowCumsum(valid) 1:
RowCumsum(valid) 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
2: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tau = tau, theta = th, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)
3: 4: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ComputeError(predictions$Observations, predictions$Predictions) embedded = embedded, validLib = validLib, noTime = noTime,
5: ignoreNan = ignoreNan, backend = backend)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 4: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ComputeError(predictions$Observations, predictions$Predictions)
embedded = embedded, validLib = validLib, noTime = noTime, 5: ignoreNan = ignoreNan, backend = backend)$predictions)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 6: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
FUN(X[[i]], ...) 6:
FUN(X[[i]], ...) 7:
lapply(X = S, FUN = FUN, ...) 7:
lapply(X = S, FUN = FUN, ...) 8:
8: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
9: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 10: tryCatchList(expr, classes, parentenv, handlers)
tryCatchList(expr, classes, parentenv, handlers)11:
tryCatch(expr, error = function(e) {11: call <- conditionCall(e)tryCatch(expr, error = function(e) { if (!is.null(call)) { call <- conditionCall(e) if (identical(call[[1L]], quote(doTryCatch))) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") LONG <- 75L if (is.na(w)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (is.na(w)) type = "b") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (w > LONG) type = "b") prefix <- paste0(prefix, "\n ") if (w > LONG) prefix <- paste0(prefix, "\n ") } } else prefix <- "Error : " else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(printDeferredWarnings()) cat(msg, file = outFile) } .Internal(printDeferredWarnings()) invisible(structure(msg, class = "try-error", condition = e))}) }
invisible(structure(msg, class = "try-error", condition = e))12: })
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
14: FUN(X[[i]], ...)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
15: 14: lapply(seq_len(cores), inner.do)FUN(X[[i]], ...)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)15:
lapply(seq_len(cores), inner.do)17:
16: doTryCatch(return(expr), name, parentenv, handler)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
Traceback:
18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 1:
17: RowCumsum(valid)19: doTryCatch(return(expr), name, parentenv, handler)
tryCatchList(expr, classes, parentenv, handlers) 2:
18: 20: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
mc.preschedule = TRUE), error = function(e) NULL) tieBreak = FALSE, verbose = verbose)
21: 19: SweepApply(theta, worker, numProcess)tryCatchList(expr, classes, parentenv, handlers) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 22: tau = tau, theta = th, exclusionRadius = exclusionRadius, unlist(SweepApply(theta, worker, numProcess)) embedded = embedded, validLib = validLib, noTime = noTime, 20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, ignoreNan = ignoreNan, backend = backend)23: mc.preschedule = TRUE), error = function(e) NULL)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 4: target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)ComputeError(predictions$Observations, predictions$Predictions)21:
SweepApply(theta, worker, numProcess) 5: 24:
eval(expr, envir)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 22:
unlist(SweepApply(theta, worker, numProcess))25:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, eval(expr, envir)23: embedded = embedded, validLib = validLib, noTime = noTime,
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 26: ignoreNan = ignoreNan, backend = backend)$predictions) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
withVisible(eval(expr, envir)) E = E, showPlot = TRUE)
6: 27: FUN(X[[i]], ...)
withCallingHandlers(code, error = function (e)
24: rlang::entrace(e), message = function (cnd) 7: eval(expr, envir){ watcher$capture_plot_and_output()lapply(X = S, FUN = FUN, ...) if (on_message$capture) {
watcher$push(cnd)25:
eval(expr, envir) }
8: doTryCatch(return(expr), name, parentenv, handler)26:
if (on_message$silence) {withVisible(eval(expr, envir))
9: 27: invokeRestart("muffleMessage")withCallingHandlers(code, error = function (e) tryCatchOne(expr, names, parentenv, handlers[[1L]])rlang::entrace(e), message = function (cnd) }}, warning = function (cnd)
{{10: watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) {tryCatchList(expr, classes, parentenv, handlers) if (on_message$capture) { return()
watcher$push(cnd)11: } } watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { if (on_message$silence) { if (on_warning$capture) { call <- conditionCall(e) invokeRestart("muffleMessage")
Traceback:
} cnd <- sanitize_call(cnd) 1: RowCumsum(valid) if (!is.null(call)) {}, warning = function (cnd) { if (identical(call[[1L]], quote(doTryCatch))) watcher$push(cnd)
} 2: call <- sys.call(-4L) if (getOption("warn") >= 2 || getOption("warn") < 0) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (on_warning$silence) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, return() dcall <- deparse(call, nlines = 1L) } invokeRestart("muffleWarning") watcher$capture_plot_and_output() tieBreak = FALSE, verbose = verbose) prefix <- paste("Error in", dcall, ": ") if (on_warning$capture) { } LONG <- 75L cnd <- sanitize_call(cnd)}, error = function (cnd) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
watcher$push(cnd){ 3: } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, watcher$capture_plot_and_output() tau = tau, theta = th, exclusionRadius = exclusionRadius, cnd <- sanitize_call(cnd) if (is.na(w)) if (on_warning$silence) { embedded = embedded, validLib = validLib, noTime = noTime, watcher$push(cnd) invokeRestart("muffleWarning") } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ignoreNan = ignoreNan, backend = backend)}, error = function (cnd) type = "b") switch(on_error, continue = invokeRestart("eval_continue"), { if (w > LONG) stop = invokeRestart("eval_stop"), error = NULL) watcher$capture_plot_and_output()
prefix <- paste0(prefix, "\n ") cnd <- sanitize_call(cnd) } watcher$push(cnd)}) switch(on_error, continue = invokeRestart("eval_continue"), 4: else prefix <- "Error : "
ComputeError(predictions$Observations, predictions$Predictions) msg <- paste0(prefix, conditionMessage(e), "\n")28:
eval(call)
stop = invokeRestart("eval_stop"), error = NULL) .Internal(seterrmessage(msg[1L])) 5: })29:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, eval(call)28: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, if (!silent && isTRUE(getOption("show.error.messages"))) { ignoreNan = ignoreNan, backend = backend)$predictions)eval(call)
6: cat(msg, file = outFile)30: FUN(X[[i]], ...) .Internal(printDeferredWarnings())with_handlers({
}
invisible(structure(msg, class = "try-error", condition = e)) 7: lapply(X = S, FUN = FUN, ...)29: for (expr in tle$exprs) {}) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()eval(call)
watcher$print_value(ev$value, ev$visible, envir) 8: 12: doTryCatch(return(expr), name, parentenv, handler)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
30:
}with_handlers({ TRUE 9: 13: for (expr in tle$exprs) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir))}, handlers) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
TRUE
10: 31: 14: doWithOneRestart(return(expr), restart)FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
32: }, handlers)withOneRestart(expr, restarts[[1L]])
15: 33:
withRestartList(expr, restarts[-nr])lapply(seq_len(cores), inner.do)11: 31:
tryCatch(expr, error = function(e) {34: call <- conditionCall(e)doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
16: 32: 35: if (!is.null(call)) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withOneRestart(expr, restarts[[1L]])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
36: dcall <- deparse(call, nlines = 1L)
17: prefix <- paste("Error in", dcall, ": ")33: doTryCatch(return(expr), name, parentenv, handler)withRestartList(expr, restarts[-nr])withRestartList(expr, restarts) LONG <- 75L
18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])34: sm <- strsplit(conditionMessage(e), "\n")[[1L]]
doWithOneRestart(return(expr), restart)37: 19: tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
withRestarts(with_handlers({ if (is.na(w))
35: 20: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], for (expr in tle$exprs) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) ev <- withVisible(eval(expr, envir)) type = "b")
if (w > LONG) watcher$capture_plot_and_output()36: watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts) mc.preschedule = TRUE), error = function(e) NULL) prefix <- paste0(prefix, "\n ") }
} else prefix <- "Error : "21: TRUESweepApply(theta, worker, numProcess)37: msg <- paste0(prefix, conditionMessage(e), "\n")withRestarts(with_handlers({
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) for (expr in tle$exprs) {22: .Internal(seterrmessage(msg[1L])) ev <- withVisible(eval(expr, envir))
if (!silent && isTRUE(getOption("show.error.messages"))) {38: unlist(SweepApply(theta, worker, numProcess)) cat(msg, file = outFile) watcher$capture_plot_and_output() .Internal(printDeferredWarnings())
evaluate::evaluate(...) watcher$print_value(ev$value, ev$visible, envir)
} TRUE }39: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)23: invisible(structure(msg, class = "try-error", condition = e))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
}) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", keep_message = if (is.numeric(options$message)) TRUE else options$message, E = E, showPlot = TRUE)38:
stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...)24:
if (options$error && options$include) 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 0L12: else 2Leval(expr, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
}, output_handler = knit_handlers(options$render, options))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)25:
if (options$error && options$include)
40: eval(expr, envir) 0L13: in_dir(input_dir(), expr)
else 2LsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }, output_handler = knit_handlers(options$render, options))26:
41: withVisible(eval(expr, envir))40: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 14:
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, in_dir(input_dir(), expr) keep_message = if (is.numeric(options$message)) TRUE else options$message, FUN(X[[i]], ...) stop_on_error = if (is.numeric(options$error)) options$error else {27:
if (options$error && options$include) 15: withCallingHandlers(code, error = function (e)
0Lrlang::entrace(e), message = function (cnd) else 2Llapply(seq_len(cores), inner.do)41: }, output_handler = knit_handlers(options$render, options)))
{
watcher$capture_plot_and_output()16: 42: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)eng_r(options) if (on_message$capture) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$push(cnd)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }43: keep_message = if (is.numeric(options$message)) TRUE else options$message,
if (on_message$silence) { stop_on_error = if (is.numeric(options$error)) options$error else {block_exec(params) invokeRestart("muffleMessage") if (options$error && options$include) 0L17:
else 2L }44: }, output_handler = knit_handlers(options$render, options)))}, warning = function (cnd)
{42: doTryCatch(return(expr), name, parentenv, handler)call_block(x) if (getOption("warn") >= 2 || getOption("warn") < 0) {
eng_r(options)
return()43: 18:
}tryCatchOne(expr, names, parentenv, handlers[[1L]])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) {19: invokeRestart("muffleWarning") }tryCatchList(expr, classes, parentenv, handlers)45: }, error = function (cnd)
process_group(group)46:
{20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 46: watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, error = function(e) { mc.preschedule = TRUE), error = function(e) NULL) cnd <- sanitize_call(cnd) if (progress && is.function(pb$interrupt)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
pb$interrupt() error = function(e) { watcher$push(cnd)21: if (progress && is.function(pb$interrupt)) switch(on_error, continue = invokeRestart("eval_continue"), SweepApply(theta, worker, numProcess) if (is_R_CMD_build() || is_R_CMD_check()) stop = invokeRestart("eval_stop"), error = NULL)
error <<- format(e)})22: pb$interrupt() })unlist(SweepApply(theta, worker, numProcess))
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) 28: error = function(e) {eval(call) error <<- format(e)23:
if (progress && is.function(pb$interrupt)) }) pb$interrupt()29:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 47: if (is_R_CMD_build() || is_R_CMD_check()) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), target = "Thrips_imaginis", lib = "1 73", pred = "1 73", eval(call) error <<- format(e) error = function(e) {
}), list(rlang_trace_top_env = knit_global())) E = E, showPlot = TRUE) if (progress && is.function(pb$interrupt))
pb$interrupt()30:
if (is_R_CMD_build() || is_R_CMD_check()) 24: 48: with_handlers({ error <<- format(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(expr, envir) error = function(e) { }), list(rlang_trace_top_env = knit_global())) for (expr in tle$exprs) {
if (progress && is.function(pb$interrupt)) ev <- withVisible(eval(expr, envir))48: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) pb$interrupt() }25: TRUExfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) {}, handlers) if (progress && is.function(pb$interrupt)) eval(expr, envir)
pb$interrupt()31:
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)doWithOneRestart(return(expr), restart) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {
}), list(rlang_trace_top_env = knit_global())), function(loc) {32: setwd(wd)26: write_utf8(res, output %n% stdout())withVisible(eval(expr, envir)) setwd(wd) paste0("\nQuitting from ", loc, if (!is.null(error)) withOneRestart(expr, restarts[[1L]]) write_utf8(res, output %n% stdout())
paste0("\n", rule(), error, "\n", rule()))
paste0("\nQuitting from ", loc, if (!is.null(error)) 33: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) paste0("\n", rule(), error, "\n", rule()))withRestartList(expr, restarts[-nr])
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
27:
34: 49: 49: doWithOneRestart(return(expr), restart)process_file(text, output)process_file(text, output)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 50: 35: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)50: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]){
watcher$capture_plot_and_output()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)36: 51: if (on_message$capture) {
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), watcher$push(cnd) output_dir = getwd(), ...)withRestartList(expr, restarts)
}51: if (on_message$silence) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), invokeRestart("muffleMessage")52:
output_dir = getwd(), ...) }
52: vweave_rmarkdown(...)37: }, warning = function (cnd) withRestarts(with_handlers({
{vweave_rmarkdown(...) for (expr in tle$exprs) {53: if (getOption("warn") >= 2 || getOption("warn") < 0) {engine$weave(file, quiet = quiet, encoding = enc) ev <- withVisible(eval(expr, envir)) return() watcher$capture_plot_and_output() }
54: watcher$print_value(ev$value, ev$visible, envir)53: watcher$capture_plot_and_output() }engine$weave(file, quiet = quiet, encoding = enc)doTryCatch(return(expr), name, parentenv, handler) TRUE if (on_warning$capture) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: cnd <- sanitize_call(cnd)evaluate::evaluate(...)55: watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }54:
doTryCatch(return(expr), name, parentenv, handler)
39:
if (on_warning$silence) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 56: invokeRestart("muffleWarning") keep_message = if (is.numeric(options$message)) TRUE else options$message, }55: }, error = function (cnd) tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) tryCatchOne(expr, names, parentenv, handlers[[1L]])57: { 0L watcher$capture_plot_and_output()
tryCatch({56: cnd <- sanitize_call(cnd) engine$weave(file, quiet = quiet, encoding = enc)tryCatchList(expr, classes, parentenv, handlers) watcher$push(cnd) setwd(startdir) switch(on_error, continue = invokeRestart("eval_continue"), output <- find_vignette_product(name, by = "weave", engine = engine) stop = invokeRestart("eval_stop"), error = NULL) else 2L if (!have.makefile && vignette_is_tex(output)) {
}) }, output_handler = knit_handlers(options$render, options))57:
texi2pdf(file = output, clean = FALSE, quiet = quiet)28: tryCatch({eval(call) output <- find_vignette_product(name, by = "texi2pdf", engine$weave(file, quiet = quiet, encoding = enc)40:
setwd(startdir)29: in_dir(input_dir(), expr)eval(call)
engine = engine) output <- find_vignette_product(name, by = "weave", engine = engine)41: }
in_input_dir(evaluate(code, envir = env, new_device = FALSE, outputs <- c(outputs, output) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (!have.makefile && vignette_is_tex(output)) { keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function(e) { texi2pdf(file = output, clean = FALSE, quiet = quiet) stop_on_error = if (is.numeric(options$error)) options$error else {30: thisOK <<- FALSE output <- find_vignette_product(name, by = "texi2pdf", if (options$error && options$include) with_handlers({ fails <<- c(fails, file) 0L engine = engine) for (expr in tle$exprs) { else 2L message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, output_handler = knit_handlers(options$render, options))) file, conditionMessage(e)))
}}) ev <- withVisible(eval(expr, envir))42:
eng_r(options) outputs <- c(outputs, output) watcher$capture_plot_and_output()}, error = function(e) {
58: watcher$print_value(ev$value, ev$visible, envir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", thisOK <<- FALSE43: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpmfyCaP/file8f1a34d4ea40.rds") fails <<- c(fails, file)
An irrecoverable exception occurred. R is aborting now ...
}block_exec(params) TRUE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, handlers)44: file, conditionMessage(e)))
call_block(x)})31:
doWithOneRestart(return(expr), restart)45:
58: 32: process_group(group)withOneRestart(expr, restarts[[1L]])
46: 33: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", withRestartList(expr, restarts[-nr]) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpmfyCaP/file8f1a34d4ea40.rds")withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
34: An irrecoverable exception occurred. R is aborting now ...
error = function(e) {doWithOneRestart(return(expr), restart)
if (progress && is.function(pb$interrupt)) 35: pb$interrupt()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
})36:
withRestartList(expr, restarts)47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {37: if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({ pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())) watcher$print_value(ev$value, ev$visible, envir)
}48: TRUExfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) error = function(e) {
if (progress && is.function(pb$interrupt)) 38: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) evaluate::evaluate(...) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {39: setwd(wd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, write_utf8(res, output %n% stdout()) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { paste0("\nQuitting from ", loc, if (!is.null(error)) if (options$error && options$include) paste0("\n", rule(), error, "\n", rule())) 0L}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) else 2L
}, output_handler = knit_handlers(options$render, options))49:
process_file(text, output)40:
in_dir(input_dir(), expr)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)41:
51: in_input_dir(evaluate(code, envir = env, new_device = FALSE, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, output_dir = getwd(), ...) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {52: if (options$error && options$include) vweave_rmarkdown(...) 0L
53: else 2L }, output_handler = knit_handlers(options$render, options)))engine$weave(file, quiet = quiet, encoding = enc)
54: 42: doTryCatch(return(expr), name, parentenv, handler)eng_r(options)
55: 43: tryCatchOne(expr, names, parentenv, handlers[[1L]])block_exec(params)
56: 44: tryCatchList(expr, classes, parentenv, handlers)call_block(x)
57: 45: tryCatch({process_group(group) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output <- find_vignette_product(name, by = "weave", engine = engine) error = function(e) { if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "texi2pdf", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) engine = engine) }) }
outputs <- c(outputs, output)47: }, error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { thisOK <<- FALSE if (progress && is.function(pb$interrupt)) fails <<- c(fails, file) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", error <<- format(e) file, conditionMessage(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) {58: if (progress && is.function(pb$interrupt)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpmfyCaP/file8f1a34d4ea40.rds") error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {An irrecoverable exception occurred. R is aborting now ...
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/RtmpmfyCaP/file8f1a34d4ea40.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