Last updated on 2026-08-13 06:55:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | OK | |||||
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.46 | 218.46 | 220.92 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 4.00 | 257.00 | 261.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.45 | 205.25 | 208.70 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 37.00 | 38.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 8.00 | 165.00 | 173.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-13 13:59:19.984 R[41156:59922] 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$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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"))) {
Traceback:
cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: verbose = verbose)FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
17: doTryCatch(return(expr), name, parentenv, handler)
18: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)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)
8: doTryCatch(return(expr), name, parentenv, handler)
9:
Traceback:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 24: eval(expr, envir)
25: eval(expr, envir) 1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e)
26: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
if (!is.null(call)) { 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] tau = tau, theta = th, exclusionRadius = exclusionRadius, withVisible(eval(expr, envir))
Traceback:
embedded = embedded, validLib = validLib, noTime = noTime,
27: withCallingHandlers(code, error = function (e) ignoreNan = ignoreNan, backend = backend)rlang::entrace(e), message = function (cnd)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 4: 1: RowCumsum(valid) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")ComputeError(predictions$Observations, predictions$Predictions)
} 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 5: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, else prefix <- "Error : "{ watcher$capture_plot_and_output() if (on_message$capture) { verbose = verbose)
3: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } watcher$push(cnd)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, } invisible(structure(msg, class = "try-error", condition = e)) tau = tau, theta = th, exclusionRadius = exclusionRadius, if (on_message$silence) {}) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: 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)$predictions)
6: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)FUN(X[[i]], ...) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
7: lapply(X = S, FUN = FUN, ...)
8: 17: doTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffleMessage")
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
18: 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
}19: 9: }, warning = function (cnd) tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {
{20: if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output()10: tryCatchList(expr, classes, parentenv, handlers) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) if (on_warning$capture) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) cnd <- sanitize_call(cnd) mc.preschedule = TRUE), error = function(e) NULL) prefix <- paste("Error in", dcall, ": ") LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]21: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], SweepApply(theta, worker, numProcess) watcher$push(cnd) if (!is.null(call)) {
22: if (identical(call[[1L]], quote(doTryCatch))) unlist(SweepApply(theta, worker, numProcess)) call <- sys.call(-4L) } dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) type = "b"){ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) stop = invokeRestart("eval_stop"), error = NULL) prefix <- paste0(prefix, "\n ")23: if (w > LONG) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", prefix <- paste0(prefix, "\n ")})
28: }eval(call) else prefix <- "Error : " } 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()) } msg <- paste0(prefix, conditionMessage(e), "\n") target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)
invisible(structure(msg, class = "try-error", condition = e))24: })eval(expr, envir)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
.Internal(seterrmessage(msg[1L]))14: if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
29: 25: FUN(X[[i]], ...)eval(expr, envir) .Internal(printDeferredWarnings())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$visible, envir) } } TRUE invisible(structure(msg, class = "try-error", condition = e))})
}, handlers)
26: 12: 15: lapply(seq_len(cores), inner.do)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)withVisible(eval(expr, envir))
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
27: 31: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart)17: if (on_message$capture) {doTryCatch(return(expr), name, parentenv, handler)
18: 32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]])13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}withRestartList(expr, restarts)
14:
FUN(X[[i]], ...) if (on_message$silence) {19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess) invokeRestart("muffleMessage") }
37: 22: }, warning = function (cnd)
unlist(SweepApply(theta, worker, numProcess)){ if (getOption("warn") >= 2 || getOption("warn") < 0) { return()15:
}lapply(seq_len(cores), inner.do)
watcher$capture_plot_and_output() if (on_warning$capture) {16: cnd <- sanitize_call(cnd)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$push(cnd) }
23: withRestarts(with_handlers({ if (on_warning$silence) { for (expr in tle$exprs) {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", invokeRestart("muffleWarning") target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
} ev <- withVisible(eval(expr, envir))24: eval(expr, envir)}, error = function (cnd)
17: 25: doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output(){eval(expr, envir) watcher$print_value(ev$value, ev$visible, envir)
26: watcher$capture_plot_and_output()withVisible(eval(expr, envir))
18: }tryCatchOne(expr, names, parentenv, handlers[[1L]]) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)19: cnd <- sanitize_call(cnd)
27: withCallingHandlers(code, error = function (e) watcher$push(cnd)rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { switch(on_error, continue = invokeRestart("eval_continue"),
watcher$push(cnd)38: evaluate::evaluate(...) stop = invokeRestart("eval_stop"), error = NULL)tryCatchList(expr, classes, parentenv, handlers) }
if (on_message$silence) {
})20: 39:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
28: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(call)22: unlist(SweepApply(theta, worker, numProcess))
23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { invokeRestart("muffleMessage")29: eval(call)
30: with_handlers({ } if (options$error && options$include) }, warning = function (cnd) 0L target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE){ for (expr in tle$exprs) { else 2L ev <- withVisible(eval(expr, envir)) }, output_handler = knit_handlers(options$render, options)) if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
}
watcher$capture_plot_and_output()40: watcher$print_value(ev$value, ev$visible, envir) }24: TRUE watcher$capture_plot_and_output()in_dir(input_dir(), expr)eval(expr, envir)}, handlers)
31:
doWithOneRestart(return(expr), restart)
if (on_warning$capture) { cnd <- sanitize_call(cnd)41: 32: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 25: eval(expr, envir)withOneRestart(expr, restarts[[1L]]) 0L watcher$push(cnd) else 2L
33: }, output_handler = knit_handlers(options$render, options))) }
42: if (on_warning$silence) { invokeRestart("muffleWarning")26: eng_r(options) }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
withRestartList(expr, restarts[-nr])
watcher$push(cnd)withVisible(eval(expr, envir))43:
block_exec(params) switch(on_error, continue = invokeRestart("eval_continue"), 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 34: doWithOneRestart(return(expr), restart){ stop = invokeRestart("eval_stop"), error = NULL)
})
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts) watcher$capture_plot_and_output()
44: 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: call_block(x)
evaluate::evaluate(...) if (on_message$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) {28:
39: 45: process_group(group) cnd <- sanitize_call(cnd)eval(call)
29: watcher$push(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }eval(call)
30: with_handlers({
keep_message = if (is.numeric(options$message)) TRUE else options$message, for (expr in tle$exprs) { if (on_warning$silence) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { invokeRestart("muffleWarning") } watcher$print_value(ev$value, ev$visible, envir)}, error = function (cnd) { watcher$capture_plot_and_output() if (options$error && options$include) cnd <- sanitize_call(cnd) } watcher$push(cnd) TRUE 0L}, handlers) else 2L }, output_handler = knit_handlers(options$render, options))46:
switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), })
error = function(e) {40: if (progress && is.function(pb$interrupt)) in_dir(input_dir(), expr) pb$interrupt()31: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
28:
doWithOneRestart(return(expr), restart)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
47: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(call)34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
keep_message = if (is.numeric(options$message)) TRUE else options$message,
36: 29: stop_on_error = if (is.numeric(options$error)) options$error else {withRestartList(expr, restarts) if (options$error && options$include)
0L else 2Leval(call)
30: 37: }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
withRestarts(with_handlers({43: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {with_handlers({block_exec(params) for (expr in tle$exprs) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() ev <- withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir) } if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) watcher$capture_plot_and_output() TRUE
44: watcher$print_value(ev$value, ev$visible, envir) }), list(rlang_trace_top_env = knit_global()))call_block(x)}, handlers)
31: doWithOneRestart(return(expr), restart)
}
32: 48: withOneRestart(expr, restarts[[1L]])
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: process_group(group)33: error = function(e) { TRUE if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr]) pb$interrupt()
34: doWithOneRestart(return(expr), restart) if (is_R_CMD_build() || is_R_CMD_check())
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
35: 46: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }), list(rlang_trace_top_env = knit_global())), function(loc) {
36: withRestartList(expr, restarts)
37: setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), paste0("\n", rule(), error, "\n", rule()))38: withRestarts(with_handlers({ error = function(e) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) for (expr in tle$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(...) error <<- format(e) })
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), evaluate::evaluate(...)49:
39: error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, process_file(text, output)
50: 39: if (progress && is.function(pb$interrupt)) 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, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
if (is_R_CMD_build() || is_R_CMD_check()) 51: if (options$error && options$include) 41: error <<- format(e)in_input_dir(evaluate(code, envir = env, new_device = FALSE, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) }), list(rlang_trace_top_env = knit_global()))
52: vweave_rmarkdown(...) 0L else 2L
48: }, output_handler = knit_handlers(options$render, options)))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {53: engine$weave(file, quiet = quiet, encoding = enc)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt))
42: eng_r(options) pb$interrupt()54: if (is_R_CMD_build() || is_R_CMD_check())
keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 43: 0LdoTryCatch(return(expr), name, parentenv, handler)
55: block_exec(params)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), 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())) else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 44:
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e) setwd(startdir)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
})call_block(x)
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)49: 45: process_group(group)
} outputs <- c(outputs, output)47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function(e) { thisOK <<- FALSE46: process_file(text, output) error = function(e) {
fails <<- c(fails, file)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 50: if (progress && is.function(pb$interrupt)) pb$interrupt() error = function(e) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
if (is_R_CMD_build() || is_R_CMD_check()) 51: if (progress && is.function(pb$interrupt)) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpnIYlrJ/file6a535e78d330.rds")
An irrecoverable exception occurred. R is aborting now ...
output_dir = getwd(), ...) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)48: })
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {54: doTryCatch(return(expr), name, parentenv, handler)
55: if (progress && is.function(pb$interrupt)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchList(expr, classes, parentenv, handlers) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
57: error = function(e) { if (progress && is.function(pb$interrupt)) tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) setwd(startdir) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) }), list(rlang_trace_top_env = knit_global())), function(loc) { output <- find_vignette_product(name, by = "weave", engine = engine) setwd(wd)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (!have.makefile && vignette_is_tex(output)) { 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: if (progress && is.function(pb$interrupt)) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) texi2pdf(file = output, clean = FALSE, quiet = quiet)51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { output_dir = getwd(), ...)
52: thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) setwd(wd)
write_utf8(res, output %n% stdout())58: paste0("\nQuitting from ", loc, if (!is.null(error)) vweave_rmarkdown(...) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpnIYlrJ/file6a535e78d330.rds")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(),
53: engine$weave(file, quiet = quiet, encoding = enc) output_dir = getwd(), ...)
54: doTryCatch(return(expr), name, parentenv, handler)An irrecoverable exception occurred. R is aborting now ...
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({52: vweave_rmarkdown(...)
engine$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/RtmpnIYlrJ/file6a535e78d330.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpnIYlrJ/file6a535e78d330.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