Last updated on 2026-08-17 13:50:22 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.57 | 226.18 | 229.75 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.49 | 225.98 | 228.47 | 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 | 3.27 | 210.37 | 213.64 | 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 | 0.00 | 6.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 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
2026-08-17 20:21:57.791 R[41404:60288] 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"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24:
Traceback:
Traceback:
1: RowCumsum(valid)eval(expr, envir)
1: RowCumsum(valid)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: 2: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose){ watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage")FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
}}, warning = function (cnd) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 3: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
Traceback:
tau = tau, theta = th, exclusionRadius = exclusionRadius, { 1: RowCumsum(valid) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) ignoreNan = ignoreNan, backend = backend)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 4: ComputeError(predictions$Observations, predictions$Predictions) verbose = verbose) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return() 4: } 5:
watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, ComputeError(predictions$Observations, predictions$Predictions) 3: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, } tau = tau, theta = th, exclusionRadius = exclusionRadius, if (on_warning$silence) { invokeRestart("muffleWarning") } embedded = embedded, validLib = validLib, noTime = noTime, }, error = function (cnd) ignoreNan = ignoreNan, backend = backend){ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, stop = invokeRestart("eval_stop"), error = NULL) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
5: 6: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, FUN(X[[i]], ...)
}) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
7: lapply(X = S, FUN = FUN, ...)
embedded = embedded, validLib = validLib, noTime = noTime, 28: eval(call)
29: 4: eval(call) ignoreNan = ignoreNan, backend = backend)$predictions)
6:
8: 30: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])ComputeError(predictions$Observations, predictions$Predictions)
FUN(X[[i]], ...)
7: with_handlers({lapply(X = S, FUN = FUN, ...) 5: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
10: 8: 31: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
32: withOneRestart(expr, restarts[[1L]])
embedded = embedded, validLib = validLib, noTime = noTime, 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
ignoreNan = ignoreNan, backend = backend)$predictions)
10: 11: 6: tryCatchList(expr, classes, parentenv, handlers)33: tryCatch(expr, error = function(e) {FUN(X[[i]], ...) call <- conditionCall(e)
if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L11: 7: lapply(X = S, FUN = FUN, ...) sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) withRestartList(expr, restarts[-nr]) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") call <- sys.call(-4L)
34:
8: doTryCatch(return(expr), name, parentenv, handler)
9: if (is.na(w)) dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
10: type = "b")tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } prefix <- paste("Error in", dcall, ": ") if (w > LONG) LONG <- 75L prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : " sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") msg <- paste0(prefix, conditionMessage(e), "\n") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")11: } TRUEtryCatch(expr, error = function(e) { else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 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]] if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") .Internal(seterrmessage(msg[1L])) if (is.na(w)) cat(msg, file = outFile) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) .Internal(printDeferredWarnings())
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") }38: evaluate::evaluate(...) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") invisible(structure(msg, class = "try-error", condition = e)) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) }
})
invisible(structure(msg, class = "try-error", condition = e)) }12: 39: }) 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, 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 13: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 13: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...) 0L
else 2L
14: FUN(X[[i]], ...) }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 15: lapply(seq_len(cores), inner.do)
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)15: lapply(seq_len(cores), inner.do)FUN(X[[i]], ...)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
15: 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 17: 17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
mc.preschedule = TRUE), error = function(e) NULL)doTryCatch(return(expr), name, parentenv, handler)
stop_on_error = if (is.numeric(options$error)) options$error else {18: 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
if (options$error && options$include) 0L mc.preschedule = TRUE), error = function(e) NULL)19:
tryCatchList(expr, classes, parentenv, handlers)
else 2L }, output_handler = knit_handlers(options$render, options)))
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: 21: 21: unlist(SweepApply(theta, worker, numProcess))42:
SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))eng_r(options)SweepApply(theta, worker, numProcess)23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
22: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)unlist(SweepApply(theta, worker, numProcess))
23: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
24: 43: eval(expr, envir) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
block_exec(params)
E = E, showPlot = TRUE)25: 44: eval(expr, envir)call_block(x)
26: 24:
45: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)withVisible(eval(expr, envir))
process_group(group)eval(expr, envir)
25:
27: withCallingHandlers(code, error = function (e) eval(expr, envir)46: 24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(expr, envir) error = function(e) {rlang::entrace(e), message = function (cnd)
25: eval(expr, envir)
if (progress && is.function(pb$interrupt)) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
26: withVisible(eval(expr, envir))
watcher$capture_plot_and_output()26: withVisible(eval(expr, envir))27:
47: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {27: watcher$push(cnd)withCallingHandlers(code, error = function (e) } if (on_message$capture) {rlang::entrace(e), message = function (cnd) if (on_message$silence) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), invokeRestart("muffleMessage"){ watcher$capture_plot_and_output() if (on_message$capture) { error = function(e) { } if (progress && is.function(pb$interrupt)) watcher$push(cnd) pb$interrupt() } watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: if (on_message$silence) { }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), invokeRestart("muffleMessage") if (on_message$silence) { 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)) }, warning = function (cnd) invokeRestart("muffleMessage") }{ if (getOption("warn") >= 2 || getOption("warn") < 0) { return()}, warning = function (cnd) } paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc){
} watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output()49: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)}, warning = function (cnd) }{process_file(text, output) if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_warning$capture) { cnd <- sanitize_call(cnd)
watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") } if (on_warning$silence) {50: }, error = function (cnd) { watcher$capture_plot_and_output() invokeRestart("muffleWarning")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
cnd <- sanitize_call(cnd) watcher$push(cnd) return()51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), switch(on_error, continue = invokeRestart("eval_continue"), }, error = function (cnd) { stop = invokeRestart("eval_stop"), error = NULL) }}) watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)
28: eval(call)
watcher$capture_plot_and_output()29: watcher$push(cnd) } if (on_warning$silence) { output_dir = getwd(), ...) invokeRestart("muffleWarning") cnd <- sanitize_call(cnd) } watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: })eval(call)52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)28:
54:
29: eval(call)
eval(call)
eval(call)29: doTryCatch(return(expr), name, parentenv, handler)30: eval(call)with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
30: with_handlers({ for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir))
30: TRUEwith_handlers({ for (expr in tle$exprs) { watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir)
55: }, handlers)
31: doWithOneRestart(return(expr), restart)
watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: 32: } TRUEwithOneRestart(expr, restarts[[1L]]) watcher$print_value(ev$value, ev$visible, envir) }}, handlers)
31: doWithOneRestart(return(expr), restart) TRUEtryCatch({
engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)32: output <- find_vignette_product(name, by = "weave", engine = engine)withOneRestart(expr, restarts[[1L]]) if (!have.makefile && vignette_is_tex(output)) {}, handlers) texi2pdf(file = output, clean = FALSE, quiet = quiet)
31: doWithOneRestart(return(expr), restart)
32: 33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart) output <- find_vignette_product(name, by = "texi2pdf",
withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
engine = engine)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,
}33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
stop_on_error = if (is.numeric(options$error)) options$error else { 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))) if (options$error && options$include) 35: })
0L else 2L }, output_handler = knit_handlers(options$render, options))
40: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) {in_dir(input_dir(), expr)
36: 58: withRestartList(expr, restarts) 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(...)
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpywZp3H/file6aee44348245.rds")
An irrecoverable exception occurred. R is aborting now ...
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
0L42: eng_r(options)
else 2L }, output_handler = knit_handlers(options$render, options)))
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
43: 38: block_exec(params)evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
42: 40: in_dir(input_dir(), expr)
41:
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, eng_r(options) if (progress && is.function(pb$interrupt))
43: block_exec(params) 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) pb$interrupt() 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42:
if (is_R_CMD_build() || is_R_CMD_check()) eng_r(options) error <<- format(e) })
43:
block_exec(params)
44: call_block(x)
45: process_group(group)
44: 46: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt()call_block(x)
error = function(e) { if (progress && is.function(pb$interrupt)) 45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() error = function(e) { if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) pb$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 = 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())) 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() error <<- format(e)
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {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() }), list(rlang_trace_top_env = knit_global()))
48: setwd(wd) write_utf8(res, output %n% stdout()) if (is_R_CMD_build() || is_R_CMD_check()) 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()) paste0("\nQuitting from ", loc, if (!is.null(error)) error <<- format(e) error <<- format(e) paste0("\n", rule(), error, "\n", rule())) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) }), 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("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
paste0("\n", rule(), error, "\n", rule()))49: process_file(text, output)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: 50: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)53:
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
57: engine$weave(file, quiet = quiet, encoding = enc)tryCatch({52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: engine$weave(file, quiet = quiet, encoding = enc)doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
setwd(startdir)54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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)56: 56: }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({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/RtmpywZp3H/file6aee44348245.rds")
engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {An irrecoverable exception occurred. R is aborting now ...
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpywZp3H/file6aee44348245.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpywZp3H/file6aee44348245.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